diff --git a/.Rbuildignore b/.Rbuildignore index 9365a9708..d2d21bce9 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -6,7 +6,6 @@ a.out.dSYM ^.*\.Rproj$ ^\.Rproj\.user$ ^\.travis\.yml$ -^NEWS\.md$ ^cran-comments\.md$ ^data-raw$ ^src/sqlite3/.*\.o$ @@ -26,3 +25,5 @@ a.out.dSYM ^clion-test\.R$ ^_pkgdown\.yml$ ^docs$ +^README\.Rmd$ +^UPDATE\.md$ diff --git a/.travis.yml b/.travis.yml index dbf5cce57..3059c7a53 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,7 +19,7 @@ matrix: - r: oldrel - r: devel - os: osx - osx_image: xcode7.2 + osx_image: xcode7.3 r: release latex: false diff --git a/DESCRIPTION b/DESCRIPTION index f6a007be1..95065d2a2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: RSQLite -Version: 1.0.9017 -Date: 2016-11-22 -Title: SQLite Interface for R +Version: 1.1 +Date: 2016-11-24 +Title: 'SQLite' Interface for R Authors@R: c( person("Kirill", "Müller", role = c("aut", "cre"), email = "krlmlr+r@mailbox.org"), person("Hadley", "Wickham", role = c("aut")), @@ -9,30 +9,30 @@ Authors@R: c( person("Seth", "Falcon", role = "aut"), person(family = "SQLite Authors", role = "ctb", comment = "for the included SQLite sources"), person("Liam", "Healy", role = "ctb", comment = "for the included SQLite sources"), + person(family = "R Consortium", role = "cph"), person(family = "RStudio", role = "cph") ) Description: Embeds the 'SQLite' database engine in R and provides an interface compliant with the 'DBI' package. The - source for the SQLite engine (version 3.8.8.2) is included. + source for the 'SQLite' engine (version 3.8.8.2) is included. Depends: R (>= 3.1.0) Suggests: - testthat, + DBItest, knitr, rmarkdown, - DBItest + testthat Imports: - methods, DBI (>= 0.4-9), - Rcpp (>= 0.12.7), - memoise + memoise, + methods, + Rcpp (>= 0.12.7) LinkingTo: Rcpp, BH, plogr -Remotes: rstats-db/DBI, rstats-db/DBItest@production, hadley/testthat Encoding: UTF-8 License: LGPL (>= 2) URL: https://github.com/rstats-db/RSQLite BugReports: https://github.com/rstats-db/RSQLite/issues -Collate: +Collate: 'RcppExports.R' 'SQLiteConnection.R' 'SQLiteDriver.R' @@ -41,6 +41,7 @@ Collate: 'copy.R' 'datasetsDb.R' 'deprecated.R' + 'dummy.R' 'extensions.R' 'query.R' 'rownames.R' diff --git a/NAMESPACE b/NAMESPACE index 6a82f70ba..400dab043 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -59,4 +59,5 @@ exportMethods(sqlData) import(DBI) import(methods) importFrom(Rcpp,sourceCpp) +importFrom(memoise,memoise) useDynLib(RSQLite) diff --git a/NEWS.md b/NEWS.md index 5235c9e50..2e21bd9a1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# RSQLite 1.1 (2016-11-25) + - New maintainer: Kirill Müller. ## Bundled SQLite @@ -14,6 +16,15 @@ - Header files for `sqlite3` are no longer installed, linking to the package is not possible anymore. Packages that require access to the low-level sqlite3 API should bundle their own copy. +## Breaking changes + +- `RSQLite()` no longer automatically attaches DBI when loaded. This is to + encourage you to use `library(DBI); dbConnect(RSQLite::SQLite())`. + +- Functions that take a table name, such as `dbWriteTable()` and `dbReadTable()`, + now quote the table name via `dbQuoteIdentifier()`. + This means that caller-quoted names should be marked as such with `DBI::SQL()`. + ## New features - RSQLite has been rewritten (essentially from scratch) in C++ with @@ -51,10 +62,7 @@ - Deprecation warnings are given only once, with a clear reference to the source. -## Breaking changes - -- `RSQLite()` no longer automatically attaches DBI when loaded. This is to - encourage you to use `library(DBI); dbConnect(RSQLite::SQLite())`. +- `datasetsDb()` now returns a read-only database, to avoid modifications to the installed file. ## Deprecated functions @@ -88,6 +96,10 @@ - Reimplemented `dbWriteTable("SQLiteConnection", "character", "character")` for import of CSV files, using a function from the old codebase (#151). +- `dbWriteTable("SQLiteConnection", "character", "data.frame")` looks + for table names already enclosed in backticks and uses these, + (with a warning), for compatibility with the sqldf package. + ## Performance - The `dbExistsTable()` function now works faster by filtering the list of tables using SQL (#166). @@ -96,15 +108,15 @@ - Start on a basic vignette: `vignette("RSQLite")` (#50). -- Using `dbExecute()` in examples. +- Reworked function and method documentation, removed old documentation (#121). + +- Using `dbExecute()` in documentation and examples. - Using both `":memory:"` and `":file::memory:"` in documentation. - Added additional documentation and unit tests for [autoincrement keys](https://www.sqlite.org/autoinc.html) (#119, @wibeasley). -- Removed old documentation (#121). - ## Internal - Avoid warning about missing `long long` data type in C++98 by using a compound data type built from two 32-bit integers, with static assert that the size is 8 indeed. diff --git a/R/dummy.R b/R/dummy.R new file mode 100644 index 000000000..32fb98f22 --- /dev/null +++ b/R/dummy.R @@ -0,0 +1,16 @@ +#' Dummy methods +#' +#' Define here so that these methods can also be imported from this package. +#' Recommended practice is to import all methods from \pkg{DBI}. +#' +#' @name dummy-methods +#' @keywords internal +NULL + +#' @rdname dummy-methods +#' @aliases dbGetQuery,NULL,ANY-method +#' @inheritParams DBI::dbGetQuery +#' @export +setMethod("dbGetQuery", "NULL", function(conn, statement, ...) { + stop("conn cannot be NULL", call. = FALSE) +}) diff --git a/R/query.R b/R/query.R index 450e8b42c..fffb1cd50 100644 --- a/R/query.R +++ b/R/query.R @@ -112,7 +112,6 @@ setMethod("dbSendQuery", c("SQLiteConnection", "character"), #' @export -#' @rawNamespace exportMethods(dbGetQuery) DBI::dbGetQuery diff --git a/R/table.R b/R/table.R index 81f1c0b4a..c252a4412 100644 --- a/R/table.R +++ b/R/table.R @@ -65,6 +65,8 @@ setMethod("dbWriteTable", c("SQLiteConnection", "character", "data.frame"), if (overwrite && append) stop("overwrite and append cannot both be TRUE", call. = FALSE) + name <- check_quoted_identifier(name) + row.names <- compatRowNames(row.names) dbBegin(conn, "dbWriteTable") @@ -270,6 +272,15 @@ string_to_utf8 <- function(value) { value } +check_quoted_identifier <- function(name) { + if (class(name)[[1L]] != "SQL" && grepl("^`.*`$", name)) { + warning_once("Quoted identifiers should have class SQL, use DBI::SQL() if the caller performs the quoting.") + name <- SQL(name) + } + + name +} + #' Read a database table #' diff --git a/R/utils.R b/R/utils.R index 0d18b3aff..389e8bc6a 100644 --- a/R/utils.R +++ b/R/utils.R @@ -14,4 +14,5 @@ warningc <- function(...) { warning(..., call. = FALSE, domain = NA) } -warning_once <- memoise::memoise(warningc) +#' @importFrom memoise memoise +warning_once <- memoise(warningc) diff --git a/cran-comments.md b/cran-comments.md index 0e105b4fa..c0686c37a 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,79 +1,41 @@ -The following notes were generated across my local OS X install and ubuntu running on travis-ci. Response to NOTEs across three platforms below. +## Test environments +* Ubuntu 16.10 (local install), R 3.3.2 +* Ubuntu 12.04 (on travis-ci), R devel, release, and oldrel +* OS X (on travis-ci), R release +* win-builder (devel and release) -* I am taking over maintenance of RSQLite. I'ved asked Seth Falcon to - email you to confirm this. +## R CMD check results -* checking CRAN incoming feasibility ... NOTE - Possibly mis-spelled words in DESCRIPTION: - DBI (14:46) - SQLite (3:8, 12:46, 13:29, 15:24) - - These are correct spellings +0 errors | 0 warnings | 2 notes -* checking compiled code ... NOTE - File ‘/Users/hadley/Documents/databases/RSQLite.Rcheck/RSQLite/libs/RSQLite.so’: - Found ‘___stderrp’, possibly from ‘stderr’ (C) - Object: ‘sqlite-all.o’ +* New maintainer: Kirill Müller, previous maintainer: Hadley Wickham. + See https://github.com/rstats-db/RSQLite/commit/1cfbce07c678de#commitcomment-18978172 + for a comment that indicates Hadley's consent. - This is in C code from the embedded SQLite database. - -I also ran R CMD check on all downstream dependencies on R-devel. All packages that I install past R CMD check without ERRORs, WARNINGs, or NOTE. (See below for packages that I couldn't install). I informed all downstream maintainers of the pending update one month ago, giving plenty of time for fixes. +* Installed size: This package comes with a bundled RSQLite library. -Downstream dependency failure --------------------------------------------------- -CITAN =================================================================== - * checking package dependencies ... ERROR -Package required but not available: ‘RGtk2’ +## Reverse dependencies -See the information on DESCRIPTION files in the chapter ‘Creating R -packages’ of the ‘Writing R Extensions’ manual. +Checked all 117 CRAN and BioConductor reverse dependencies on Ubuntu 16.04. +A few CRAN packages show errors in this version but succeed with RSQLite v1.0.0: -marmap ================================================================== - * checking package dependencies ... ERROR -Package required but not available: ‘ncdf’ +- ecd (0.8.2) imports RSQLite <= 1.0.0, contacted maintainer several times, + last time on Oct 20 -See the information on DESCRIPTION files in the chapter ‘Creating R -packages’ of the ‘Writing R Extensions’ manual. +- poplite (0.99.16), errors fixed in development version: + https://github.com/dbottomly/poplite/issues/2 -MUCflights ============================================================== - * checking package dependencies ... ERROR -Package required but not available: ‘XML’ +- tigreBrowserWriter (0.1.2), contacted maintainer on Nov 17, no response so far. + The code is using a prepared SQL query with more parameters than the query expects. + RSQLite is now intentially stricter about such errors, and I believe that a + downstream fix will be beneficial for the tigreBrowserWriter package. -See the information on DESCRIPTION files in the chapter ‘Creating R -packages’ of the ‘Writing R Extensions’ manual. - -pitchRx ================================================================= - * checking package dependencies ... ERROR -Package required but not available: ‘XML2R’ - -Package suggested but not available for checking: ‘rgl’ - -See the information on DESCRIPTION files in the chapter ‘Creating R -packages’ of the ‘Writing R Extensions’ manual. - -rangeMapper ============================================================= - * checking package dependencies ... ERROR -Package required but not available: ‘rgdal’ - -Package suggested but not available for checking: ‘rgeos’ - -See the information on DESCRIPTION files in the chapter ‘Creating R -packages’ of the ‘Writing R Extensions’ manual. - -RQDA ==================================================================== - * checking package dependencies ... ERROR -Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’ - -Package which this enhances but not available for checking: ‘rjpod’ - -See the information on DESCRIPTION files in the chapter ‘Creating R -packages’ of the ‘Writing R Extensions’ manual. - -snplist ================================================================= - * checking package dependencies ... ERROR -Package required but not available: ‘biomaRt’ - -See the information on DESCRIPTION files in the chapter ‘Creating R -packages’ of the ‘Writing R Extensions’ manual. +I couldn't check RQDA and vmsbase, they consistently fail checks with both +versions of RSQLite on my system but succeed checks on CRAN. +All other packages are consistent in their checking behavior for both RSQLite 1.0.0 +and 1.1. +See https://github.com/rstats-db/RSQLite/blob/r-1.1/revdep/README.md for check results and https://github.com/rstats-db/RSQLite/blob/r-1.1/revdep/problems.md +for results for packages with problems only. diff --git a/man/dummy-methods.Rd b/man/dummy-methods.Rd new file mode 100644 index 000000000..d308f75f3 --- /dev/null +++ b/man/dummy-methods.Rd @@ -0,0 +1,24 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/dummy.R +\docType{methods} +\name{dummy-methods} +\alias{dummy-methods} +\alias{dbGetQuery,NULL,ANY-method} +\title{Dummy methods} +\usage{ +\S4method{dbGetQuery}{`NULL`,ANY}(conn, statement, ...) +} +\arguments{ +\item{conn}{A \code{\linkS4class{DBIConnection}} object, as produced by +\code{\link[=dbConnect]{dbConnect()}}.} + +\item{statement}{a character vector of length 1 containing SQL.} + +\item{...}{Other parameters passed on to methods.} +} +\description{ +Define here so that these methods can also be imported from this package. +Recommended practice is to import all methods from \pkg{DBI}. +} +\keyword{internal} + diff --git a/revdep/README-master.md b/revdep/README-master.md deleted file mode 100644 index eb396c262..000000000 --- a/revdep/README-master.md +++ /dev/null @@ -1,3300 +0,0 @@ -# Setup - -## Platform - -|setting |value | -|:--------|:----------------------------| -|version |R version 3.3.1 (2016-06-21) | -|system |x86_64, linux-gnu | -|ui |X11 | -|language |(EN) | -|collate |en_US.UTF-8 | -|tz |Zulu | -|date |2016-10-19 | - -## Packages - -|package |* |version |date |source | -|:---------|:--|:----------|:----------|:----------------------------------| -|BH | |1.60.0-2 |2016-05-07 |cran (@1.60.0-) | -|DBI | |0.5-12 |2016-10-06 |Github (rstats-db/DBI@4f00863) | -|DBItest | |1.3-10 |2016-10-06 |Github (rstats-db/DBItest@9e87611) | -|knitr | |1.14 |2016-08-13 |cran (@1.14) | -|memoise | |1.0.0 |2016-01-29 |CRAN (R 3.3.1) | -|plogr | |0.1-1 |2016-09-24 |cran (@0.1-1) | -|Rcpp | |0.12.7 |2016-09-05 |cran (@0.12.7) | -|rmarkdown | |1.0 |2016-07-08 |cran (@1.0) | -|RSQLite | |1.0.0 |2014-10-25 |CRAN (R 3.3.1) | -|testthat | |1.0.2.9000 |2016-08-25 |Github (hadley/testthat@46d15da) | - -# Check results - -112 packages - -|package |version | errors| warnings| notes| -|:------------------|:---------|------:|--------:|-----:| -|affycoretools |1.46.0 | 0| 0| 0| -|AnnotationDbi |1.36.0 | 0| 1| 5| -|AnnotationForge |1.16.0 | 0| 0| 2| -|AnnotationHubData |1.4.0 | 1| 0| 3| -|AnnotationHub |2.6.0 | 0| 0| 2| -|APSIM |0.9.1 | 0| 0| 0| -|archivist |2.1 | 0| 0| 2| -|BatchExperiments |1.4.1 | 0| 0| 2| -|BatchJobs |1.6 | 0| 0| 0| -|bibliospec |0.0.4 | 0| 0| 0| -|biglm |0.9-1 | 0| 0| 5| -|bioassayR |1.12.0 | 0| 0| 1| -|BoSSA |2.0 | 0| 0| 0| -|caroline |0.7.6 | 0| 0| 2| -|Category |2.40.0 | 0| 0| 1| -|ChemmineR |2.26.0 | 1| 0| 0| -|chunked |0.3 | 0| 0| 0| -|CITAN |2015.12-2 | 0| 0| 0| -|clstutils |1.22.0 | 0| 2| 5| -|CNEr |1.10.0 | 0| 2| 2| -|CollapsABEL |0.10.8 | 0| 0| 0| -|cummeRbund |2.16.0 | 0| 0| 6| -|customProDB |1.14.0 | 0| 0| 3| -|DBI |0.5-1 | 0| 0| 1| -|DECIPHER |2.2.0 | 0| 0| 3| -|dplyr |0.5.0 | 0| 0| 1| -|ecd |0.8.2 | 1| 0| 0| -|emuR |0.1.9 | 0| 0| 0| -|ensembldb |1.6.0 | 0| 0| 2| -|etl |0.3.3.1 | 0| 0| 0| -|ETLUtils |1.3 | 0| 0| 0| -|filehashSQLite |0.2-4 | 0| 0| 3| -|filematrix |1.1.0 | 0| 1| 0| -|freqweights |1.0.2 | 0| 0| 1| -|gcbd |0.2.6 | 0| 1| 1| -|GeneAnswers |2.16.0 | 1| 3| 6| -|GenomicFeatures |1.26.0 | 0| 0| 2| -|Genominator |1.28.0 | 0| 0| 4| -|GEOmetadb |1.34.0 | 0| 0| 3| -|GWASTools |1.20.0 | 0| 0| 1| -|imputeMulti |0.6.3 | 0| 0| 1| -|iontree |1.20.0 | 0| 0| 5| -|macleish |0.3.0 | 0| 0| 0| -|maGUI |1.0 | 1| 0| 0| -|manta |1.20.0 | 0| 0| 7| -|marmap |0.9.5 | 0| 0| 0| -|MeSHDbi |1.10.0 | 0| 0| 2| -|metagenomeFeatures |1.4.0 | 0| 2| 2| -|MetaIntegrator |1.0.3 | 0| 0| 0| -|metaseqR |1.14.0 | 1| 1| 4| -|mgsa |1.22.0 | 0| 1| 5| -|miRNAtap |1.8.0 | 0| 0| 2| -|MmPalateMiRNA |1.24.0 | 0| 0| 4| -|MonetDBLite |0.3.1 | 0| 0| 1| -|MUCflights |0.0-3 | 0| 0| 3| -|nutshell.bbdb |1.0 | 0| 0| 2| -|nutshell |2.0 | 0| 0| 3| -|oai |0.2.0 | 0| 0| 0| -|oce |0.9-19 | 1| 0| 1| -|oligoClasses |1.36.0 | 0| 1| 4| -|oligo |1.38.0 | 1| 0| 9| -|OrganismDbi |1.16.0 | 0| 0| 2| -|PAnnBuilder |1.38.0 | 0| 3| 1| -|pdInfoBuilder |1.38.0 | 0| 0| 1| -|PGA |1.4.0 | 0| 0| 3| -|pitchRx |1.8.2 | 0| 0| 1| -|plethy |1.12.0 | 2| 1| 3| -|poplite |0.99.16 | 1| 0| 1| -|ProjectTemplate |0.7 | 0| 0| 0| -|quantmod |0.4-6 | 0| 0| 1| -|rangeMapper |0.3-0 | 0| 0| 0| -|RecordLinkage |0.4-10 | 0| 0| 0| -|recoup |1.2.0 | 2| 0| 1| -|refGenome |1.7.0 | 0| 0| 0| -|rgrass7 |0.1-9 | 0| 0| 0| -|RImmPort |1.2.0 | 0| 1| 1| -|RObsDat |16.03 | 0| 0| 0| -|rplexos |1.1.8 | 0| 0| 0| -|RQDA |0.2-7 | 1| 0| 1| -|rTRM |1.12.0 | 0| 0| 1| -|rvertnet |0.5.0 | 0| 0| 0| -|scrime |1.3.3 | 0| 0| 2| -|SEERaBomb |2016.1 | 0| 0| 0| -|seqplots |1.12.0 | 0| 0| 3| -|SGP |1.5-0.0 | 0| 0| 0| -|smnet |2.1 | 0| 0| 0| -|snplist |0.15 | 0| 0| 0| -|specL |1.8.0 | 0| 1| 3| -|sqldf |0.4-10 | 1| 1| 2| -|sqliter |0.1.0 | 0| 0| 0| -|SRAdb |1.31.0 | 0| 0| 6| -|srvyr |0.2.0 | 0| 0| 0| -|SSN |1.1.8 | 0| 0| 0| -|storr |1.0.1 | 0| 0| 0| -|stream |1.2-3 | 0| 0| 1| -|survey |3.31-2 | 0| 0| 0| -|taRifx |1.0.6 | 0| 0| 4| -|tcpl |1.2.2 | 0| 0| 1| -|TFBSTools |1.12.0 | 0| 1| 2| -|tigre |1.28.0 | 0| 0| 2| -|trackeR |0.0.3 | 0| 1| 0| -|TSdata |2016.8-1 | 0| 1| 0| -|TSSQLite |2015.4-1 | 0| 0| 0| -|TSsql |2015.1-2 | 0| 0| 1| -|tweet2r |1.0 | 0| 0| 0| -|twitteR |1.1.9 | 0| 0| 0| -|UniProt.ws |2.14.0 | 0| 0| 1| -|Uniquorn |1.2.0 | 0| 0| 2| -|UPMASK |1.0 | 0| 0| 1| -|VariantFiltering |1.10.0 | 0| 2| 4| -|vegdata |0.9 | 0| 0| 0| -|vmsbase |2.1.3 | 1| 0| 0| - -## affycoretools (1.46.0) -Maintainer: James W. MacDonald - -0 errors | 0 warnings | 0 notes - -## AnnotationDbi (1.36.0) -Maintainer: Bioconductor Package Maintainer - - -0 errors | 1 warning | 5 notes - -``` -checking for unstated dependencies in ‘tests’ ... WARNING -'library' or 'require' call not declared from: ‘org.testing.db’ - -checking installed package size ... NOTE - installed size is 8.6Mb - sub-directories of 1Mb or more: - extdata 6.0Mb - -checking DESCRIPTION meta-information ... NOTE -Packages listed in more than one of Depends, Imports, Suggests, Enhances: - ‘methods’ ‘utils’ ‘stats4’ ‘BiocGenerics’ ‘Biobase’ ‘IRanges’ ‘DBI’ ‘RSQLite’ -A package should be listed in only one of these fields. - -checking dependencies in R code ... NOTE -'library' or 'require' calls in package code: - ‘GO.db’ ‘KEGG.db’ ‘RSQLite’ ‘graph’ - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. -Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’ - See the note in ?`:::` about the use of this operator. - -checking R code for possible problems ... NOTE -.selectInp8: no visible global function definition for ‘.resort’ -annotMessage: no visible binding for global variable ‘pkgName’ -createORGANISMSeeds: no visible global function definition for - ‘makeAnnDbMapSeeds’ -makeGOGraph: no visible binding for global variable ‘GOBPPARENTS’ -makeGOGraph: no visible binding for global variable ‘GOMFPARENTS’ -makeGOGraph: no visible binding for global variable ‘GOCCPARENTS’ -makeGOGraph: no visible global function definition for ‘ftM2graphNEL’ -Undefined global functions or variables: - .resort GOBPPARENTS GOCCPARENTS GOMFPARENTS ftM2graphNEL - makeAnnDbMapSeeds pkgName - -checking Rd line widths ... NOTE -Rd file 'inpIDMapper.Rd': - \examples lines wider than 100 characters: - YeastUPSingles = inpIDMapper(ids, "HOMSA", "SACCE", destIDType="UNIPROT", keepMultDestIDMatches = FALSE) - -These lines will be truncated in the PDF manual. -``` - -## AnnotationForge (1.16.0) -Maintainer: Bioconductor Package Maintainer - -0 errors | 0 warnings | 2 notes - -``` -checking installed package size ... NOTE - installed size is 6.0Mb - sub-directories of 1Mb or more: - AnnDbPkg-templates 1.7Mb - extdata 3.3Mb - -checking dependencies in R code ... NOTE -Unexported object imported by a ':::' call: ‘AnnotationDbi:::NCBIORG_DB_SeedGenerator’ - See the note in ?`:::` about the use of this operator. -``` - -## AnnotationHubData (1.4.0) -Maintainer: Bioconductor Package Maintainer - -1 error | 0 warnings | 3 notes - -``` -checking tests ... ERROR -Running the tests in ‘tests/AnnotationHubData_unit_tests.R’ failed. -Last 13 lines of output: - ERROR in test_UCSC2BitPreparer_recipe: Error in ahms[[1]] : subscript out of bounds - ERROR in test_UCSCChainPreparer_recipe: Error in ahms[[1]] : subscript out of bounds - - Test files with failing tests - - test_recipe.R - test_UCSC2BitPreparer_recipe - test_UCSCChainPreparer_recipe - - - Error in BiocGenerics:::testPackage("AnnotationHubData") : - unit tests failed for package AnnotationHubData - Execution halted - -checking top-level files ... NOTE -Non-standard file/directory found at top level: - ‘appveyor.yml’ - -checking dependencies in R code ... NOTE -Missing object imported by a ':::' call: ‘AnnotationHub:::.db_connection’ -Unexported object imported by a ':::' call: ‘OrganismDbi:::.packageTaxIds’ - See the note in ?`:::` about the use of this operator. - -checking R code for possible problems ... NOTE -.NCBIMetadataFromUrl: no visible binding for global variable ‘results’ -.NCBIMetadataFromUrl: no visible binding for global variable ‘specData’ -.makeComplexGR: no visible binding for global variable ‘seqname’ -jsonPath: no visible binding for global variable ‘SourceFile’ -jsonPath: no visible binding for global variable ‘HubRoot’ -makeAnnotationHubMetadata : : no visible binding for global - variable ‘Title’ -makeAnnotationHubMetadata : : no visible binding for global - variable ‘Description’ -... 52 lines ... - SourceFile SourceType SourceUrl SourceVersion Species TaxonomyId - Title ahroot bucket checkTrue read.csv results seqname specData - suppresWarnings -Consider adding - importFrom("utils", "read.csv") -to your NAMESPACE file. - -Found the following calls to data() loading into the global environment: -File ‘AnnotationHubData/R/makeNCBIToOrgDbs.R’: - data(specData, package = "GenomeInfoDb") -See section ‘Good practice’ in ‘?data’. -``` - -## AnnotationHub (2.6.0) -Maintainer: Bioconductor Package Maintainer - -0 errors | 0 warnings | 2 notes - -``` -checking R code for possible problems ... NOTE -.get1,EpiExpressionTextResource: no visible global function definition - for ‘read.table’ -Undefined global functions or variables: - read.table -Consider adding - importFrom("utils", "read.table") -to your NAMESPACE file. - -checking Rd files ... NOTE -prepare_Rd: listResources.Rd:44-45: Dropping empty section \seealso -``` - -## APSIM (0.9.1) -Maintainer: Justin Fainges - -0 errors | 0 warnings | 0 notes - -## archivist (2.1) -Maintainer: Przemyslaw Biecek -Bug reports: https://github.com/pbiecek/archivist/issues - -0 errors | 0 warnings | 2 notes - -``` -checking package dependencies ... NOTE -Package which this enhances but not available for checking: ‘archivist.github’ - -checking Rd cross-references ... NOTE -Package unavailable to check Rd xrefs: ‘archivist.github’ -``` - -## BatchExperiments (1.4.1) -Maintainer: Michel Lang -Bug reports: https://github.com/tudo-r/BatchExperiments/issues - -0 errors | 0 warnings | 2 notes - -``` -checking dependencies in R code ... NOTE -Unexported objects imported by ':::' calls: - ‘BatchJobs:::addIntModulo’ ‘BatchJobs:::buffer’ - ‘BatchJobs:::checkDir’ ‘BatchJobs:::checkId’ ‘BatchJobs:::checkIds’ - ‘BatchJobs:::checkPart’ ‘BatchJobs:::createShardedDirs’ - ‘BatchJobs:::dbConnectToJobsDB’ ‘BatchJobs:::dbCreateJobStatusTable’ - ‘BatchJobs:::dbDoQuery’ ‘BatchJobs:::dbFindDone’ - ‘BatchJobs:::dbFindRunning’ ‘BatchJobs:::dbRemoveJobs’ - ‘BatchJobs:::dbSelectWithIds’ ‘BatchJobs:::getJobDirs’ - ‘BatchJobs:::getJobInfoInternal’ ‘BatchJobs:::getKillJob’ - ‘BatchJobs:::getListJobs’ ‘BatchJobs:::getRandomSeed’ - ‘BatchJobs:::getResult’ ‘BatchJobs:::isRegistryDir’ - ‘BatchJobs:::makeRegistryInternal’ ‘BatchJobs:::saveRegistry’ - ‘BatchJobs:::seeder’ ‘BatchJobs:::syncRegistry’ - See the note in ?`:::` about the use of this operator. - -checking R code for possible problems ... NOTE -addExperiments.ExperimentRegistry: no visible global function - definition for ‘is’ -applyJobFunction.ExperimentRegistry: no visible global function - definition for ‘setNames’ -calcDynamic: no visible global function definition for ‘setNames’ -checkExperimentRegistry: no visible global function definition for - ‘head’ -dbSummarizeExperiments: no visible global function definition for - ‘setNames’ -designIterator: no visible global function definition for ‘setNames’ -getIndex : exprToIndex: no visible global function definition for - ‘capture.output’ -getProblemFilePaths: no visible global function definition for - ‘setNames’ -updateRegistry.ExperimentRegistry: no visible global function - definition for ‘packageVersion’ -Undefined global functions or variables: - capture.output head is packageVersion setNames -Consider adding - importFrom("methods", "is") - importFrom("stats", "setNames") - importFrom("utils", "capture.output", "head", "packageVersion") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). -``` - -## BatchJobs (1.6) -Maintainer: Bernd Bischl -Bug reports: https://github.com/tudo-r/BatchJobs/issues - -0 errors | 0 warnings | 0 notes - -## bibliospec (0.0.4) -Maintainer: Witold E. Wolski -Bug reports: https://github.com/protViz/bibliospec/issues - -0 errors | 0 warnings | 0 notes - -## biglm (0.9-1) -Maintainer: Thomas Lumley - -0 errors | 0 warnings | 5 notes - -``` -checking DESCRIPTION meta-information ... NOTE -Malformed Description field: should contain one or more complete sentences. - -checking top-level files ... NOTE -Non-standard file/directory found at top level: - ‘test’ - -checking dependencies in R code ... NOTE -Packages in Depends field not imported from: - ‘DBI’ ‘methods’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - -checking foreign function calls ... NOTE -Call with DUP: - .Fortran("regcf", as.integer(p), as.integer(p * p/2), bigQR$D, - bigQR$rbar, bigQR$thetab, bigQR$tol, beta = numeric(p), nreq = as.integer(nvar), - ier = integer(1), DUP = FALSE) -DUP is no longer supported and will be ignored. - -checking R code for possible problems ... NOTE -bigglm.RODBC: no visible global function definition for ‘odbcQuery’ -bigglm.RODBC : chunk: no visible global function definition for - ‘odbcQuery’ -bigglm.RODBC : chunk: no visible global function definition for - ‘sqlGetResults’ -bigglm,ANY-DBIConnection: no visible global function definition for - ‘dbSendQuery’ -bigglm,ANY-DBIConnection: no visible global function definition for - ‘dbClearResult’ -bigglm,ANY-DBIConnection : chunk: no visible global function definition - for ‘dbClearResult’ -bigglm,ANY-DBIConnection : chunk: no visible global function definition - for ‘dbSendQuery’ -bigglm,ANY-DBIConnection : chunk: no visible global function definition - for ‘fetch’ -Undefined global functions or variables: - dbClearResult dbSendQuery fetch odbcQuery sqlGetResults - -Found the following calls to data() loading into the global environment: -File ‘biglm/R/bigglm.R’: - data(reset = TRUE) - data(reset = FALSE) -See section ‘Good practice’ in ‘?data’. -``` - -## bioassayR (1.12.0) -Maintainer: Tyler Backman -Bug reports: https://github.com/TylerBackman/bioassayR/issues - -0 errors | 0 warnings | 1 note - -``` -checking R code for possible problems ... NOTE -crossReactivityPrior: no visible global function definition for ‘sd’ -crossReactivityProbability : : no visible global function - definition for ‘pbeta’ -Undefined global functions or variables: - pbeta sd -Consider adding - importFrom("stats", "pbeta", "sd") -to your NAMESPACE file. -``` - -## BoSSA (2.0) -Maintainer: pierre lefeuvre - -0 errors | 0 warnings | 0 notes - -## caroline (0.7.6) -Maintainer: David Schruth - -0 errors | 0 warnings | 2 notes - -``` -checking dependencies in R code ... NOTE -'library' or 'require' calls in package code: - ‘MASS’ ‘RSQLite’ ‘grid’ ‘sm’ - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. - -checking R code for possible problems ... NOTE -.ci.median: no visible global function definition for ‘qbinom’ -.ci.median: no visible global function definition for ‘median’ -.ci.median: no visible global function definition for ‘pbinom’ -.description: no visible global function definition for ‘var’ -.description: no visible global function definition for ‘shapiro.test’ -.description: no visible global function definition for ‘quantile’ -.huber.NR: no visible global function definition for ‘median’ -.kurtosis: no visible global function definition for ‘var’ -.kurtosys: no visible global function definition for ‘var’ -... 104 lines ... - importFrom("graphics", "axis", "box", "identify", "image", "lines", - "locator", "mtext", "par", "plot", "plot.new", - "plot.window", "points", "polygon", "rect", "segments", - "text", "title") - importFrom("methods", "as") - importFrom("stats", "median", "pbinom", "qbinom", "qnorm", "quantile", - "runif", "sd", "shapiro.test", "var") - importFrom("utils", "browseURL", "count.fields", "head", "read.delim", - "write.table") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). -``` - -## Category (2.40.0) -Maintainer: Bioconductor Package Maintainer - -0 errors | 0 warnings | 1 note - -``` -checking R code for possible problems ... NOTE -.linearMTestInternal: no visible global function definition for - ‘setNames’ -Undefined global functions or variables: - setNames -Consider adding - importFrom("stats", "setNames") -to your NAMESPACE file. -``` - -## ChemmineR (2.26.0) -Maintainer: Thomas Girke - -1 error | 0 warnings | 0 notes - -``` -checking whether package ‘ChemmineR’ can be installed ... ERROR -Installation failed. -See ‘/home/muelleki/git/R/RSQLite/revdep/checks/ChemmineR.Rcheck/00install.out’ for details. -``` - -## chunked (0.3) -Maintainer: Edwin de Jonge -Bug reports: https://github.com/edwindj/chunked/issues - -0 errors | 0 warnings | 0 notes - -## CITAN (2015.12-2) -Maintainer: Marek Gagolewski -Bug reports: https://github.com/Rexamine/CITAN/issues - -0 errors | 0 warnings | 0 notes - -## clstutils (1.22.0) -Maintainer: Noah Hoffman - -0 errors | 2 warnings | 5 notes - -``` -checking for GNU extensions in Makefiles ... WARNING -Found the following file(s) containing GNU extensions: - tests/unit/Makefile -Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), -$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in -the ‘Writing R Extensions’ manual. - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Loading required package: clst -Loading required package: rjson -Loading required package: ape -Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : - Running 'texi2dvi' on 'pplacerDemo.tex' failed. -LaTeX errors: -! Package auto-pst-pdf Error: - "shell escape" (or "write18") is not enabled: - auto-pst-pdf will not work! -. -Calls: buildVignettes -> texi2pdf -> texi2dvi -Execution halted - - -checking DESCRIPTION meta-information ... NOTE -Malformed Title field: should not end in a period. - -checking top-level files ... NOTE -Non-standard file/directory found at top level: - ‘devmakefile’ - -checking dependencies in R code ... NOTE -'library' or 'require' call to ‘rjson’ which was already attached by Depends. - Please remove these calls from your code. -'library' or 'require' call to ‘RSVGTipsDevice’ in package code. - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. -Packages in Depends field not imported from: - ‘ape’ ‘rjson’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - -checking foreign function calls ... NOTE -Foreign function call to a different package: - .Call("seq_root2tip", ..., PACKAGE = "ape") -See chapter ‘System and foreign language interfaces’ in the ‘Writing R -Extensions’ manual. - -checking R code for possible problems ... NOTE -edgeMap: no visible global function definition for ‘fromJSON’ -findOutliers: no visible global function definition for ‘quantile’ -findOutliers: no visible binding for global variable ‘median’ -maxDists: no visible binding for global variable ‘median’ -placeData: no visible global function definition for ‘read.table’ -prettyTree: no visible binding for global variable ‘par’ -prettyTree: no visible global function definition for ‘plot’ -prettyTree: no visible binding for global variable ‘.PlotPhyloEnv’ -prettyTree: no visible binding for global variable ‘points’ -... 19 lines ... -taxonomyFromRefpkg: no visible global function definition for - ‘read.csv’ -Undefined global functions or variables: - .PlotPhyloEnv dev.off devSVGTips fromJSON legend median par plot - points quantile read.csv read.table setSVGShapeToolTip text -Consider adding - importFrom("grDevices", "dev.off") - importFrom("graphics", "legend", "par", "plot", "points", "text") - importFrom("stats", "median", "quantile") - importFrom("utils", "read.csv", "read.table") -to your NAMESPACE file. -``` - -## CNEr (1.10.0) -Maintainer: Ge Tan -Bug reports: https://github.com/ge11232002/CNEr/issues - -0 errors | 2 warnings | 2 notes - -``` -checking compiled code ... WARNING -File ‘CNEr/libs/CNEr.so’: - Found ‘abort’, possibly from ‘abort’ (C) - Object: ‘ucsc/errabort.o’ - Found ‘exit’, possibly from ‘exit’ (C) - Objects: ‘ucsc/errabort.o’, ‘ucsc/pipeline.o’ - Found ‘printf’, possibly from ‘printf’ (C) - Objects: ‘ceScan.o’, ‘ucsc/pipeline.o’ - Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C) - Object: ‘ucsc/pipeline.o’ - Found ‘rand’, possibly from ‘rand’ (C) - Object: ‘ucsc/obscure.o’ - Found ‘stderr’, possibly from ‘stderr’ (C) - Objects: ‘ucsc/axt.o’, ‘ucsc/errabort.o’, ‘ucsc/obscure.o’, - ‘ucsc/verbose.o’, ‘ucsc/os.o’ - Found ‘stdout’, possibly from ‘stdout’ (C) - Objects: ‘ucsc/common.o’, ‘ucsc/errabort.o’, ‘ucsc/verbose.o’, - ‘ucsc/os.o’ - -Compiled code should not call entry points which might terminate R nor -write to stdout/stderr instead of to the console, nor the system RNG. - -See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because CNEr.Rmd appears to be an R Markdown v2 document. -Quitting from lines 2-15 (CNEr.Rmd) -Error: processing vignette 'CNEr.Rmd' failed with diagnostics: -could not find function "doc_date" -Execution halted - - -checking installed package size ... NOTE - installed size is 28.4Mb - sub-directories of 1Mb or more: - R 11.0Mb - extdata 15.9Mb - -checking dependencies in R code ... NOTE -Unexported objects imported by ':::' calls: - ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::make_zero_col_DataFrame’ - See the note in ?`:::` about the use of this operator. -``` - -## CollapsABEL (0.10.8) -Maintainer: Kaiyin Zhong -Bug reports: https://bitbucket.org/kindlychung/collapsabel2/issues - -0 errors | 0 warnings | 0 notes - -## cummeRbund (2.16.0) -Maintainer: Loyal A. Goff - -0 errors | 0 warnings | 6 notes - -``` -checking package dependencies ... NOTE -Depends: includes the non-default packages: - ‘BiocGenerics’ ‘RSQLite’ ‘ggplot2’ ‘reshape2’ ‘fastcluster’ - ‘rtracklayer’ ‘Gviz’ -Adding so many packages to the search path is excessive and importing -selectively is preferable. - -checking installed package size ... NOTE - installed size is 11.5Mb - sub-directories of 1Mb or more: - R 4.1Mb - doc 1.6Mb - extdata 5.6Mb - -checking DESCRIPTION meta-information ... NOTE -Malformed Title field: should not end in a period. -Packages listed in more than one of Depends, Imports, Suggests, Enhances: - ‘BiocGenerics’ ‘plyr’ -A package should be listed in only one of these fields. - -checking dependencies in R code ... NOTE -'library' or 'require' calls in package code: - 'NMFN' 'cluster' 'rjson' 'stringr' - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. -Packages in Depends field not imported from: - 'Gviz' 'RSQLite' 'fastcluster' 'ggplot2' 'reshape2' 'rtracklayer' - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - -checking R code for possible problems ... NOTE -.CVdensity: no visible global function definition for 'ggplot' -.CVdensity: no visible global function definition for 'geom_density' -.CVdensity: no visible global function definition for 'aes' -.CVdensity: no visible binding for global variable 'CV' -.CVdensity: no visible binding for global variable 'sample_name' -.CVdensity: no visible global function definition for 'scale_x_log10' -.MAplot: no visible global function definition for 'ggplot' -.MAplot: no visible global function definition for 'geom_point' -.MAplot: no visible global function definition for 'aes' -... 1188 lines ... - scale_y_log10 seqnames significant stat_density stat_smooth stat_sum - stat_summary stdev str_split_fixed strand theme theme_bw toJSON - tracking_id tracks unit v1 v2 value variable varnames write.table x - xlab xlim y ylab -Consider adding - importFrom("graphics", "plot") - importFrom("stats", "as.dendrogram", "as.dist", "as.formula", - "cmdscale", "dist", "hclust", "order.dendrogram", - "p.adjust", "prcomp") - importFrom("utils", "read.delim", "read.table", "write.table") -to your NAMESPACE file. - -checking Rd line widths ... NOTE -Rd file 'MAplot.Rd': - \examples lines wider than 100 characters: - a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data - -Rd file 'QCplots.Rd': - \examples lines wider than 100 characters: - a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create CuffSet object - -Rd file 'csBoxplot.Rd': -... 96 lines ... - isoformFPKM = "isoforms.fpkm_tracking", isoformDiff = "isoform_exp.diff", isoformCount="isoforms.count_ ... [TRUNCATED] - TSSFPKM = "tss_groups.fpkm_tracking", TSSDiff = "tss_group_exp.diff", TSSCount="tss_groups.count_tracki ... [TRUNCATED] - CDSFPKM = "cds.fpkm_tracking", CDSExpDiff = "cds_exp.diff", CDSCount="cds.count_tracking", CDSRep="cds. ... [TRUNCATED] - \examples lines wider than 100 characters: - a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data in sample directory and creates CuffSet obj ... [TRUNCATED] - -Rd file 'sigMatrix.Rd': - \examples lines wider than 100 characters: - a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data - -These lines will be truncated in the PDF manual. -``` - -## customProDB (1.14.0) -Maintainer: xiaojing wang - -0 errors | 0 warnings | 3 notes - -``` -checking DESCRIPTION meta-information ... NOTE -Malformed Title field: should not end in a period. -Malformed Description field: should contain one or more complete sentences. -Packages listed in more than one of Depends, Imports, Suggests, Enhances: - ‘IRanges’ ‘biomaRt’ ‘AnnotationDbi’ -A package should be listed in only one of these fields. - -checking dependencies in R code ... NOTE -Unexported objects imported by ':::' calls: - ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’ - See the note in ?`:::` about the use of this operator. - -checking R code for possible problems ... NOTE -.Ensembl.getTable: no visible global function definition for - ‘download.file’ -.Ensembl.getTable: no visible global function definition for - ‘read.table’ -.getDatasetAttrGroups: no visible global function definition for ‘is’ -.makeBiomartChrominfo: no visible global function definition for ‘is’ -.parseBMMartParams: no visible global function definition for ‘is’ -Bed2Range: no visible global function definition for ‘read.table’ -Bed2Range: no visible binding for global variable ‘V5’ -... 54 lines ... - definition for ‘as’ -Undefined global functions or variables: - V5 aapos aaref aavar alleleCount alleles allsample as cds_end - cds_start chrom download.file ensembl_gene_id genename is jun_type - mrnaAcc name pro_name proname protAcc read.table rsid saveDb - transcript txname write.table -Consider adding - importFrom("methods", "as", "is") - importFrom("utils", "download.file", "read.table", "write.table") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). -``` - -## DBI (0.5-1) -Maintainer: Kirill Müller -Bug reports: https://github.com/rstats-db/DBI/issues - -0 errors | 0 warnings | 1 note - -``` -checking S3 generic/method consistency ... NOTE -Found the following apparent S3 methods exported but not registered: - print.list.pairs -See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ -manual. -``` - -## DECIPHER (2.2.0) -Maintainer: Erik Wright - -0 errors | 0 warnings | 3 notes - -``` -checking installed package size ... NOTE - installed size is 8.8Mb - sub-directories of 1Mb or more: - data 2.5Mb - doc 3.8Mb - extdata 1.4Mb - -checking foreign function calls ... NOTE -Registration problems: - symbol ‘functionCall’ in the local frame: - .Call(functionCall, myXStringSet, as.numeric(subMatrix), gapOpening, - gapExtension, gapLetter, shiftPenalty, threshold, weight, - PACKAGE = "DECIPHER") - symbol ‘consensusProfile’ in the local frame: - .Call(consensusProfile, pattern, p.weight, NULL, PACKAGE = "DECIPHER") - symbol ‘consensusProfile’ in the local frame: - .Call(consensusProfile, subject, s.weight, NULL, PACKAGE = "DECIPHER") -... 11 lines ... - structureMatrix) - Evaluating ‘compression[1]’ during check gives error -‘object 'compression' not found’: - .Call(compression[1], x, 2L - length(compression), compressRepeats, - processors, PACKAGE = "DECIPHER") - Evaluating ‘compression[1]’ during check gives error -‘object 'compression' not found’: - .Call(compression[1], x, 2L - length(compression), processors, - PACKAGE = "DECIPHER") -See chapter ‘System and foreign language interfaces’ in the ‘Writing R -Extensions’ manual. - -checking R code for possible problems ... NOTE -DesignSignatures: no visible binding for global variable ‘deltaHrules’ -Undefined global functions or variables: - deltaHrules -``` - -## dplyr (0.5.0) -Maintainer: Hadley Wickham -Bug reports: https://github.com/hadley/dplyr/issues - -0 errors | 0 warnings | 1 note - -``` -checking installed package size ... NOTE - installed size is 16.0Mb - sub-directories of 1Mb or more: - libs 13.9Mb -``` - -## ecd (0.8.2) -Maintainer: Stephen H-T. Lihn - -1 error | 0 warnings | 0 notes - -``` -checking package dependencies ... ERROR -Package required and available but unsuitable version: ‘RSQLite’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -``` - -## emuR (0.1.9) -Maintainer: Raphael Winkelmann -Bug reports: https://github.com/IPS-LMU/emuR/issues - -0 errors | 0 warnings | 0 notes - -## ensembldb (1.6.0) -Maintainer: Johannes Rainer -Bug reports: https://github.com/jotsetung/ensembldb/issues - -0 errors | 0 warnings | 2 notes - -``` -checking dependencies in R code ... NOTE -Unexported objects imported by ':::' calls: - 'GenomicFeatures:::fetchChromLengthsFromEnsembl' - 'GenomicFeatures:::fetchChromLengthsFromEnsemblPlants' - See the note in ?`:::` about the use of this operator. - -checking Rd line widths ... NOTE -Rd file 'EnsDb.Rd': - \examples lines wider than 100 characters: - dbcon <- dbConnect(MySQL(), user = my_user, pass = my_pass, host = my_host, dbname = "ensdb_hsapiens_v75") - -These lines will be truncated in the PDF manual. -``` - -## etl (0.3.3.1) -Maintainer: Ben Baumer -Bug reports: https://github.com/beanumber/etl/issues - -0 errors | 0 warnings | 0 notes - -## ETLUtils (1.3) -Maintainer: Jan Wijffels - -0 errors | 0 warnings | 0 notes - -## filehashSQLite (0.2-4) -Maintainer: Roger D. Peng - -0 errors | 0 warnings | 3 notes - -``` -checking DESCRIPTION meta-information ... NOTE -Malformed Description field: should contain one or more complete sentences. -Packages listed in more than one of Depends, Imports, Suggests, Enhances: - ‘filehash’ ‘DBI’ -A package should be listed in only one of these fields. - -checking dependencies in R code ... NOTE -Packages in Depends field not imported from: - ‘RSQLite’ ‘methods’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - -checking R code for possible problems ... NOTE -createSQLite: no visible global function definition for ‘dbDriver’ -createSQLite: no visible global function definition for ‘dbConnect’ -createSQLite: no visible global function definition for - ‘dbUnloadDriver’ -createSQLite: no visible global function definition for ‘dbGetQuery’ -initializeSQLite: no visible global function definition for ‘dbDriver’ -initializeSQLite: no visible global function definition for ‘dbConnect’ -initializeSQLite: no visible global function definition for ‘new’ -dbDelete,filehashSQLite-character: no visible global function -... 7 lines ... - definition for ‘dbGetQuery’ -dbList,filehashSQLite: no visible global function definition for - ‘dbGetQuery’ -dbMultiFetch,filehashSQLite-character: no visible global function - definition for ‘dbGetQuery’ -Undefined global functions or variables: - dbConnect dbDriver dbGetQuery dbUnloadDriver new -Consider adding - importFrom("methods", "new") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). -``` - -## filematrix (1.1.0) -Maintainer: Andrey A Shabalin -Bug reports: https://github.com/andreyshabalin/filematrix/issues - -0 errors | 1 warning | 0 notes - -``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because Best_Prectices.Rmd appears to be an R Markdown v2 document. -Quitting from lines 2-23 (Best_Prectices.Rmd) -Error: processing vignette 'Best_Prectices.Rmd' failed with diagnostics: -could not find function "doc_date" -Execution halted - -``` - -## freqweights (1.0.2) -Maintainer: Emilio Torres-Manzanera - -0 errors | 0 warnings | 1 note - -``` -checking R code for possible problems ... NOTE -.corfreq: no visible global function definition for ‘complete.cases’ -.covfreq: no visible global function definition for ‘complete.cases’ -.hclustvfreq: no visible global function definition for - ‘complete.cases’ -.quantilefreq : : no visible global function definition for - ‘approx’ -coef.biglmfreq: no visible global function definition for ‘coef’ -predict.biglmfreq: no visible global function definition for ‘predict’ -predict.lmfreq: no visible global function definition for ‘predict’ -summary.lmfreq: no visible global function definition for ‘coef’ -summary.lmfreq: no visible global function definition for ‘pt’ -summary.lmfreq: no visible global function definition for ‘AIC’ -update.biglmfreq: no visible global function definition for ‘update’ -Undefined global functions or variables: - AIC approx coef complete.cases predict pt update -Consider adding - importFrom("stats", "AIC", "approx", "coef", "complete.cases", - "predict", "pt", "update") -to your NAMESPACE file. -``` - -## gcbd (0.2.6) -Maintainer: Dirk Eddelbuettel - -0 errors | 1 warning | 1 note - -``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning in packageDescription("gputools") : - no package 'gputools' was found -Error: processing vignette 'gcbd.Rnw' failed with diagnostics: -at gcbd.Rnw:860, subscript out of bounds -Execution halted - - -checking package dependencies ... NOTE -Package suggested but not available for checking: ‘gputools’ -``` - -## GeneAnswers (2.16.0) -Maintainer: Lei Huang and Gang Feng - -1 error | 3 warnings | 6 notes - -``` -checking examples ... ERROR -Running examples in ‘GeneAnswers-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: chartPlots -> ### Title: Pie Chart and Bar Plots -> ### Aliases: chartPlots -> ### Keywords: methods -> -> ### ** Examples -> -> x <- matrix(c(6,9,3,30,13,2,15,20), nrow = 4, ncol=2, byrow=FALSE, -+ dimnames = list(c("group1", "group2", "group3", "group4"), -+ c("value1", "value2"))) -> chartPlots(x, chartType='all', specifiedCol = "value2", top = 3) -Error in x11() : screen devices should not be used in examples etc -Calls: chartPlots -> x11 -Execution halted - -checking whether package ‘GeneAnswers’ can be installed ... WARNING -Found the following significant warnings: - Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’ - Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’ -See ‘/home/muelleki/git/R/RSQLite/revdep/checks/GeneAnswers.Rcheck/00install.out’ for details. - -checking sizes of PDF files under ‘inst/doc’ ... WARNING - ‘gs+qpdf’ made some significant size reductions: - compacted ‘geneAnswers.pdf’ from 1373Kb to 600Kb - consider running tools::compactPDF(gs_quality = "ebook") on these files - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’ -Loading required package: org.Hs.eg.db - -Loading required package: GO.db - -Loading required package: KEGG.db - -... 8 lines ... -Loading required package: org.Mm.eg.db - -Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : - Running 'texi2dvi' on 'geneAnswers.tex' failed. -LaTeX errors: -! Package auto-pst-pdf Error: - "shell escape" (or "write18") is not enabled: - auto-pst-pdf will not work! -. -Calls: buildVignettes -> texi2pdf -> texi2dvi -Execution halted - -checking package dependencies ... NOTE -Depends: includes the non-default packages: - ‘igraph’ ‘RCurl’ ‘annotate’ ‘Biobase’ ‘XML’ ‘RSQLite’ ‘MASS’ - ‘Heatplus’ ‘RColorBrewer’ -Adding so many packages to the search path is excessive and importing -selectively is preferable. - -checking installed package size ... NOTE - installed size is 36.1Mb - sub-directories of 1Mb or more: - External 32.4Mb - data 1.1Mb - doc 1.6Mb - -checking DESCRIPTION meta-information ... NOTE -Package listed in more than one of Depends, Imports, Suggests, Enhances: - ‘annotate’ -A package should be listed in only one of these fields. - -checking dependencies in R code ... NOTE -'library' or 'require' calls to packages already attached by Depends: - ‘Biobase’ ‘Heatplus’ ‘MASS’ ‘RColorBrewer’ ‘XML’ ‘igraph’ - Please remove these calls from your code. -'library' or 'require' calls in package code: - ‘GO.db’ ‘KEGG.db’ ‘biomaRt’ ‘reactome.db’ - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. - -checking R code for possible problems ... NOTE -Found an obsolete/platform-specific call in the following functions: - ‘chartPlots’ ‘drawTable’ -Found the platform-specific device: - ‘x11’ -dev.new() is the preferred way to open a new device, in the unlikely -event one is needed. -File ‘GeneAnswers/R/zzz.R’: - .onLoad calls: - require(Biobase) -... 78 lines ... - data("DmIALite", package = "GeneAnswers") -File ‘GeneAnswers/R/getDOLiteTerms.R’: - data("DOLiteTerm", package = "GeneAnswers") -File ‘GeneAnswers/R/zzz.R’: - data("DOLite", package = "GeneAnswers") - data("DOLiteTerm", package = "GeneAnswers") - data("HsIALite", package = "GeneAnswers") - data("MmIALite", package = "GeneAnswers") - data("RnIALite", package = "GeneAnswers") - data("DmIALite", package = "GeneAnswers") -See section ‘Good practice’ in ‘?data’. - -checking Rd line widths ... NOTE -Rd file 'GeneAnswers-class.Rd': - \examples lines wider than 100 characters: - x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db', categoryType='GO.BP', testType='hyperG', pvalueT=0.01, FDR.correct=TRUE, geneEx ... [TRUNCATED] - -Rd file 'GeneAnswers-package.Rd': - \examples lines wider than 100 characters: - x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db', categoryType='GO.BP', testType='hyperG', pvalueT=0.01, FDR.correct=TRUE, geneEx ... [TRUNCATED] - -Rd file 'buildNet.Rd': -... 144 lines ... - ## Not run: topDOLITEGenes(x, geneSymbol=TRUE, orderby='pvalue', top=10, topGenes='ALL', genesOrderBy='pValue', file=TRUE) - -Rd file 'topPATHGenes.Rd': - \examples lines wider than 100 characters: - ## Not run: topPATHGenes(x, geneSymbol=TRUE, orderby='genenum', top=6, topGenes=8, genesOrderBy='foldChange') - -Rd file 'topREACTOME.PATHGenes.Rd': - \examples lines wider than 100 characters: - ## Not run: topREACTOME.PATHGenes(x, geneSymbol=TRUE, orderby='pvalue', top=10, topGenes='ALL', genesOrderBy='pValue', file=TRUE) - -These lines will be truncated in the PDF manual. -``` - -## GenomicFeatures (1.26.0) -Maintainer: Bioconductor Package Maintainer - -0 errors | 0 warnings | 2 notes - -``` -checking package dependencies ... NOTE -Depends: includes the non-default packages: - ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’ - ‘AnnotationDbi’ -Adding so many packages to the search path is excessive and importing -selectively is preferable. - -checking dependencies in R code ... NOTE -Unexported objects imported by ':::' calls: - ‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.valid.colnames’ - ‘AnnotationDbi:::.valid.metadata.table’ - ‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’ - ‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’ - ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’ - ‘rtracklayer:::resourceDescription’ ‘rtracklayer:::ucscTableOutputs’ - See the note in ?`:::` about the use of this operator. -``` - -## Genominator (1.28.0) -Maintainer: James Bullard - -0 errors | 0 warnings | 4 notes - -``` -checking dependencies in R code ... NOTE -'library' or 'require' calls to packages already attached by Depends: - ‘GenomeGraphs’ ‘IRanges’ - Please remove these calls from your code. -'library' or 'require' call to ‘ShortRead’ in package code. - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. -Packages in Depends field not imported from: - ‘GenomeGraphs’ ‘RSQLite’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - -checking S3 generic/method consistency ... NOTE -Found the following apparent S3 methods exported but not registered: - plot.genominator.coverage plot.genominator.goodness.of.fit -See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ -manual. - -checking R code for possible problems ... NOTE -addPrimingWeights: no visible global function definition for - ‘varLabels’ -addPrimingWeights: no visible global function definition for - ‘alignData’ -addPrimingWeights: no visible global function definition for ‘subseq’ -addPrimingWeights: no visible global function definition for ‘sread’ -addPrimingWeights: no visible global function definition for - ‘AlignedDataFrame’ -addPrimingWeights: no visible global function definition for ‘pData’ -... 46 lines ... - function definition for ‘qunif’ -plot.genominator.goodness.of.fit : : no visible global - function definition for ‘qqplot’ -Undefined global functions or variables: - AlignedDataFrame DisplayPars alignData chromosome gdPlot - geneRegionBiomart makeAnnotationTrack makeBaseTrack makeGenericArray - makeGenomeAxis mkAllStrings pData position ppoints qchisq qqplot - qunif readAligned sread subseq tables varLabels varMetadata -Consider adding - importFrom("stats", "ppoints", "qchisq", "qqplot", "qunif") -to your NAMESPACE file. - -checking Rd line widths ... NOTE -Rd file 'makeGeneRepresentation.Rd': - \usage lines wider than 90 characters: - "background"), gene.id = "ensembl_gene_id", transcript.id = "ensembl_transcript_id", bind.columns, ignoreStrand = TRUE, verbose = getOp ... [TRUNCATED] - -These lines will be truncated in the PDF manual. -``` - -## GEOmetadb (1.34.0) -Maintainer: Jack Zhu - -0 errors | 0 warnings | 3 notes - -``` -checking for hidden files and directories ... NOTE -Found the following hidden files and directories: - .travis.yml -These were most likely included in error. See section ‘Package -structure’ in the ‘Writing R Extensions’ manual. - -checking R code for possible problems ... NOTE -getSQLiteFile: no visible global function definition for - ‘download.file’ -Undefined global functions or variables: - download.file -Consider adding - importFrom("utils", "download.file") -to your NAMESPACE file. - -checking Rd line widths ... NOTE -Rd file 'geoConvert.Rd': - \usage lines wider than 90 characters: - geoConvert(in_list, out_type = c("gse", "gpl", "gsm", "gds", "smatrix"), sqlite_db_name = "GEOmetadb.sqlite") - -These lines will be truncated in the PDF manual. -``` - -## GWASTools (1.20.0) -Maintainer: Stephanie M. Gogarten , Adrienne Stilp - -0 errors | 0 warnings | 1 note - -``` -checking Rd line widths ... NOTE -Rd file 'assocRegression.Rd': - \examples lines wider than 100 characters: - scanAnnot$blood.pressure[scanAnnot$case.cntl.status==1] <- rnorm(sum(scanAnnot$case.cntl.status==1), mean=100, sd=10) - scanAnnot$blood.pressure[scanAnnot$case.cntl.status==0] <- rnorm(sum(scanAnnot$case.cntl.status==0), mean=90, sd=5) - -Rd file 'createDataFile.Rd': - \usage lines wider than 90 characters: - precision="single", compress="ZIP_RA:8M", compress.geno="ZIP_RA", compress.annot="ZIP_RA", - -These lines will be truncated in the PDF manual. -``` - -## imputeMulti (0.6.3) -Maintainer: Alex Whitworth - -0 errors | 0 warnings | 1 note - -``` -checking dependencies in R code ... NOTE -There are ::: calls to the package's namespace in its code. A package - almost never needs to use ::: for its own objects: - ‘count_compare’ -``` - -## iontree (1.20.0) -Maintainer: Mingshu Cao - -0 errors | 0 warnings | 5 notes - -``` -checking for hidden files and directories ... NOTE -Found the following hidden files and directories: - .BBSoptions -These were most likely included in error. See section ‘Package -structure’ in the ‘Writing R Extensions’ manual. - -checking top-level files ... NOTE -File - LICENSE -is not mentioned in the DESCRIPTION file. - -checking R code for possible problems ... NOTE -buildIonTree: no visible binding for global variable ‘median’ -metaDataImport: no visible global function definition for - ‘flush.console’ -metaDataImport: no visible global function definition for ‘fix’ -plotSpectrum: no visible global function definition for ‘text’ -plotSpectrum: no visible global function definition for ‘identify’ -saveMSnRaw: no visible global function definition for ‘flush.console’ -searchMS2: no visible global function definition for ‘par’ -plot,iontree: no visible global function definition for ‘par’ -plot,iontree: no visible global function definition for ‘layout’ -Undefined global functions or variables: - fix flush.console identify layout median par text -Consider adding - importFrom("graphics", "identify", "layout", "par", "text") - importFrom("stats", "median") - importFrom("utils", "fix", "flush.console") -to your NAMESPACE file. - -checking Rd files ... NOTE -prepare_Rd: buildIonTree.Rd:18-19: Dropping empty section \details -prepare_Rd: buildIonTree.Rd:20-26: Dropping empty section \value -prepare_Rd: buildIonTree.Rd:27-29: Dropping empty section \references -prepare_Rd: buildIonTree.Rd:37-39: Dropping empty section \seealso -prepare_Rd: createDB.Rd:19-20: Dropping empty section \details -prepare_Rd: createDB.Rd:30-32: Dropping empty section \note -prepare_Rd: createDB.Rd:24-26: Dropping empty section \references -prepare_Rd: createDB.Rd:34-36: Dropping empty section \seealso -prepare_Rd: distMS2.Rd:18-19: Dropping empty section \details -... 50 lines ... -prepare_Rd: saveMSnRaw.Rd:33-35: Dropping empty section \note -prepare_Rd: saveMSnRaw.Rd:27-29: Dropping empty section \references -prepare_Rd: saveMSnRaw.Rd:36-38: Dropping empty section \seealso -prepare_Rd: searchMS2.Rd:23-25: Dropping empty section \details -prepare_Rd: searchMS2.Rd:35-36: Dropping empty section \note -prepare_Rd: searchMS2.Rd:29-31: Dropping empty section \references -prepare_Rd: searchMS2.Rd:38-40: Dropping empty section \seealso -prepare_Rd: searchMS2.Rd:41-42: Dropping empty section \examples -prepare_Rd: topIons.Rd:17-19: Dropping empty section \details -prepare_Rd: topIons.Rd:29-31: Dropping empty section \note -prepare_Rd: topIons.Rd:23-25: Dropping empty section \references - -checking Rd line widths ... NOTE -Rd file 'searchMS2.Rd': - \usage lines wider than 90 characters: - searchMS2(querySpec, premz, dbname = "mzDB.db", scoreFun = "distMS2", output.record = 5, plot.top = TRUE) - -These lines will be truncated in the PDF manual. -``` - -## macleish (0.3.0) -Maintainer: Ben Baumer - -0 errors | 0 warnings | 0 notes - -## maGUI (1.0) -Maintainer: Dhammapal Bharne - -1 error | 0 warnings | 0 notes - -``` -checking whether package ‘maGUI’ can be installed ... ERROR -Installation failed. -See ‘/home/muelleki/git/R/RSQLite/revdep/checks/maGUI.Rcheck/00install.out’ for details. -``` - -## manta (1.20.0) -Maintainer: Chris Berthiaume , Adrian Marchetti - - -0 errors | 0 warnings | 7 notes - -``` -checking installed package size ... NOTE - installed size is 5.5Mb - sub-directories of 1Mb or more: - doc 1.4Mb - extdata 4.0Mb - -checking top-level files ... NOTE -File - LICENSE -is not mentioned in the DESCRIPTION file. - -checking dependencies in R code ... NOTE -'library' or 'require' calls in package code: - ‘RSQLite’ ‘plotrix’ - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. -Package in Depends field not imported from: ‘methods’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. -There are ::: calls to the package's namespace in its code. A package - almost never needs to use ::: for its own objects: - ‘.meta2metasum’ - -checking S3 generic/method consistency ... NOTE -Found the following apparent S3 methods exported but not registered: - plot.manta summary.manta -See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ -manual. - -checking R code for possible problems ... NOTE -.MTDheatplot: no visible global function definition for ‘gray’ -.MTDheatplot: no visible global function definition for - ‘colorRampPalette’ -.MTDheatplot: no visible global function definition for ‘abline’ -.MTDheatplot: no visible global function definition for ‘segments’ -.MTDheatplot: no visible global function definition for ‘par’ -.MTDheatplot: no visible global function definition for ‘plot’ -.aggBinCounts: no visible global function definition for ‘hist’ -.aggDESigCumDist: no visible global function definition for ‘hist’ -... 51 lines ... - importFrom("graphics", "abline", "boxplot", "hist", "legend", "par", - "plot", "segments") - importFrom("methods", "new") - importFrom("stats", "aggregate", "anova", "lm", "p.adjust", "var") - importFrom("utils", "read.delim") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). - -Found the following assignments to the global environment: -File ‘manta/R/Util.R’: - assign(keys[i], value, envir = .GlobalEnv) - -checking Rd line widths ... NOTE -Rd file 'compbiasPlot.Rd': - \usage lines wider than 90 characters: - compbiasPlot(x, pair=nv(levels(x$samples$group)[1:2] , c('ref','obs')), meta.lev='phylum', meta.lev.lim=nrow(x$meta.sum[[meta.lev]]), ... [TRUNCATED] - -Rd file 'compbiasTest.Rd': - \usage lines wider than 90 characters: - compbiasTest(x, pair=nv(levels(x$samples$group)[1:2] , c('ref','obs')), meta.lev='phylum', meta.lev.lim=min(10,nrow(x$meta.sum[[meta.l ... [TRUNCATED] - -Rd file 'in2manta.Rd': -... 9 lines ... - -Rd file 'plot.manta.Rd': - \usage lines wider than 90 characters: - meta.level=names(x$meta.sum)[1], meta.lgnd.lim=6, lgd.pos='topright', lgd.cex=.75, lgd.trunk=FALSE, pie.lwd=1, - -Rd file 'readSeastar.Rd': - \usage lines wider than 90 characters: - clmn.names=c('seq_id','bit_score','read_count','raw_abundance','fractional_abundance','mean_coverage','mean_read_length','seq_len','gc_ ... [TRUNCATED] - name.clmn='seq_id', ret.df=FALSE, ret.clmn='read_count', ct.calc=expression(raw_abundance*seq_len), header = FALSE, ...) - -These lines will be truncated in the PDF manual. - -checking Rd \usage sections ... NOTE -S3 methods shown with full name in documentation object 'summary.manta': - ‘summary.manta’ - -The \usage entries for S3 methods should use the \method markup and not -their full name. -See chapter ‘Writing R documentation files’ in the ‘Writing R -Extensions’ manual. -``` - -## marmap (0.9.5) -Maintainer: Eric Pante - -0 errors | 0 warnings | 0 notes - -## MeSHDbi (1.10.0) -Maintainer: Koki Tsuyuzaki - -0 errors | 0 warnings | 2 notes - -``` -checking R code for possible problems ... NOTE -.div: no visible global function definition for ‘na.omit’ -Undefined global functions or variables: - na.omit -Consider adding - importFrom("stats", "na.omit") -to your NAMESPACE file. - -checking Rd line widths ... NOTE -Rd file 'makeMeSHPackage.Rd': - \examples lines wider than 100 characters: - maintainer = "Koki Tsuyuzaki ", - -These lines will be truncated in the PDF manual. -``` - -## metagenomeFeatures (1.4.0) -Maintainer: Nathan D. Olson -Bug reports: https://github.com/HCBravoLab/metagenomeFeatures/issues - -0 errors | 2 warnings | 2 notes - -``` -checking for missing documentation entries ... WARNING -Undocumented S4 methods: - generic 'taxa_columns' and siglist 'MgDb' - generic 'taxa_keys' and siglist 'MgDb' - generic 'taxa_keytypes' and siglist 'MgDb' -All user-level objects in a package (including S4 classes and methods) -should have documentation entries. -See chapter ‘Writing R documentation files’ in the ‘Writing R -Extensions’ manual. - -checking Rd \usage sections ... WARNING -Undocumented arguments in documentation object 'annotateFeatures' - ‘query_key’ -Documented arguments not in \usage in documentation object 'annotateFeatures': - ‘db_keys’ ‘query_df’ - -Functions with \usage entries need to have the appropriate \alias -entries, and all their arguments documented. -The \usage entries must correspond to syntactically valid R code. -See chapter ‘Writing R documentation files’ in the ‘Writing R -Extensions’ manual. - -checking installed package size ... NOTE - installed size is 6.3Mb - sub-directories of 1Mb or more: - R 1.1Mb - extdata 3.4Mb - -checking R code for possible problems ... NOTE -.mgDb_annotateFeatures: no visible binding for global variable - ‘db_keys’ -.select.taxa: no visible binding for global variable ‘Keys’ -.select.taxa: no visible binding for global variable ‘.’ -aggregate_taxa: no visible binding for global variable ‘.’ -aggregate_taxa: no visible binding for global variable ‘index’ -aggregate_taxa: no visible global function definition for - ‘newMRexperiment’ -vignette_pheno_data: no visible global function definition for - ‘read.csv’ -Undefined global functions or variables: - . Keys db_keys index newMRexperiment read.csv -Consider adding - importFrom("utils", "read.csv") -to your NAMESPACE file. -``` - -## MetaIntegrator (1.0.3) -Maintainer: Winston A. Haynes - -0 errors | 0 warnings | 0 notes - -## metaseqR (1.14.0) -Maintainer: Panagiotis Moulos - -1 error | 1 warning | 4 notes - -``` -checking tests ... ERROR -Running the tests in ‘tests/runTests.R’ failed. -Last 13 lines of output: - - Test files with failing tests - - test_estimate_aufc_weights.R - test_estimate_aufc_weights - - test_metaseqr.R - test_metaseqr - - - Error in BiocGenerics:::testPackage("metaseqR") : - unit tests failed for package metaseqR - Execution halted - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... - -The following objects are masked from 'package:ShortRead': - - left, right - -Loading required package: lattice - Welcome to 'DESeq'. For improved performance, usability and -... 8 lines ... - plotMA - -The following object is masked from 'package:BiocGenerics': - - plotMA - -Loading required package: qvalue -Quitting from lines 119-159 (metaseqr-pdf.Rnw) -Error: processing vignette 'metaseqr-pdf.Rnw' failed with diagnostics: -13 simultaneous processes spawned -Execution halted - -checking package dependencies ... NOTE -Package which this enhances but not available for checking: ‘TCC’ - -checking DESCRIPTION meta-information ... NOTE -Malformed Title field: should not end in a period. - -checking dependencies in R code ... NOTE -'library' or 'require' calls in package code: - ‘BSgenome’ ‘BiocInstaller’ ‘GenomicRanges’ ‘RMySQL’ ‘RSQLite’ - ‘Rsamtools’ ‘TCC’ ‘VennDiagram’ ‘parallel’ ‘rtracklayer’ ‘survcomp’ - ‘zoo’ - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. - -checking R code for possible problems ... NOTE -biasPlotToJSON: no visible binding for global variable ‘nams’ -cddat: no visible global function definition for ‘assayData’ -cddat: no visible global function definition for ‘ks.test’ -cddat: no visible global function definition for ‘p.adjust’ -cdplot: no visible global function definition for ‘plot’ -cdplot: no visible global function definition for ‘lines’ -countsBioToJSON: no visible binding for global variable ‘nams’ -diagplot.avg.ftd : : no visible binding for global variable - ‘sd’ -... 246 lines ... - "dev.off", "jpeg", "pdf", "png", "postscript", "tiff") - importFrom("graphics", "abline", "arrows", "axis", "grid", "lines", - "mtext", "par", "plot", "plot.new", "plot.window", "points", - "text", "title") - importFrom("methods", "as", "new") - importFrom("stats", "as.dist", "cmdscale", "cor", "end", "ks.test", - "mad", "median", "model.matrix", "na.exclude", "optimize", - "p.adjust", "p.adjust.methods", "pchisq", "quantile", - "rexp", "rnbinom", "runif", "sd", "start", "var") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). -``` - -## mgsa (1.22.0) -Maintainer: Sebastian Bauer - -0 errors | 1 warning | 5 notes - -``` -checking for GNU extensions in Makefiles ... WARNING -Found the following file(s) containing GNU extensions: - src/Makevars - src/Makevars.in -Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), -$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in -the ‘Writing R Extensions’ manual. - -checking top-level files ... NOTE -Non-standard files/directories found at top level: - ‘acinclude.m4’ ‘aclocal.m4’ ‘script’ - -checking whether the namespace can be loaded with stated dependencies ... NOTE -Warning: no function found corresponding to methods exports from ‘mgsa’ for: ‘show’ - -A namespace must be able to be loaded with just the base namespace -loaded: otherwise if the namespace gets loaded by a saved object, the -session will be unable to start. - -Probably some imports need to be declared in the NAMESPACE file. - -checking dependencies in R code ... NOTE -'library' or 'require' call to ‘gplots’ which was already attached by Depends. - Please remove these calls from your code. -'library' or 'require' calls in package code: - ‘DBI’ ‘GO.db’ ‘RSQLite’ - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. -Packages in Depends field not imported from: - ‘gplots’ ‘methods’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - -checking R code for possible problems ... NOTE -createMgsaGoSets: no visible global function definition for ‘new’ -mcmcSummary: no visible binding for global variable ‘sd’ -mgsa.wrapper: no visible global function definition for ‘str’ -mgsa.wrapper: no visible global function definition for ‘new’ -readGAF: no visible global function definition for ‘read.delim’ -readGAF: no visible global function definition for ‘na.omit’ -readGAF: no visible global function definition for ‘new’ -initialize,MgsaSets: no visible global function definition for - ‘callNextMethod’ -... 10 lines ... - ‘close.screen’ -Undefined global functions or variables: - barplot2 callNextMethod close.screen na.omit new par read.delim - relist screen sd split.screen str -Consider adding - importFrom("graphics", "close.screen", "par", "screen", "split.screen") - importFrom("methods", "callNextMethod", "new") - importFrom("stats", "na.omit", "sd") - importFrom("utils", "read.delim", "relist", "str") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). - -checking compiled code ... NOTE -File ‘mgsa/libs/mgsa.so’: - Found ‘printf’, possibly from ‘printf’ (C) - Object: ‘mgsa.o’ - -Compiled code should not call entry points which might terminate R nor -write to stdout/stderr instead of to the console, nor the system RNG. - -See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. -``` - -## miRNAtap (1.8.0) -Maintainer: Maciej Pajak - -0 errors | 0 warnings | 2 notes - -``` -checking dependencies in R code ... NOTE -'library' or 'require' call to ‘miRNAtap.db’ in package code. - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. - -checking R code for possible problems ... NOTE -getTargetsFromSource: no visible binding for global variable - ‘miRNAtap.db’ -getTargetsFromSource : : no visible binding for global - variable ‘miRNAtap.db’ -translate: no visible binding for global variable ‘miRNAtap.db’ -Undefined global functions or variables: - miRNAtap.db -``` - -## MmPalateMiRNA (1.24.0) -Maintainer: Guy Brock - -0 errors | 0 warnings | 4 notes - -``` -checking package dependencies ... NOTE -Depends: includes the non-default packages: - ‘Biobase’ ‘xtable’ ‘limma’ ‘statmod’ ‘lattice’ ‘vsn’ -Adding so many packages to the search path is excessive and importing -selectively is preferable. - -checking DESCRIPTION meta-information ... NOTE -Packages listed in more than one of Depends, Imports, Suggests, Enhances: - ‘limma’ ‘lattice’ ‘Biobase’ -A package should be listed in only one of these fields. - -checking dependencies in R code ... NOTE -Packages in Depends field not imported from: - ‘methods’ ‘statmod’ ‘vsn’ ‘xtable’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - -checking R code for possible problems ... NOTE -clustPlot: no visible global function definition for ‘par’ -clustPlot: no visible global function definition for ‘plot’ -clustPlot: no visible global function definition for ‘axis’ -clustPlot: no visible global function definition for ‘lines’ -clustPlot: no visible global function definition for ‘legend’ -fixOutliers : : no visible global function definition for - ‘sd’ -imputeKNN: no visible global function definition for ‘sd’ -imputeKNN: no visible global function definition for ‘cor’ -... 36 lines ... - definition for ‘assayData’ -levelplot,list-missing: no visible global function definition for - ‘median’ -Undefined global functions or variables: - RG.MA as.formula assayData axis cor featureData legend lines mad - median pData par plot sd stack -Consider adding - importFrom("graphics", "axis", "legend", "lines", "par", "plot") - importFrom("stats", "as.formula", "cor", "mad", "median", "sd") - importFrom("utils", "stack") -to your NAMESPACE file. -``` - -## MonetDBLite (0.3.1) -Maintainer: Hannes Muehleisen -Bug reports: https://github.com/hannesmuehleisen/MonetDBLite/issues - -0 errors | 0 warnings | 1 note - -``` -checking installed package size ... NOTE - installed size is 8.4Mb - sub-directories of 1Mb or more: - libs 8.1Mb -``` - -## MUCflights (0.0-3) -Maintainer: Manuel Eugster - -0 errors | 0 warnings | 3 notes - -``` -checking dependencies in R code ... NOTE -'library' or 'require' call to ‘XML’ which was already attached by Depends. - Please remove these calls from your code. -Packages in Depends field not imported from: - ‘NightDay’ ‘RSQLite’ ‘XML’ ‘geosphere’ ‘sp’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - -checking R code for possible problems ... NOTE -drawMap: no visible global function definition for ‘plot’ -drawMap: no visible global function definition for ‘box’ -drawMap: no visible global function definition for ‘points’ -getFlights: no visible binding for global variable ‘htmlTreeParse’ -getFlights: no visible binding for global variable ‘xpathSApply’ -getFlights: no visible binding for global variable ‘xmlAttrs’ -getFlights: no visible binding for global variable ‘free’ -movie.routes: no visible global function definition for - ‘txtProgressBar’ -... 16 lines ... -routes: no visible global function definition for ‘gcIntermediate’ -Undefined global functions or variables: - box data dev.off distHaversine free gcIntermediate htmlTreeParse jpeg - lines mtext plot points setTxtProgressBar text txtProgressBar - xmlAttrs xpathSApply -Consider adding - importFrom("grDevices", "dev.off", "jpeg") - importFrom("graphics", "box", "lines", "mtext", "plot", "points", - "text") - importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar") -to your NAMESPACE file. - -checking Rd line widths ... NOTE -Rd file 'flights.Rd': - \usage lines wider than 90 characters: - flights(from = NULL, to = NULL, path = system.file("MUCflights.RData", package = "MUCflights")) - -These lines will be truncated in the PDF manual. -``` - -## nutshell.bbdb (1.0) -Maintainer: Joseph Adler - -0 errors | 0 warnings | 2 notes - -``` -checking installed package size ... NOTE - installed size is 39.0Mb - sub-directories of 1Mb or more: - extdata 38.9Mb - -checking DESCRIPTION meta-information ... NOTE -Malformed Description field: should contain one or more complete sentences. -Deprecated license: CC BY-NC-ND 3.0 US -``` - -## nutshell (2.0) -Maintainer: Joseph Adler - -0 errors | 0 warnings | 3 notes - -``` -checking installed package size ... NOTE - installed size is 8.8Mb - sub-directories of 1Mb or more: - data 8.7Mb - -checking DESCRIPTION meta-information ... NOTE -Malformed Description field: should contain one or more complete sentences. -Deprecated license: CC BY-NC-ND 3.0 US - -checking dependencies in R code ... NOTE -Packages in Depends field not imported from: - ‘nutshell.audioscrobbler’ ‘nutshell.bbdb’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. -``` - -## oai (0.2.0) -Maintainer: Scott Chamberlain -Bug reports: https://github.com/sckott/oai/issues - -0 errors | 0 warnings | 0 notes - -## oce (0.9-19) -Maintainer: Dan Kelley -Bug reports: https://github.com/dankelley/oce/issues - -1 error | 0 warnings | 1 note - -``` -checking examples ... ERROR -Running examples in ‘oce-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: read.oce -> ### Title: Read an Oceanographic Data File -> ### Aliases: read.oce -> -> ### ** Examples -> -> -> library(oce) -> x <- read.oce(system.file("extdata", "ctd.cnv", package="oce")) -> plot(x) # summary with TS and profiles -Error in if (!is.null(x@metadata$startTime) && 4 < nchar(x@metadata$startTime, : - missing value where TRUE/FALSE needed -Calls: plot -> plot -> .local -Execution halted - -checking installed package size ... NOTE - installed size is 5.1Mb - sub-directories of 1Mb or more: - help 2.0Mb -``` - -## oligoClasses (1.36.0) -Maintainer: Benilton Carvalho and Robert Scharpf - -0 errors | 1 warning | 4 notes - -``` -checking for missing documentation entries ... WARNING -Undocumented S4 methods: - generic '[' and siglist 'CNSet,ANY,ANY,ANY' - generic '[' and siglist 'gSetList,ANY,ANY,ANY' -All user-level objects in a package (including S4 classes and methods) -should have documentation entries. -See chapter ‘Writing R documentation files’ in the ‘Writing R -Extensions’ manual. - -checking package dependencies ... NOTE -Packages which this enhances but not available for checking: - ‘doMC’ ‘doMPI’ ‘doSNOW’ ‘doRedis’ - -checking dependencies in R code ... NOTE -Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’ - See the note in ?`:::` about the use of this operator. - -checking R code for possible problems ... NOTE -getSequenceLengths: no visible binding for global variable ‘seqlengths’ -pdPkgFromBioC: no visible binding for global variable ‘contrib.url’ -pdPkgFromBioC: no visible global function definition for - ‘available.packages’ -pdPkgFromBioC: no visible global function definition for - ‘install.packages’ -chromosome,gSetList: no visible global function definition for - ‘chromosomeList’ -coerce,CNSet-CopyNumberSet: no visible global function definition for - ‘totalCopynumber’ -geometry,FeatureSet: no visible global function definition for ‘getPD’ -Undefined global functions or variables: - available.packages chromosomeList contrib.url getPD install.packages - seqlengths totalCopynumber -Consider adding - importFrom("utils", "available.packages", "contrib.url", - "install.packages") -to your NAMESPACE file. - -checking Rd line widths ... NOTE -Rd file 'AssayDataList.Rd': - \examples lines wider than 100 characters: - r <- lapply(r, function(x,dns) {dimnames(x) <- dns; return(x)}, dns=list(letters[1:5], LETTERS[1:5])) - -Rd file 'GenomeAnnotatedDataFrameFrom-methods.Rd': - \examples lines wider than 100 characters: - dimnames=list(c("rs10000092","rs1000055", "rs100016", "rs10003241", "rs10004197"), NULL)) - -Rd file 'largeObjects.Rd': - \usage lines wider than 90 characters: - initializeBigMatrix(name=basename(tempfile()), nr=0L, nc=0L, vmode = "integer", initdata = NA) - -Rd file 'oligoSetExample.Rd': - \examples lines wider than 100 characters: - copyNumber=integerMatrix(log2(locusLevelData[["copynumber"]]/100), 100), - -These lines will be truncated in the PDF manual. -``` - -## oligo (1.38.0) -Maintainer: Benilton Carvalho - -1 error | 0 warnings | 9 notes - -``` -checking examples ... ERROR -Running examples in ‘oligo-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: MAplot -> ### Title: MA plots -> ### Aliases: MAplot MAplot-methods MAplot,FeatureSet-method -> ### MAplot,TilingFeatureSet-method MAplot,PLMset-method -> ### MAplot,ExpressionSet-method MAplot,matrix-method -... 8 lines ... -+ groups <- factor(rep(c('brain', 'UnivRef'), each=3)) -+ data.frame(sampleNames(nimbleExpressionFS), groups) -+ MAplot(nimbleExpressionFS, pairs=TRUE, ylim=c(-.5, .5), groups=groups) -+ } -Loading required package: oligoData -Loading required package: pd.hg18.60mer.expr -Loading required package: RSQLite -Loading required package: DBI -Error in loadNamespace(name) : there is no package called ‘KernSmooth’ -Calls: MAplot ... tryCatch -> tryCatchList -> tryCatchOne -> -Execution halted - -checking package dependencies ... NOTE -Packages which this enhances but not available for checking: ‘doMC’ ‘doMPI’ - -checking installed package size ... NOTE - installed size is 30.2Mb - sub-directories of 1Mb or more: - R 1.2Mb - doc 12.9Mb - scripts 15.7Mb - -checking DESCRIPTION meta-information ... NOTE -Packages listed in more than one of Depends, Imports, Suggests, Enhances: - ‘biomaRt’ ‘AnnotationDbi’ ‘GenomeGraphs’ ‘RCurl’ ‘ff’ -A package should be listed in only one of these fields. - -checking top-level files ... NOTE -Non-standard file/directory found at top level: - ‘TODO.org’ - -checking whether the namespace can be loaded with stated dependencies ... NOTE -Warning: no function found corresponding to methods exports from ‘oligo’ for: ‘show’ - -A namespace must be able to be loaded with just the base namespace -loaded: otherwise if the namespace gets loaded by a saved object, the -session will be unable to start. - -Probably some imports need to be declared in the NAMESPACE file. - -checking dependencies in R code ... NOTE -Unexported object imported by a ':::' call: ‘Biobase:::annotatedDataFrameFromMatrix’ - See the note in ?`:::` about the use of this operator. - -checking foreign function calls ... NOTE -Foreign function calls to a different package: - .Call("ReadHeader", ..., PACKAGE = "affyio") - .Call("read_abatch", ..., PACKAGE = "affyio") -See chapter ‘System and foreign language interfaces’ in the ‘Writing R -Extensions’ manual. - -checking R code for possible problems ... NOTE -image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]): - partial argument match of 'nr' to 'nrow' -image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]): - partial argument match of 'nc' to 'ncol' -NUSE: no visible global function definition for ‘abline’ -RLE: no visible global function definition for ‘abline’ -basicMvApairsPlot: no visible binding for global variable - ‘smoothScatter’ -basicMvApairsPlot: no visible global function definition for ‘frame’ -... 36 lines ... -Undefined global functions or variables: - IQR abline aggregate approx complete.cases data frame intensities - loess man_fsetid mtext predict rnorm smooth.spline smoothScatter - splinefun text -Consider adding - importFrom("graphics", "abline", "frame", "mtext", "smoothScatter", - "text") - importFrom("stats", "IQR", "aggregate", "approx", "complete.cases", - "loess", "predict", "rnorm", "smooth.spline", "splinefun") - importFrom("utils", "data") -to your NAMESPACE file. - -checking Rd line widths ... NOTE -Rd file 'basicRMA.Rd': - \usage lines wider than 90 characters: - basicRMA(pmMat, pnVec, normalize = TRUE, background = TRUE, bgversion = 2, destructive = FALSE, verbose = TRUE, ...) - -Rd file 'fitProbeLevelModel.Rd': - \usage lines wider than 90 characters: - fitProbeLevelModel(object, background=TRUE, normalize=TRUE, target="core", method="plm", verbose=TRUE, S4=TRUE, ...) - -Rd file 'getProbeInfo.Rd': - \usage lines wider than 90 characters: - getProbeInfo(object, field, probeType = "pm", target = "core", sortBy = c("fid", "man_fsetid", "none"), ...) - \examples lines wider than 100 characters: - agenGene <- getProbeInfo(affyGeneFS, field=c('fid', 'fsetid', 'type'), target='probeset', subset= type == 'control->bgp->antigenomic ... [TRUNCATED] - -Rd file 'preprocessTools.Rd': - \usage lines wider than 90 characters: - backgroundCorrect(object, method=backgroundCorrectionMethods(), copy=TRUE, extra, subset=NULL, target='core', verbose=TRUE) - normalize(object, method=normalizationMethods(), copy=TRUE, subset=NULL,target='core', verbose=TRUE, ...) - -These lines will be truncated in the PDF manual. -``` - -## OrganismDbi (1.16.0) -Maintainer: Biocore Data Team - -0 errors | 0 warnings | 2 notes - -``` -checking dependencies in R code ... NOTE -Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’ - See the note in ?`:::` about the use of this operator. -There are ::: calls to the package's namespace in its code. A package - almost never needs to use ::: for its own objects: - ‘.biocAnnPackages’ ‘.extractPkgsAndCols’ ‘.gentlyExtractDbFiles’ - ‘.lookupDbNameFromKeytype’ ‘.mungeGraphData’ ‘.taxIdToOrgDb’ - ‘.taxIdToOrgDbName’ ‘.testGraphData’ ‘.testKeys’ ‘OrganismDb’ - -checking R code for possible problems ... NOTE -Found the following assignments to the global environment: -File ‘OrganismDbi/R/createOrganismPackage.R’: - assign(txdbName, txdb, .GlobalEnv) - assign(orgdbName, orgdb, .GlobalEnv) - assign(orgdbName, orgdb, .GlobalEnv) -``` - -## PAnnBuilder (1.38.0) -Maintainer: Li Hong - -0 errors | 3 warnings | 1 note - -``` -checking dependencies in R code ... WARNING -'library' or 'require' call to ‘Biobase’ which was already attached by Depends. - Please remove these calls from your code. -':::' calls which should be '::': - ‘AnnotationDbi:::as.list’ ‘base:::get’ ‘tools:::list_files_with_type’ - See the note in ?`:::` about the use of this operator. -Unexported objects imported by ':::' calls: - ‘AnnotationDbi:::createAnnDbBimaps’ - ‘AnnotationDbi:::prefixAnnObjNames’ ‘tools:::makeLazyLoadDB’ - See the note in ?`:::` about the use of this operator. - Including base/recommended package(s): - ‘tools’ -There are ::: calls to the package's namespace in its code. A package - almost never needs to use ::: for its own objects: - ‘getShortSciName’ ‘twoStepSplit’ - -checking R code for possible problems ... WARNING -Found an obsolete/platform-specific call in the following function: - ‘makeLLDB’ -Found the defunct/removed function: - ‘.saveRDS’ - -In addition to the above warning(s), found the following notes: - -File ‘PAnnBuilder/R/zzz.R’: - .onLoad calls: - require(Biobase) - -Package startup functions should not change the search path. -See section ‘Good practice’ in '?.onAttach'. - -Found the following calls to data() loading into the global environment: -File ‘PAnnBuilder/R/writeManPage.R’: - data("descriptionInfo") - data("descriptionInfo") -See section ‘Good practice’ in ‘?data’. - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... - } - - -trying URL 'http://gpcr2.biocomp.unibo.it/bacello/dataset.htm' -Content type 'text/html; charset=iso-8859-1' length 5062 bytes -================================================== -downloaded 5062 bytes -... 8 lines ... -Warning in rsqlite_disconnect(conn@ptr) : - There are 1 result in use. The connection will be released when they are closed -Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : - Running 'texi2dvi' on 'PAnnBuilder.tex' failed. -LaTeX errors: -! Package auto-pst-pdf Error: - "shell escape" (or "write18") is not enabled: - auto-pst-pdf will not work! -. -Calls: buildVignettes -> texi2pdf -> texi2dvi -Execution halted - -checking DESCRIPTION meta-information ... NOTE -Packages listed in more than one of Depends, Imports, Suggests, Enhances: - ‘methods’ ‘utils’ ‘Biobase’ ‘RSQLite’ ‘AnnotationDbi’ -A package should be listed in only one of these fields. -``` - -## pdInfoBuilder (1.38.0) -Maintainer: Benilton Carvalho - -0 errors | 0 warnings | 1 note - -``` -checking R code for possible problems ... NOTE -cdf2table: no visible global function definition for ‘getDoParWorkers’ -cdf2table: no visible global function definition for ‘%dopar%’ -cdf2table: no visible global function definition for ‘foreach’ -cdf2table: no visible binding for global variable ‘unitLst’ -cdfUnits2table: no visible global function definition for ‘%do%’ -cdfUnits2table: no visible global function definition for ‘foreach’ -cdfUnits2table: no visible binding for global variable ‘i’ -createChrDict: no visible global function definition for ‘na.omit’ -getAllFSetMpsTables: no visible global function definition for - ‘%dopar%’ -getAllFSetMpsTables: no visible global function definition for - ‘foreach’ -getAllFSetMpsTables: no visible binding for global variable ‘i’ -parseBpmapCel: no visible global function definition for ‘aggregate’ -parseCdfSeqAnnotSnp: no visible global function definition for - ‘aggregate’ -parseNgsTrio: no visible global function definition for ‘aggregate’ -Undefined global functions or variables: - %do% %dopar% aggregate foreach getDoParWorkers i na.omit unitLst -Consider adding - importFrom("stats", "aggregate", "na.omit") -to your NAMESPACE file. -``` - -## PGA (1.4.0) -Maintainer: Bo Wen , Shaohang Xu - -0 errors | 0 warnings | 3 notes - -``` -checking installed package size ... NOTE - installed size is 5.6Mb - sub-directories of 1Mb or more: - extdata 1.8Mb - -checking dependencies in R code ... NOTE -Unexported objects imported by ':::' calls: - ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’ - ‘customProDB:::makeTranscriptDbFromBiomart_archive’ - See the note in ?`:::` about the use of this operator. - -checking R code for possible problems ... NOTE -.base_transfer: no visible binding for global variable ‘peptide’ -.base_transfer: no visible binding for global variable ‘refbase’ -.base_transfer: no visible binding for global variable ‘varbase’ -.base_transfer: no visible binding for global variable ‘aaref’ -.base_transfer: no visible binding for global variable ‘aavar’ -.base_transfer: no visible binding for global variable ‘Type’ -.base_transfer: no visible binding for global variable ‘Freq’ -.get_30aa_splited_seq: no visible global function definition for ‘.’ -.get_30aa_splited_seq: no visible binding for global variable ‘id’ -... 216 lines ... -reportSNV: no visible binding for global variable ‘abc’ -reportSNV: no visible binding for global variable ‘xyz’ -Undefined global functions or variables: - . .I .N .SD CUFF_ID Change Class Evalue Frame Freq ID Index Mass - MutNum Query Qvalue Strand Substring Type aapos aaref aavar abc - alleleCount alleles charge chr chrom cumlen delta_da delta_ppm evalue - gene_name genename genome<- id isSAP isUnique junType jun_type label - miss mods mrnaAcc mz name output pep peptide pincoding position - pro_name proname prot protAcc protein rbindlist readAAStringSet - readDNAStringSet refbase rsid seqlengths seqlevels seqlevels<- subseq - transcript tx_name txid txname varbase writeXStringSet x xyz y -``` - -## pitchRx (1.8.2) -Maintainer: Carson Sievert -Bug reports: http://github.com/cpsievert/pitchRx/issues - -0 errors | 0 warnings | 1 note - -``` -checking package dependencies ... NOTE -Package suggested but not available for checking: ‘ggsubplot’ -``` - -## plethy (1.12.0) -Maintainer: Daniel Bottomly - -2 errors | 1 warning | 3 notes - -``` -checking examples ... ERROR -Running examples in ‘plethy-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: BuxcoDB-class -> ### Title: Class '"BuxcoDB"' -> ### Aliases: BuxcoDB-class BuxcoDB addAnnotation,BuxcoDB-method -> ### addAnnotation annoTable,BuxcoDB-method annoTable -> ### annoCols,BuxcoDB-method annoCols annoLevels,BuxcoDB-method annoLevels -... 53 lines ... -> -> tables(bux.db) -[1] "WBPth" -> -> variables(bux.db) - [1] "f" "TVb" "MVb" "Penh" "PAU" "Rpef" "Comp" "PIFb" "PEFb" -[10] "Ti" "Te" "EF50" "Tr" "Tbody" "Tc" "RH" "Rinx" -> -> addAnnotation(bux.db, query=day.infer.query, index=FALSE) -Error: is.null(dbGetQuery(db.con, i)) is not TRUE -Execution halted - -checking tests ... ERROR -Running the tests in ‘tests/runTests.R’ failed. -Last 13 lines of output: - test.db.insert.autoincrement - test.dbImport - test.examine.table.lines - test.get.err.breaks - test.parse.buxco - test.retrieveData - test.summaryMeasures - test.write.sample.db - - - Error in BiocGenerics:::testPackage("plethy") : - unit tests failed for package plethy - Execution halted - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... - - IQR, mad, xtabs - -The following objects are masked from ‘package:base’: - - Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, - cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, -... 8 lines ... -Attaching package: ‘S4Vectors’ - -The following objects are masked from ‘package:base’: - - colMeans, colSums, expand.grid, rowMeans, rowSums - - -Error: processing vignette 'plethy.Rnw' failed with diagnostics: - chunk 3 -Error : is.null(dbGetQuery(db.con, query.list[[i]])) is not TRUE -Execution halted - -checking dependencies in R code ... NOTE -There are ::: calls to the package's namespace in its code. A package - almost never needs to use ::: for its own objects: - ‘csv.to.table’ ‘find.break.ranges.integer’ ‘fix.time’ ‘multi.grep’ - -checking R code for possible problems ... NOTE -generate.sample.buxco : : : : - : no visible global function definition for ‘rnorm’ -make.db.package: no visible global function definition for - ‘packageDescription’ -mvtsplot.data.frame: no visible global function definition for ‘colors’ -mvtsplot.data.frame: no visible global function definition for ‘par’ -mvtsplot.data.frame: no visible global function definition for ‘layout’ -mvtsplot.data.frame: no visible global function definition for - ‘strwidth’ -... 14 lines ... -tsplot,BuxcoDB: no visible binding for global variable ‘Sample_Name’ -Undefined global functions or variables: - Axis Days Sample_Name Value abline bxp colors layout legend lines - median mtext packageDescription par plot rnorm strwidth terms -Consider adding - importFrom("grDevices", "colors") - importFrom("graphics", "Axis", "abline", "bxp", "layout", "legend", - "lines", "mtext", "par", "plot", "strwidth") - importFrom("stats", "median", "rnorm", "terms") - importFrom("utils", "packageDescription") -to your NAMESPACE file. - -checking Rd line widths ... NOTE -Rd file 'parsing.Rd': - \usage lines wider than 90 characters: - parse.buxco(file.name = NULL, table.delim = "Table", burn.in.lines = c("Measurement", "Create measurement", "Waiting for", "Site Acknow ... [TRUNCATED] - chunk.size = 500, db.name = "bux_test.db", max.run.time.minutes = 60, overwrite = TRUE, verbose=TRUE, make.package = F, author = NULL ... [TRUNCATED] - parse.buxco.basic(file.name=NULL, table.delim="Table", burn.in.lines=c("Measurement", "Create measurement", "Waiting for", "Site Acknow ... [TRUNCATED] - -Rd file 'utilities.Rd': - \usage lines wider than 90 characters: - get.err.breaks(bux.db, max.exp.count=150, max.acc.count=900, vary.perc=.1, label.val="ERR") - proc.sanity(bux.db, max.exp.time=300, max.acc.time=1800, max.exp.count=150, max.acc.count=900) - \examples lines wider than 100 characters: - err.dta <- data.frame(samples=samples, count=count, measure_break=measure_break, table_break=table_break, phase=phase, stringsAsFactors ... [TRUNCATED] - sample.labels <- data.frame(samples=c("sample_1","sample_3"), response_type=c("high", "low"),stringsAsFactors=FALSE) - -These lines will be truncated in the PDF manual. -``` - -## poplite (0.99.16) -Maintainer: Daniel Bottomly - -1 error | 0 warnings | 1 note - -``` -checking tests ... ERROR -Running the tests in ‘tests/testthat.R’ failed. -Last 13 lines of output: - 1. Failure: createTable (@test-poplite.R#252) - 2. Failure: createTable (@test-poplite.R#252) - 3. Failure: createTable (@test-poplite.R#252) - 4. Failure: createTable (@test-poplite.R#252) - 5. Failure: insertStatement (@test-poplite.R#330) - 6. Failure: insertStatement (@test-poplite.R#350) - 7. Failure: insertStatement (@test-poplite.R#330) - 8. Failure: insertStatement (@test-poplite.R#350) - 9. Failure: insertStatement (@test-poplite.R#330) - 1. ... - - Error: testthat unit tests failed - Execution halted - -checking R code for possible problems ... NOTE -filter_.Database: no visible global function definition for ‘stack’ -get.starting.point : : no visible global function definition - for ‘na.omit’ -select_.Database: no visible global function definition for ‘stack’ -tsl.to.graph: no visible global function definition for ‘stack’ -join,Database: no visible global function definition for ‘stack’ -join,Database : .get.select.cols: no visible global function definition - for ‘setNames’ -join,Database: no visible binding for global variable ‘new.ancil’ -join,Database: no visible global function definition for ‘setNames’ -Undefined global functions or variables: - na.omit new.ancil setNames stack -Consider adding - importFrom("stats", "na.omit", "setNames") - importFrom("utils", "stack") -to your NAMESPACE file. -``` - -## ProjectTemplate (0.7) -Maintainer: Kenton White -Bug reports: https://github.com/johnmyleswhite/ProjectTemplate/issues - -0 errors | 0 warnings | 0 notes - -## quantmod (0.4-6) -Maintainer: Joshua M. Ulrich -Bug reports: https://github.com/joshuaulrich/quantmod/issues - -0 errors | 0 warnings | 1 note - -``` -checking R code for possible problems ... NOTE -Found the following calls to attach(): -File ‘quantmod/R/attachSymbols.R’: - attach(NULL, pos = pos, name = DB$name) - attach(NULL, pos = pos, name = DB$name) -See section ‘Good practice’ in ‘?attach’. -``` - -## rangeMapper (0.3-0) -Maintainer: Mihai Valcu - -0 errors | 0 warnings | 0 notes - -## RecordLinkage (0.4-10) -Maintainer: Andreas Borg - -0 errors | 0 warnings | 0 notes - -## recoup (1.2.0) -Maintainer: Panagiotis Moulos - -2 errors | 0 warnings | 1 note - -``` -checking examples ... ERROR -Running examples in ‘recoup-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: calcCoverage -> ### Title: Calculate coverages over a genomic region -> ### Aliases: calcCoverage -> -> ### ** Examples -> -> # Load some data -> data("recoup_test_data",package="recoup") -> -> # Calculate coverage Rle -> mask <- makeGRangesFromDataFrame(df=test.genome, -+ keep.extra.columns=TRUE) -> small.cov <- calcCoverage(test.input[[1]]$ranges,mask) -Error in .check_ncores(cores) : 16 simultaneous processes spawned -Calls: calcCoverage ... splitBySeqname -> cmclapply -> mclapply -> .check_ncores -Execution halted -** found \donttest examples: check also with --run-donttest - -checking tests ... ERROR -Running the tests in ‘tests/runTests.R’ failed. -Last 13 lines of output: - 1 Test Suite : - recoup RUnit Tests - 1 test function, 1 error, 0 failures - ERROR in test_recoup: Error in .check_ncores(cores) : 16 simultaneous processes spawned - - Test files with failing tests - - test_recoup.R - test_recoup - - - Error in BiocGenerics:::testPackage("recoup") : - unit tests failed for package recoup - Execution halted - -checking R code for possible problems ... NOTE -areColors : : no visible global function definition for - ‘col2rgb’ -buildAnnotationStore: no visible global function definition for - ‘Seqinfo’ -calcCoverage: no visible global function definition for ‘is’ -calcDesignPlotProfiles : : no visible global function - definition for ‘smooth.spline’ -calcPlotProfiles : : no visible global function definition - for ‘smooth.spline’ -... 94 lines ... -Consider adding - importFrom("grDevices", "bmp", "col2rgb", "dev.new", "dev.off", "jpeg", - "pdf", "png", "postscript", "tiff") - importFrom("graphics", "plot") - importFrom("methods", "as", "is") - importFrom("stats", "approx", "kmeans", "lowess", "quantile", - "smooth.spline", "spline", "var") - importFrom("utils", "download.file", "packageVersion", "read.delim", - "unzip") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). -``` - -## refGenome (1.7.0) -Maintainer: Wolfgang Kaisers - -0 errors | 0 warnings | 0 notes - -## rgrass7 (0.1-9) -Maintainer: Roger Bivand - -0 errors | 0 warnings | 0 notes - -## RImmPort (1.2.0) -Maintainer: Ravi Shankar - -0 errors | 1 warning | 1 note - -``` -checking sizes of PDF files under ‘inst/doc’ ... WARNING - ‘gs+qpdf’ made some significant size reductions: - compacted ‘RImmPort_Article.pdf’ from 731Kb to 336Kb - consider running tools::compactPDF(gs_quality = "ebook") on these files - -checking R code for possible problems ... NOTE -getCellularQuantification: no visible binding for global variable - ‘experiment_sample_accession’ -getCellularQuantification: no visible binding for global variable - ‘control_files_names’ -getCellularQuantification: no visible binding for global variable - ‘ZBREFIDP’ -getGeneticsFindings: no visible binding for global variable - ‘experiment_sample_accession’ -getNucleicAcidQuantification: no visible binding for global variable - ‘experiment_sample_accession’ -getProteinQuantification: no visible binding for global variable - ‘experiment_sample_accession’ -getTiterAssayResults: no visible binding for global variable - ‘experiment_sample_accession’ -Undefined global functions or variables: - ZBREFIDP control_files_names experiment_sample_accession -``` - -## RObsDat (16.03) -Maintainer: Dominik Reusser - -0 errors | 0 warnings | 0 notes - -## rplexos (1.1.8) -Maintainer: Clayton Barrows -Bug reports: https://github.com/NREL/rplexos/issues - -0 errors | 0 warnings | 0 notes - -## RQDA (0.2-7) -Maintainer: HUANG Ronggui - -1 error | 0 warnings | 1 note - -``` -checking whether package ‘RQDA’ can be installed ... ERROR -Installation failed. -See ‘/home/muelleki/git/R/RSQLite/revdep/checks/RQDA.Rcheck/00install.out’ for details. - -checking package dependencies ... NOTE -Packages which this enhances but not available for checking: - ‘rjpod’ ‘d3Network’ -``` - -## rTRM (1.12.0) -Maintainer: Diego Diez -Bug reports: https://github.com/ddiez/rTRM/issues - -0 errors | 0 warnings | 1 note - -``` -checking Rd line widths ... NOTE -Rd file 'findTRM.Rd': - \usage lines wider than 90 characters: - findTRM(g, target, query, method = "nsa", max.bridge = 1, extended = FALSE, strict = FALSE, type = "igraph") - -Rd file 'plotGraph.Rd': - \usage lines wider than 90 characters: - plotGraph(g, layout = layout.fruchterman.reingold, mar = .5, vertex.pch = 21, vertex.cex, vertex.col, vertex.bg, vertex.lwd, edge.col, ... [TRUNCATED] - -Rd file 'plotTRM.Rd': - \usage lines wider than 90 characters: - plotTRM(g, layout = layout.fruchterman.reingold, mar = .5, vertex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TR ... [TRUNCATED] - -Rd file 'processBiogrid.Rd': - \usage lines wider than 90 characters: - processBiogrid(dblist, org = "human", simplify = TRUE, type = "physical", mimic.old = FALSE) - -These lines will be truncated in the PDF manual. -``` - -## rvertnet (0.5.0) -Maintainer: Scott Chamberlain -Bug reports: https://github.com/ropensci/rvertnet/issues - -0 errors | 0 warnings | 0 notes - -## scrime (1.3.3) -Maintainer: Holger Schwender - -0 errors | 0 warnings | 2 notes - -``` -checking dependencies in R code ... NOTE -'library' or 'require' calls in package code: - ‘MASS’ ‘oligoClasses’ - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. - -checking R code for possible problems ... NOTE -abf: no visible global function definition for ‘qnorm’ -abf: no visible global function definition for ‘dnorm’ -analyse.models: no visible global function definition for ‘read.table’ -buildSNPannotation: no visible global function definition for ‘db’ -buildSNPannotation: no visible global function definition for - ‘dbListFields’ -buildSNPannotation: no visible global function definition for - ‘dbGetQuery’ -chisqClass2: no visible global function definition for ‘pchisq’ -... 48 lines ... -Undefined global functions or variables: - as.dist db dbGetQuery dbListFields dist dnorm glm is mvrnorm pchisq - pnorm predict qnorm rbinom read.table rgamma runif sd write.table -Consider adding - importFrom("methods", "is") - importFrom("stats", "as.dist", "dist", "dnorm", "glm", "pchisq", - "pnorm", "predict", "qnorm", "rbinom", "rgamma", "runif", - "sd") - importFrom("utils", "read.table", "write.table") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). -``` - -## SEERaBomb (2016.1) -Maintainer: Tomas Radivoyevitch - -0 errors | 0 warnings | 0 notes - -## seqplots (1.12.0) -Maintainer: Przemyslaw Stempor -Bug reports: http://github.com/przemol/seqplots/issues - -0 errors | 0 warnings | 3 notes - -``` -checking installed package size ... NOTE - installed size is 9.1Mb - sub-directories of 1Mb or more: - R 1.2Mb - doc 2.4Mb - seqplots 4.9Mb - -checking foreign function calls ... NOTE -Foreign function call to a different package: - .Call("BWGFile_summary", ..., PACKAGE = "rtracklayer") -See chapter ‘System and foreign language interfaces’ in the ‘Writing R -Extensions’ manual. - -checking R code for possible problems ... NOTE -getPlotSetArray : : no visible global function definition - for ‘qt’ -getSF : : no visible global function definition for ‘approx’ -ggHeatmapPlotWrapper: no visible global function definition for - ‘colorRampPalette’ -ggHeatmapPlotWrapper: no visible binding for global variable ‘Var2’ -ggHeatmapPlotWrapper: no visible binding for global variable ‘Var1’ -ggHeatmapPlotWrapper: no visible binding for global variable ‘value’ -heatmapPlotWrapper: no visible global function definition for -... 39 lines ... - capture.output colorRampPalette cutree dist hclust image kmeans - layout lines mtext par plot.new qt rainbow rect rgb title value -Consider adding - importFrom("grDevices", "adjustcolor", "colorRampPalette", "rainbow", - "rgb") - importFrom("graphics", "abline", "axis", "box", "image", "layout", - "lines", "mtext", "par", "plot.new", "rect", "title") - importFrom("stats", "approx", "as.dendrogram", "cutree", "dist", - "hclust", "kmeans", "qt") - importFrom("utils", "capture.output") -to your NAMESPACE file. -``` - -## SGP (1.5-0.0) -Maintainer: Damian W. Betebenner -Bug reports: https://github.com/CenterForAssessment/SGP/issues - -0 errors | 0 warnings | 0 notes - -## smnet (2.1) -Maintainer: Alastair Rushworth - -0 errors | 0 warnings | 0 notes - -## snplist (0.15) -Maintainer: Alexander Sibley - -0 errors | 0 warnings | 0 notes - -## specL (1.8.0) -Maintainer: Christian Panse , Witold E. Wolski -Bug reports: https://github.com/fgcz/specL/issues - -0 errors | 1 warning | 3 notes - -``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because cdsw.Rmd appears to be an R Markdown v2 document. -Quitting from lines 2-25 (cdsw.Rmd) -Error: processing vignette 'cdsw.Rmd' failed with diagnostics: -could not find function "doc_date" -Execution halted - - -checking S3 generic/method consistency ... NOTE -Found the following apparent S3 methods exported but not registered: - merge.specLSet plot.psm plot.psmSet summary.psmSet -See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ -manual. - -checking R code for possible problems ... NOTE -.onAttach: no visible global function definition for ‘packageVersion’ -plot,specLSet: no visible global function definition for ‘draw.circle’ -summary,specLSet : : no visible binding for global variable - ‘iRTpeptides’ -Undefined global functions or variables: - draw.circle iRTpeptides packageVersion -Consider adding - importFrom("utils", "packageVersion") -to your NAMESPACE file. - -checking Rd files ... NOTE -prepare_Rd: ms1.p2069.Rd:28-32: Dropping empty section \references -prepare_Rd: ms1.p2069.Rd:23-26: Dropping empty section \examples -``` - -## sqldf (0.4-10) -Maintainer: G. Grothendieck -Bug reports: http://groups.google.com/group/sqldf - -1 error | 1 warning | 2 notes - -``` -checking examples ... ERROR -Running examples in ‘sqldf-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: sqldf -> ### Title: SQL select on data frames -> ### Aliases: sqldf -> ### Keywords: manip -> -... 6 lines ... -> # in R without SQL and then again with SQL -> # -> -> # head -> a1r <- head(warpbreaks) -> a1s <- sqldf("select * from warpbreaks limit 6") -Loading required package: tcltk -Error in eval(substitute(expr), envir, enclos) : - no such table: warpbreaks -Calls: sqldf ... initialize -> initialize -> rsqlite_send_query -> .Call -Execution halted - -checking whether package ‘sqldf’ can be installed ... WARNING -Found the following significant warnings: - Warning: no DISPLAY variable so Tk is not available -See ‘/home/muelleki/git/R/RSQLite/revdep/checks/sqldf.Rcheck/00install.out’ for details. - -checking dependencies in R code ... NOTE -'library' or 'require' call to ‘tcltk’ in package code. - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. - -checking R code for possible problems ... NOTE -read.csv.sql: no visible global function definition for ‘download.file’ -sqldf: no visible global function definition for ‘modifyList’ -sqldf: no visible global function definition for ‘head’ -Undefined global functions or variables: - download.file head modifyList -Consider adding - importFrom("utils", "download.file", "head", "modifyList") -to your NAMESPACE file. -``` - -## sqliter (0.1.0) -Maintainer: Wilson Freitas - -0 errors | 0 warnings | 0 notes - -## SRAdb (1.31.0) -Maintainer: Jack Zhu -Bug reports: https://github.com/seandavi/SRAdb/issues/new - -0 errors | 0 warnings | 6 notes - -``` -checking for hidden files and directories ... NOTE -Found the following hidden files and directories: - .BBSoptions -These were most likely included in error. See section ‘Package -structure’ in the ‘Writing R Extensions’ manual. - -checking top-level files ... NOTE -Non-standard file/directory found at top level: - ‘SRAdb-package.Rd’ - -checking for left-over files ... NOTE -The following files look like leftovers: - ‘SRAdb/SRAdb-package.Rd’ -Please remove them from your package. - -checking dependencies in R code ... NOTE -'library' or 'require' call to ‘RCurl’ which was already attached by Depends. - Please remove these calls from your code. -Packages in Depends field not imported from: - ‘RSQLite’ ‘graph’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - -checking R code for possible problems ... NOTE -.socketWrite: no visible global function definition for ‘write.socket’ -.socketWrite: no visible global function definition for ‘read.socket’ -IGVsocket: no visible global function definition for ‘make.socket’ -colDescriptions: no visible global function definition for ‘dbGetQuery’ -entityGraph: no visible global function definition for ‘na.omit’ -entityGraph: no visible global function definition for ‘new’ -entityGraph : : no visible global function definition for - ‘addEdge’ -getFASTQfile: no visible global function definition for ‘download.file’ -... 11 lines ... -startIGV: no visible global function definition for ‘browseURL’ -Undefined global functions or variables: - SQLite addEdge browseURL dbConnect dbDisconnect dbGetQuery - download.file make.socket na.omit new read.socket write.socket -Consider adding - importFrom("methods", "new") - importFrom("stats", "na.omit") - importFrom("utils", "browseURL", "download.file", "make.socket", - "read.socket", "write.socket") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). - -checking Rd line widths ... NOTE -Rd file 'IGVsession.Rd': - \examples lines wider than 100 characters: - ## Wait until IGV fully launched and make sure the listen port for IGV is open (If not configured in IGV, follow these steops: ... [TRUNCATED] - -Rd file 'IGVsnapshot.Rd': - \examples lines wider than 100 characters: - ## Create a snapshot of the current IGV window, which is usually the first launched IGV with listen port 60151 open - -Rd file 'SRAdb-package.Rd': -... 68 lines ... -Rd file 'sraConvert.Rd': - \usage lines wider than 90 characters: - sraConvert(in_acc, out_type = c("sra", "submission", "study", "sample", "experiment", "run"), sra_con) - \examples lines wider than 100 characters: - a <- sraConvert( in_acc=c(" SRR000137", "SRR000138 "), out_type=c('sample'), sra_con=sra_con ) - -Rd file 'sraGraph.Rd': - \examples lines wider than 100 characters: - ## create a graphNEL object from SRA accessions, which are full text search results of terms 'primary thyroid cell line' - -These lines will be truncated in the PDF manual. -``` - -## srvyr (0.2.0) -Maintainer: Greg Freedman Ellis -Bug reports: https://github.com/gergness/srvyr/issues - -0 errors | 0 warnings | 0 notes - -## SSN (1.1.8) -Maintainer: Jay Ver Hoef - -0 errors | 0 warnings | 0 notes - -## storr (1.0.1) -Maintainer: Rich FitzJohn - -0 errors | 0 warnings | 0 notes - -## stream (1.2-3) -Maintainer: Michael Hahsler -Bug reports: https://github.com/mhahsler/stream/issues - -0 errors | 0 warnings | 1 note - -``` -checking installed package size ... NOTE - installed size is 5.6Mb - sub-directories of 1Mb or more: - doc 1.6Mb - libs 3.6Mb -``` - -## survey (3.31-2) -Maintainer: "Thomas Lumley" - -0 errors | 0 warnings | 0 notes - -## taRifx (1.0.6) -Maintainer: Ari B. Friedman - -0 errors | 0 warnings | 4 notes - -``` -checking DESCRIPTION meta-information ... NOTE -Malformed Title field: should not end in a period. - -checking dependencies in R code ... NOTE -'library' or 'require' calls in package code: - ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’ - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. - -checking S3 generic/method consistency ... NOTE -Found the following apparent S3 methods exported but not registered: - as.matrix.by stack.list -See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ -manual. - -checking R code for possible problems ... NOTE -as.data.frame.by: no visible global function definition for ‘na.omit’ -autoplot.microbenchmark : uq: no visible global function definition for - ‘quantile’ -autoplot.microbenchmark : lq: no visible global function definition for - ‘quantile’ -autoplot.microbenchmark: no visible global function definition for - ‘ggplot’ -autoplot.microbenchmark: no visible global function definition for - ‘aes’ -... 90 lines ... - grid.points grid.polyline grid.rect grid.segments grid.text - interleave label<- latticeParseFormula median na.omit opts - panel.densityplot panel.lines panel.xyplot par pf plot.new - popViewport pushViewport quantile sd seekViewport stat_summary terms - text theme_text time unit upViewport viewport write.csv xtable -Consider adding - importFrom("graphics", "barplot", "par", "plot.new", "text") - importFrom("stats", "ecdf", "median", "na.omit", "pf", "quantile", - "sd", "terms", "time") - importFrom("utils", "write.csv") -to your NAMESPACE file. -``` - -## tcpl (1.2.2) -Maintainer: Dayne L Filer - -0 errors | 0 warnings | 1 note - -``` -checking installed package size ... NOTE - installed size is 9.9Mb - sub-directories of 1Mb or more: - sql 8.7Mb -``` - -## TFBSTools (1.12.0) -Maintainer: Ge Tan -Bug reports: https://github.com/ge11232002/TFBSTools/issues - -0 errors | 1 warning | 2 notes - -``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because TFBSTools.Rmd appears to be an R Markdown v2 document. -Quitting from lines 2-16 (TFBSTools.Rmd) -Error: processing vignette 'TFBSTools.Rmd' failed with diagnostics: -could not find function "doc_date" -Execution halted - - -checking installed package size ... NOTE - installed size is 12.1Mb - sub-directories of 1Mb or more: - R 11.3Mb - -checking dependencies in R code ... NOTE -Unexported objects imported by ':::' calls: - ‘S4Vectors:::new_SimpleList_from_list’ ‘seqLogo:::pwm2ic’ - See the note in ?`:::` about the use of this operator. -``` - -## tigre (1.28.0) -Maintainer: Antti Honkela -Bug reports: https://github.com/ahonkela/tigre/issues - -0 errors | 0 warnings | 2 notes - -``` -checking top-level files ... NOTE -Non-standard file/directory found at top level: - ‘demos’ - -checking R code for possible problems ... NOTE -GPPlot: no visible global function definition for ‘polygon’ -export.scores: no visible global function definition for ‘png’ -export.scores: no visible global function definition for ‘dev.off’ -gpdisimLogLikeGradients: no visible global function definition for - ‘tail’ -[,scoreList: no visible global function definition for ‘slotNames’ -c,scoreList: no visible global function definition for ‘slotNames’ -Undefined global functions or variables: - dev.off png polygon slotNames tail -Consider adding - importFrom("grDevices", "dev.off", "png") - importFrom("graphics", "polygon") - importFrom("methods", "slotNames") - importFrom("utils", "tail") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). -``` - -## trackeR (0.0.3) -Maintainer: Hannah Frick - -0 errors | 1 warning | 0 notes - -``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning in readLines(con) : - incomplete final line found on 'TourDetrackeR.Rmd' -Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because TourDetrackeR.Rmd appears to be an R Markdown v2 document. -Loading required package: zoo - -Attaching package: 'zoo' - -... 7 lines ... -Attaching package: 'trackeR' - -The following object is masked from 'package:base': - - append - -Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&sensor=false -Quitting from lines 96-97 (TourDetrackeR.Rmd) -Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics: -there is no package called 'webshot' -Execution halted -``` - -## TSdata (2016.8-1) -Maintainer: Paul Gilbert - -0 errors | 1 warning | 0 notes - -``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Oct 19, 2016 3:29:25 PM it.bancaditalia.oss.sdmx.util.Configuration init -INFO: Configuration file: /home/muelleki/R/x86_64-pc-linux-gnu-library/3.3/RJSDMX/configuration.properties -Oct 19, 2016 3:29:25 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Oct 19, 2016 3:29:25 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Oct 19, 2016 3:29:26 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -... 8 lines ... -Oct 19, 2016 3:29:27 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/data/ESTAT,ei_nama_q,1.0/Q.MIO-EUR.NSA.CP.NA-P72.IT -Oct 19, 2016 3:29:27 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData -INFO: The sdmx call returned messages in the footer: - Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]] - -Error: processing vignette 'Guide.Stex' failed with diagnostics: - chunk 5 -Error in .local(serIDs, con, ...) : - ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider. -Execution halted -``` - -## TSSQLite (2015.4-1) -Maintainer: Paul Gilbert - -0 errors | 0 warnings | 0 notes - -## TSsql (2015.1-2) -Maintainer: Paul Gilbert - -0 errors | 0 warnings | 1 note - -``` -checking R code for possible problems ... NOTE -TSgetSQL: no visible global function definition for ‘ts’ -TSputSQL: no visible global function definition for ‘is.ts’ -TSputSQL: no visible global function definition for ‘frequency’ -TSputSQL: no visible global function definition for ‘time’ -TSquery: no visible global function definition for ‘ts’ -Undefined global functions or variables: - frequency is.ts time ts -Consider adding - importFrom("stats", "frequency", "is.ts", "time", "ts") -to your NAMESPACE file. -``` - -## tweet2r (1.0) -Maintainer: Pau Aragó - -0 errors | 0 warnings | 0 notes - -## twitteR (1.1.9) -Maintainer: Jeff Gentry - -0 errors | 0 warnings | 0 notes - -## UniProt.ws (2.14.0) -Maintainer: Bioconductor Package Maintainer - -0 errors | 0 warnings | 1 note - -``` -checking R code for possible problems ... NOTE -.getSomeUniprotGoodies: no visible global function definition for - ‘head’ -.tryReadResult: no visible global function definition for ‘read.delim’ -.tryReadResult: no visible global function definition for ‘URLencode’ -availableUniprotSpecies: no visible global function definition for - ‘read.delim’ -availableUniprotSpecies: no visible global function definition for - ‘head’ -lookupUniprotSpeciesFromTaxId: no visible global function definition - for ‘read.delim’ -Undefined global functions or variables: - URLencode head read.delim -Consider adding - importFrom("utils", "URLencode", "head", "read.delim") -to your NAMESPACE file. -``` - -## Uniquorn (1.2.0) -Maintainer: 'Raik Otto' - -0 errors | 0 warnings | 2 notes - -``` -checking DESCRIPTION meta-information ... NOTE -Malformed Description field: should contain one or more complete sentences. - -checking top-level files ... NOTE -Non-standard file/directory found at top level: - ‘unitTests’ -``` - -## UPMASK (1.0) -Maintainer: Alberto Krone-Martins - -0 errors | 0 warnings | 1 note - -``` -checking R code for possible problems ... NOTE -UPMASKfile: no visible global function definition for ‘read.table’ -UPMASKfile: no visible global function definition for ‘write.table’ -analyse_randomKde2d: no visible global function definition for ‘hist’ -analyse_randomKde2d: no visible global function definition for ‘lines’ -analyse_randomKde2d_AutoCalibrated: no visible global function - definition for ‘hist’ -analyse_randomKde2d_AutoCalibrated: no visible global function - definition for ‘lines’ -create_randomKde2d: no visible global function definition for ‘image’ -... 18 lines ... -kde2dForSubset: no visible global function definition for ‘image’ -kde2dForSubset: no visible global function definition for ‘points’ -Undefined global functions or variables: - contour dev.new hist image lines pairs par plot points rainbow - read.table rgb write.table -Consider adding - importFrom("grDevices", "dev.new", "rainbow", "rgb") - importFrom("graphics", "contour", "hist", "image", "lines", "pairs", - "par", "plot", "points") - importFrom("utils", "read.table", "write.table") -to your NAMESPACE file. -``` - -## VariantFiltering (1.10.0) -Maintainer: Robert Castelo -Bug reports: https://github.com/rcastelo/VariantFiltering/issues - -0 errors | 2 warnings | 4 notes - -``` -checking sizes of PDF files under ‘inst/doc’ ... WARNING - ‘gs+qpdf’ made some significant size reductions: - compacted ‘usingVariantFiltering.pdf’ from 415Kb to 153Kb - consider running tools::compactPDF(gs_quality = "ebook") on these files - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Loading required package: Biostrings -Loading required package: XVector - -Attaching package: ‘VariantAnnotation’ - -The following object is masked from ‘package:base’: - -... 8 lines ... -Error in eval(expr, envir, enclos) : database disk image is malformed -Error in eval(expr, envir, enclos) : database disk image is malformed -Error : .onLoad failed in loadNamespace() for 'MafDb.1Kgenomes.phase3.hs37d5', details: - call: eval(expr, envir, enclos) - error: database disk image is malformed - -Error: processing vignette 'usingVariantFiltering.Rnw' failed with diagnostics: - chunk 3 -Error in VariantFilteringParam(vcfFilenames = CEUvcf) : - package MafDb.1Kgenomes.phase3.hs37d5 could not be loaded. -Execution halted - -checking installed package size ... NOTE - installed size is 7.8Mb - sub-directories of 1Mb or more: - R 3.5Mb - extdata 3.5Mb - -checking dependencies in R code ... NOTE -Unexported objects imported by ':::' calls: - 'S4Vectors:::labeledLine' 'VariantAnnotation:::.checkArgs' - 'VariantAnnotation:::.consolidateHits' - 'VariantAnnotation:::.returnEmpty' - See the note in ?`:::` about the use of this operator. -There are ::: calls to the package's namespace in its code. A package - almost never needs to use ::: for its own objects: - '.adjustForStrandSense' - -checking Rd line widths ... NOTE -Rd file 'MafDb-class.Rd': - \examples lines wider than 100 characters: - ## founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression. - -Rd file 'MafDb2-class.Rd': - \examples lines wider than 100 characters: - ## founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression. - -Rd file 'VariantFilteringParam-class.Rd': -... 19 lines ... - -Rd file 'autosomalRecessiveHeterozygous.Rd': - \usage lines wider than 90 characters: - BPPARAM=bpparam("SerialParam")) - -Rd file 'autosomalRecessiveHomozygous.Rd': - \usage lines wider than 90 characters: - use=c("everything", "complete.obs", "all.obs"), - BPPARAM=bpparam("SerialParam")) - -These lines will be truncated in the PDF manual. - -checking Rd cross-references ... NOTE -Package unavailable to check Rd xrefs: ‘phastCons100way.UCSC.hg38’ -``` - -## vegdata (0.9) -Maintainer: Florian Jansen - -0 errors | 0 warnings | 0 notes - -## vmsbase (2.1.3) -Maintainer: Lorenzo D'Andrea - -1 error | 0 warnings | 0 notes - -``` -checking whether package ‘vmsbase’ can be installed ... ERROR -Installation failed. -See ‘/home/muelleki/git/R/RSQLite/revdep/checks/vmsbase.Rcheck/00install.out’ for details. -``` - diff --git a/revdep/README-f-revdep.md b/revdep/README-r-1.1.md similarity index 97% rename from revdep/README-f-revdep.md rename to revdep/README-r-1.1.md index cef304840..8c04a9f4c 100644 --- a/revdep/README-f-revdep.md +++ b/revdep/README-r-1.1.md @@ -10,26 +10,26 @@ |language |(EN) | |collate |en_US.UTF-8 | |tz |Universal | -|date |2016-11-18 | +|date |2016-11-25 | ## Packages |package |* |version |date |source | |:---------|:--|:----------|:----------|:----------------------------------| -|BH | |1.60.0-2 |2016-05-07 |cran (@1.60.0-) | +|BH | |1.62.0-1 |2016-11-19 |cran (@1.62.0-) | |DBI | |0.5-12 |2016-10-06 |Github (rstats-db/DBI@4f00863) | |DBItest | |1.3-10 |2016-10-06 |Github (rstats-db/DBItest@9e87611) | -|knitr | |1.15 |2016-11-09 |cran (@1.15) | +|knitr | |1.15.1 |2016-11-22 |cran (@1.15.1) | |memoise | |1.0.0 |2016-01-29 |CRAN (R 3.3.1) | |plogr | |0.1-1 |2016-09-24 |cran (@0.1-1) | -|Rcpp | |0.12.7 |2016-09-05 |cran (@0.12.7) | -|rmarkdown | |1.1 |2016-10-16 |cran (@1.1) | +|Rcpp | |0.12.8 |2016-11-17 |cran (@0.12.8) | +|rmarkdown | |1.2 |2016-11-21 |cran (@1.2) | |RSQLite | |1.0.0 |2014-10-25 |CRAN (R 3.3.1) | |testthat | |1.0.2.9000 |2016-08-25 |Github (hadley/testthat@46d15da) | # Check results -116 packages +117 packages |package |version | errors| warnings| notes| |:------------------|:---------|------:|--------:|-----:| @@ -37,9 +37,9 @@ |AnnotationDbi |1.36.0 | 0| 1| 5| |AnnotationForge |1.16.0 | 0| 0| 2| |AnnotationHubData |1.4.0 | 1| 0| 3| -|AnnotationHub |2.6.2 | 0| 0| 1| +|AnnotationHub |2.6.4 | 0| 0| 1| |APSIM |0.9.1 | 0| 0| 0| -|archivist |2.1 | 1| 0| 2| +|archivist |2.1.1 | 0| 0| 2| |BatchExperiments |1.4.1 | 0| 0| 2| |BatchJobs |1.6 | 0| 0| 0| |bibliospec |0.0.4 | 0| 0| 0| @@ -76,6 +76,7 @@ |GWASTools |1.20.0 | 0| 0| 1| |imputeMulti |0.6.3 | 0| 0| 1| |iontree |1.20.0 | 0| 0| 5| +|KoNLP |0.80.0 | 0| 0| 1| |lumi |2.26.3 | 0| 1| 3| |macleish |0.3.0 | 0| 0| 0| |maGUI |1.0 | 1| 0| 0| @@ -92,8 +93,8 @@ |MUCflights |0.0-3 | 0| 0| 3| |nutshell.bbdb |1.0 | 0| 0| 2| |nutshell |2.0 | 0| 0| 3| -|oai |0.2.0 | 0| 0| 0| -|oce |0.9-19 | 1| 0| 1| +|oai |0.2.2 | 0| 0| 0| +|oce |0.9-20 | 1| 0| 1| |oligoClasses |1.36.0 | 0| 1| 4| |oligo |1.38.0 | 1| 0| 9| |OrganismDbi |1.16.0 | 0| 0| 2| @@ -124,7 +125,7 @@ |smnet |2.1 | 0| 0| 0| |snplist |0.16 | 0| 0| 0| |specL |1.8.0 | 0| 1| 3| -|sqldf |0.4-10 | 1| 1| 2| +|sqldf |0.4-10 | 0| 1| 2| |sqliter |0.1.0 | 0| 0| 0| |SRAdb |1.32.0 | 0| 0| 6| |srvyr |0.2.0 | 0| 0| 0| @@ -146,7 +147,7 @@ |UniProt.ws |2.14.0 | 0| 0| 1| |Uniquorn |1.2.0 | 0| 0| 2| |UPMASK |1.0 | 0| 0| 1| -|VariantFiltering |1.10.0 | 0| 1| 4| +|VariantFiltering |1.10.1 | 0| 1| 4| |vegdata |0.9 | 0| 0| 0| |vmsbase |2.1.3 | 1| 0| 0| @@ -277,7 +278,7 @@ File ‘AnnotationHubData/R/makeNCBIToOrgDbs.R’: See section ‘Good practice’ in ‘?data’. ``` -## AnnotationHub (2.6.2) +## AnnotationHub (2.6.4) Maintainer: Bioconductor Package Maintainer 0 errors | 0 warnings | 1 note @@ -292,33 +293,13 @@ Maintainer: Justin Fainges 0 errors | 0 warnings | 0 notes -## archivist (2.1) +## archivist (2.1.1) Maintainer: Przemyslaw Biecek Bug reports: https://github.com/pbiecek/archivist/issues -1 error | 0 warnings | 2 notes +0 errors | 0 warnings | 2 notes ``` -checking examples ... ERROR -Running examples in ‘archivist-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: aread -> ### Title: Read Artifacts Given as md5hashes from the Repository -> ### Aliases: aread -> -> ### ** Examples -> -> # read the object from local directory -> setLocalRepo(system.file("graphGallery", package = "archivist")) -> pl <- aread("f05f0ed0662fe01850ec1b928830ef32") -> # plot it -> pl -Error: ScalesList was built with an incompatible version of ggproto. -Please reinstall the package that provides this extension. -Execution halted - checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘archivist.github’ @@ -1372,6 +1353,19 @@ Rd file 'searchMS2.Rd': These lines will be truncated in the PDF manual. ``` +## KoNLP (0.80.0) +Maintainer: Heewon Jeon +Bug reports: https://github.com/haven-jeon/KoNLP/issues + +0 errors | 0 warnings | 1 note + +``` +checking installed package size ... NOTE + installed size is 6.4Mb + sub-directories of 1Mb or more: + java 5.9Mb +``` + ## lumi (2.26.3) Maintainer: Pan Du @@ -1918,13 +1912,13 @@ Packages in Depends field not imported from: for when this namespace is loaded but not attached. ``` -## oai (0.2.0) +## oai (0.2.2) Maintainer: Scott Chamberlain -Bug reports: https://github.com/sckott/oai/issues +Bug reports: https://github.com/ropensci/oai/issues 0 errors | 0 warnings | 0 notes -## oce (0.9-19) +## oce (0.9-20) Maintainer: Dan Kelley Bug reports: https://github.com/dankelley/oce/issues @@ -1952,9 +1946,9 @@ Calls: plot -> plot -> .local Execution halted checking installed package size ... NOTE - installed size is 5.3Mb + installed size is 5.4Mb sub-directories of 1Mb or more: - help 2.0Mb + help 2.1Mb ``` ## oligoClasses (1.36.0) @@ -2820,32 +2814,9 @@ prepare_Rd: ms1.p2069.Rd:23-26: Dropping empty section \examples Maintainer: G. Grothendieck Bug reports: http://groups.google.com/group/sqldf -1 error | 1 warning | 2 notes +0 errors | 1 warning | 2 notes ``` -checking examples ... ERROR -Running examples in ‘sqldf-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: sqldf -> ### Title: SQL select on data frames -> ### Aliases: sqldf -> ### Keywords: manip -> -... 6 lines ... -> # in R without SQL and then again with SQL -> # -> -> # head -> a1r <- head(warpbreaks) -> a1s <- sqldf("select * from warpbreaks limit 6") -Loading required package: tcltk -Error in eval(substitute(expr), envir, enclos) : - no such table: warpbreaks -Calls: sqldf ... initialize -> initialize -> rsqlite_send_query -> .Call -Execution halted - checking whether package ‘sqldf’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available @@ -3096,7 +3067,7 @@ Warning: Named parameters not used in query: dname > closeDb(db) Warning: Named parameters not used in query: parent_id, name Warning: Named parameters not used in query: name, parent_id -Error in eval(substitute(expr), envir, enclos) : +Error in rsqlite_bind_rows(res@ptr, params) : Query requires 1 params; 2 supplied. Calls: closeDb ... -> db_bind -> rsqlite_bind_rows -> .Call Execution halted @@ -3172,24 +3143,24 @@ Maintainer: Paul Gilbert checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.util.Configuration init INFO: Configuration file: /home/muelleki/R/x86_64-pc-linux-gnu-library/3.3/RJSDMX/configuration.properties -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 25, 2016 12:03:42 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 25, 2016 12:03:43 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 25, 2016 12:03:43 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetData/QNA/CAN.B1_GE.CARSA.Q?format=compact_v2 ... 8 lines ... -Nov 18, 2016 3:53:59 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/data/ESTAT,ei_nama_q,1.0/Q.MIO-EUR.NSA.CP.NA-P72.IT -Nov 18, 2016 3:53:59 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData -INFO: The sdmx call returned messages in the footer: - Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]] +SEVERE: Connection failed. HTTP error code : 500, message: Internal Server Error +SDMX meaning: Error on the provider side. +Nov 25, 2016 12:03:44 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getDataFlowStructure +SEVERE: Exception caught parsing results from call to provider Eurostat Error: processing vignette 'Guide.Stex' failed with diagnostics: chunk 5 Error in .local(serIDs, con, ...) : - ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider. + ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: Exception. Class: it.bancaditalia.oss.sdmx.util.SdmxException .Message: Connection failed. HTTP error code : 500, message: Internal Server Error +SDMX meaning: Error on the provider side. Execution halted ``` @@ -3295,7 +3266,7 @@ Consider adding to your NAMESPACE file. ``` -## VariantFiltering (1.10.0) +## VariantFiltering (1.10.1) Maintainer: Robert Castelo Bug reports: https://github.com/rcastelo/VariantFiltering/issues diff --git a/revdep/README-v1.0.0.md b/revdep/README-v1.0.0.md index 7d20828ba..e515adba5 100644 --- a/revdep/README-v1.0.0.md +++ b/revdep/README-v1.0.0.md @@ -10,7 +10,7 @@ |language |(EN) | |collate |en_US.UTF-8 | |tz |Universal | -|date |2016-11-18 | +|date |2016-11-24 | ## Packages @@ -22,7 +22,7 @@ # Check results -116 packages +117 packages |package |version | errors| warnings| notes| |:------------------|:---------|------:|--------:|-----:| @@ -32,7 +32,7 @@ |AnnotationHubData |1.4.0 | 1| 0| 3| |AnnotationHub |2.6.2 | 0| 0| 1| |APSIM |0.9.1 | 0| 0| 0| -|archivist |2.1 | 1| 0| 2| +|archivist |2.1.1 | 0| 0| 2| |BatchExperiments |1.4.1 | 0| 0| 2| |BatchJobs |1.6 | 0| 0| 0| |bibliospec |0.0.4 | 0| 0| 0| @@ -69,6 +69,7 @@ |GWASTools |1.20.0 | 0| 0| 1| |imputeMulti |0.6.3 | 0| 0| 1| |iontree |1.20.0 | 0| 0| 5| +|KoNLP |0.80.0 | 0| 0| 1| |lumi |2.26.3 | 0| 1| 3| |macleish |0.3.0 | 0| 0| 0| |maGUI |1.0 | 1| 0| 0| @@ -85,8 +86,8 @@ |MUCflights |0.0-3 | 0| 0| 3| |nutshell.bbdb |1.0 | 0| 0| 2| |nutshell |2.0 | 0| 0| 3| -|oai |0.2.0 | 0| 0| 0| -|oce |0.9-19 | 1| 0| 1| +|oai |0.2.2 | 0| 0| 0| +|oce |0.9-20 | 1| 0| 1| |oligoClasses |1.36.0 | 0| 1| 4| |oligo |1.38.0 | 1| 0| 9| |OrganismDbi |1.16.0 | 0| 0| 2| @@ -136,10 +137,10 @@ |TSsql |2015.1-2 | 0| 0| 1| |tweet2r |1.0 | 0| 0| 0| |twitteR |1.1.9 | 0| 0| 0| -|UniProt.ws |2.14.0 | 1| 0| 1| +|UniProt.ws |2.14.0 | 0| 0| 1| |Uniquorn |1.2.0 | 0| 0| 2| |UPMASK |1.0 | 0| 0| 1| -|VariantFiltering |1.10.0 | 0| 1| 4| +|VariantFiltering |1.10.1 | 0| 1| 4| |vegdata |0.9 | 0| 0| 0| |vmsbase |2.1.3 | 1| 0| 0| @@ -223,15 +224,15 @@ Maintainer: Bioconductor Package Maintainer checking tests ... ERROR Running the tests in ‘tests/AnnotationHubData_unit_tests.R’ failed. Last 13 lines of output: + ERROR in test_UCSCChainPreparer_recipe: Error : 1: Unknown IO error2: failed to load external entity "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=&retmax=0" + + Test files with failing tests test_recipe.R test_UCSC2BitPreparer_recipe test_UCSCChainPreparer_recipe - test_webAccessFunctions.R - test_listRemoteFiles - Error in BiocGenerics:::testPackage("AnnotationHubData") : unit tests failed for package AnnotationHubData @@ -285,33 +286,13 @@ Maintainer: Justin Fainges 0 errors | 0 warnings | 0 notes -## archivist (2.1) +## archivist (2.1.1) Maintainer: Przemyslaw Biecek Bug reports: https://github.com/pbiecek/archivist/issues -1 error | 0 warnings | 2 notes +0 errors | 0 warnings | 2 notes ``` -checking examples ... ERROR -Running examples in ‘archivist-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: aread -> ### Title: Read Artifacts Given as md5hashes from the Repository -> ### Aliases: aread -> -> ### ** Examples -> -> # read the object from local directory -> setLocalRepo(system.file("graphGallery", package = "archivist")) -> pl <- aread("f05f0ed0662fe01850ec1b928830ef32") -> # plot it -> pl -Error: ScalesList was built with an incompatible version of ggproto. -Please reinstall the package that provides this extension. -Execution halted - checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘archivist.github’ @@ -863,9 +844,9 @@ Bug reports: https://github.com/hadley/dplyr/issues ``` checking installed package size ... NOTE - installed size is 23.4Mb + installed size is 23.5Mb sub-directories of 1Mb or more: - libs 21.3Mb + libs 21.4Mb checking dependencies in R code ... NOTE Missing or unexported object: ‘RSQLite::rsqliteVersion’ @@ -1368,6 +1349,19 @@ Rd file 'searchMS2.Rd': These lines will be truncated in the PDF manual. ``` +## KoNLP (0.80.0) +Maintainer: Heewon Jeon +Bug reports: https://github.com/haven-jeon/KoNLP/issues + +0 errors | 0 warnings | 1 note + +``` +checking installed package size ... NOTE + installed size is 6.4Mb + sub-directories of 1Mb or more: + java 5.9Mb +``` + ## lumi (2.26.3) Maintainer: Pan Du @@ -1914,13 +1908,13 @@ Packages in Depends field not imported from: for when this namespace is loaded but not attached. ``` -## oai (0.2.0) +## oai (0.2.2) Maintainer: Scott Chamberlain -Bug reports: https://github.com/sckott/oai/issues +Bug reports: https://github.com/ropensci/oai/issues 0 errors | 0 warnings | 0 notes -## oce (0.9-19) +## oce (0.9-20) Maintainer: Dan Kelley Bug reports: https://github.com/dankelley/oce/issues @@ -1948,9 +1942,9 @@ Calls: plot -> plot -> .local Execution halted checking installed package size ... NOTE - installed size is 5.3Mb + installed size is 5.4Mb sub-directories of 1Mb or more: - help 2.0Mb + help 2.1Mb ``` ## oligoClasses (1.36.0) @@ -2328,7 +2322,7 @@ The error most likely occurred in: > temp.db.file <- tempfile() > write(sim.bux.lines, file=temp.file) > test.bux.db <- parse.buxco(file.name=temp.file, db.name=temp.db.file, chunk.size=10000) -Processing /tmp/RtmpUmYjPW/filed52c298e3ea2 in chunks of 10000 +Processing /tmp/RtmpcwL4RG/filee779641e173e in chunks of 10000 Starting chunk 1 Reached breakpoint change Processing breakpoint 1 @@ -2351,7 +2345,7 @@ Last 13 lines of output: Error in BiocGenerics:::testPackage("plethy") : unit tests failed for package plethy In addition: Warning message: - closing unused connection 3 (/tmp/RtmpmtQQ3m/filed6117e71fb4f) + closing unused connection 3 (/tmp/RtmppOK3Wi/filee8f02e70ec78) Execution halted checking dependencies in R code ... NOTE @@ -3079,24 +3073,24 @@ Maintainer: Paul Gilbert checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... -Nov 18, 2016 3:21:19 PM it.bancaditalia.oss.sdmx.util.Configuration init +Loading required package: TSdbi +Nov 24, 2016 3:15:47 PM it.bancaditalia.oss.sdmx.util.Configuration init INFO: Configuration file: /home/muelleki/R/x86_64-pc-linux-gnu-library/3.3/RJSDMX/configuration.properties -Nov 18, 2016 3:21:19 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 24, 2016 3:15:47 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Nov 18, 2016 3:21:20 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 24, 2016 3:15:48 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Nov 18, 2016 3:21:20 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -... 8 lines ... -Nov 18, 2016 3:21:22 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/data/ESTAT,ei_nama_q,1.0/Q.MIO-EUR.NSA.CP.NA-P72.IT -Nov 18, 2016 3:21:22 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData -INFO: The sdmx call returned messages in the footer: - Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]] +... 6 lines ... +INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest +Nov 24, 2016 3:18:01 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +SEVERE: Exception. Class: java.net.ConnectException .Message: Connection timed out (Connection timed out) +Nov 24, 2016 3:18:01 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient getDataflow +SEVERE: Exception caught parsing results from call to provider Eurostat Error: processing vignette 'Guide.Stex' failed with diagnostics: chunk 5 Error in .local(serIDs, con, ...) : - ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider. + ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: Exception. Class: it.bancaditalia.oss.sdmx.util.SdmxException .Message: Exception. Class: java.net.ConnectException .Message: Connection timed out (Connection timed out) Execution halted ``` @@ -3137,26 +3131,9 @@ Maintainer: Jeff Gentry ## UniProt.ws (2.14.0) Maintainer: Bioconductor Package Maintainer -1 error | 0 warnings | 1 note +0 errors | 0 warnings | 1 note ``` -checking tests ... ERROR -Running the tests in ‘tests/UniProt.ws_unit_tests.R’ failed. -Last 13 lines of output: - UniProt.ws RUnit Tests - 14 test functions, 0 errors, 1 failure - FAILURE in test_mapUniprot: Error in checkTrue(res[1, 1] == "1") : Test not TRUE - - - Test files with failing tests - - test_serviceAccessors.R - test_mapUniprot - - - Error in BiocGenerics:::testPackage("UniProt.ws") : - unit tests failed for package UniProt.ws - Execution halted - checking R code for possible problems ... NOTE .getSomeUniprotGoodies: no visible global function definition for ‘head’ @@ -3219,7 +3196,7 @@ Consider adding to your NAMESPACE file. ``` -## VariantFiltering (1.10.0) +## VariantFiltering (1.10.1) Maintainer: Robert Castelo Bug reports: https://github.com/rcastelo/VariantFiltering/issues diff --git a/revdep/README.md b/revdep/README.md index cef304840..8c04a9f4c 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -10,26 +10,26 @@ |language |(EN) | |collate |en_US.UTF-8 | |tz |Universal | -|date |2016-11-18 | +|date |2016-11-25 | ## Packages |package |* |version |date |source | |:---------|:--|:----------|:----------|:----------------------------------| -|BH | |1.60.0-2 |2016-05-07 |cran (@1.60.0-) | +|BH | |1.62.0-1 |2016-11-19 |cran (@1.62.0-) | |DBI | |0.5-12 |2016-10-06 |Github (rstats-db/DBI@4f00863) | |DBItest | |1.3-10 |2016-10-06 |Github (rstats-db/DBItest@9e87611) | -|knitr | |1.15 |2016-11-09 |cran (@1.15) | +|knitr | |1.15.1 |2016-11-22 |cran (@1.15.1) | |memoise | |1.0.0 |2016-01-29 |CRAN (R 3.3.1) | |plogr | |0.1-1 |2016-09-24 |cran (@0.1-1) | -|Rcpp | |0.12.7 |2016-09-05 |cran (@0.12.7) | -|rmarkdown | |1.1 |2016-10-16 |cran (@1.1) | +|Rcpp | |0.12.8 |2016-11-17 |cran (@0.12.8) | +|rmarkdown | |1.2 |2016-11-21 |cran (@1.2) | |RSQLite | |1.0.0 |2014-10-25 |CRAN (R 3.3.1) | |testthat | |1.0.2.9000 |2016-08-25 |Github (hadley/testthat@46d15da) | # Check results -116 packages +117 packages |package |version | errors| warnings| notes| |:------------------|:---------|------:|--------:|-----:| @@ -37,9 +37,9 @@ |AnnotationDbi |1.36.0 | 0| 1| 5| |AnnotationForge |1.16.0 | 0| 0| 2| |AnnotationHubData |1.4.0 | 1| 0| 3| -|AnnotationHub |2.6.2 | 0| 0| 1| +|AnnotationHub |2.6.4 | 0| 0| 1| |APSIM |0.9.1 | 0| 0| 0| -|archivist |2.1 | 1| 0| 2| +|archivist |2.1.1 | 0| 0| 2| |BatchExperiments |1.4.1 | 0| 0| 2| |BatchJobs |1.6 | 0| 0| 0| |bibliospec |0.0.4 | 0| 0| 0| @@ -76,6 +76,7 @@ |GWASTools |1.20.0 | 0| 0| 1| |imputeMulti |0.6.3 | 0| 0| 1| |iontree |1.20.0 | 0| 0| 5| +|KoNLP |0.80.0 | 0| 0| 1| |lumi |2.26.3 | 0| 1| 3| |macleish |0.3.0 | 0| 0| 0| |maGUI |1.0 | 1| 0| 0| @@ -92,8 +93,8 @@ |MUCflights |0.0-3 | 0| 0| 3| |nutshell.bbdb |1.0 | 0| 0| 2| |nutshell |2.0 | 0| 0| 3| -|oai |0.2.0 | 0| 0| 0| -|oce |0.9-19 | 1| 0| 1| +|oai |0.2.2 | 0| 0| 0| +|oce |0.9-20 | 1| 0| 1| |oligoClasses |1.36.0 | 0| 1| 4| |oligo |1.38.0 | 1| 0| 9| |OrganismDbi |1.16.0 | 0| 0| 2| @@ -124,7 +125,7 @@ |smnet |2.1 | 0| 0| 0| |snplist |0.16 | 0| 0| 0| |specL |1.8.0 | 0| 1| 3| -|sqldf |0.4-10 | 1| 1| 2| +|sqldf |0.4-10 | 0| 1| 2| |sqliter |0.1.0 | 0| 0| 0| |SRAdb |1.32.0 | 0| 0| 6| |srvyr |0.2.0 | 0| 0| 0| @@ -146,7 +147,7 @@ |UniProt.ws |2.14.0 | 0| 0| 1| |Uniquorn |1.2.0 | 0| 0| 2| |UPMASK |1.0 | 0| 0| 1| -|VariantFiltering |1.10.0 | 0| 1| 4| +|VariantFiltering |1.10.1 | 0| 1| 4| |vegdata |0.9 | 0| 0| 0| |vmsbase |2.1.3 | 1| 0| 0| @@ -277,7 +278,7 @@ File ‘AnnotationHubData/R/makeNCBIToOrgDbs.R’: See section ‘Good practice’ in ‘?data’. ``` -## AnnotationHub (2.6.2) +## AnnotationHub (2.6.4) Maintainer: Bioconductor Package Maintainer 0 errors | 0 warnings | 1 note @@ -292,33 +293,13 @@ Maintainer: Justin Fainges 0 errors | 0 warnings | 0 notes -## archivist (2.1) +## archivist (2.1.1) Maintainer: Przemyslaw Biecek Bug reports: https://github.com/pbiecek/archivist/issues -1 error | 0 warnings | 2 notes +0 errors | 0 warnings | 2 notes ``` -checking examples ... ERROR -Running examples in ‘archivist-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: aread -> ### Title: Read Artifacts Given as md5hashes from the Repository -> ### Aliases: aread -> -> ### ** Examples -> -> # read the object from local directory -> setLocalRepo(system.file("graphGallery", package = "archivist")) -> pl <- aread("f05f0ed0662fe01850ec1b928830ef32") -> # plot it -> pl -Error: ScalesList was built with an incompatible version of ggproto. -Please reinstall the package that provides this extension. -Execution halted - checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘archivist.github’ @@ -1372,6 +1353,19 @@ Rd file 'searchMS2.Rd': These lines will be truncated in the PDF manual. ``` +## KoNLP (0.80.0) +Maintainer: Heewon Jeon +Bug reports: https://github.com/haven-jeon/KoNLP/issues + +0 errors | 0 warnings | 1 note + +``` +checking installed package size ... NOTE + installed size is 6.4Mb + sub-directories of 1Mb or more: + java 5.9Mb +``` + ## lumi (2.26.3) Maintainer: Pan Du @@ -1918,13 +1912,13 @@ Packages in Depends field not imported from: for when this namespace is loaded but not attached. ``` -## oai (0.2.0) +## oai (0.2.2) Maintainer: Scott Chamberlain -Bug reports: https://github.com/sckott/oai/issues +Bug reports: https://github.com/ropensci/oai/issues 0 errors | 0 warnings | 0 notes -## oce (0.9-19) +## oce (0.9-20) Maintainer: Dan Kelley Bug reports: https://github.com/dankelley/oce/issues @@ -1952,9 +1946,9 @@ Calls: plot -> plot -> .local Execution halted checking installed package size ... NOTE - installed size is 5.3Mb + installed size is 5.4Mb sub-directories of 1Mb or more: - help 2.0Mb + help 2.1Mb ``` ## oligoClasses (1.36.0) @@ -2820,32 +2814,9 @@ prepare_Rd: ms1.p2069.Rd:23-26: Dropping empty section \examples Maintainer: G. Grothendieck Bug reports: http://groups.google.com/group/sqldf -1 error | 1 warning | 2 notes +0 errors | 1 warning | 2 notes ``` -checking examples ... ERROR -Running examples in ‘sqldf-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: sqldf -> ### Title: SQL select on data frames -> ### Aliases: sqldf -> ### Keywords: manip -> -... 6 lines ... -> # in R without SQL and then again with SQL -> # -> -> # head -> a1r <- head(warpbreaks) -> a1s <- sqldf("select * from warpbreaks limit 6") -Loading required package: tcltk -Error in eval(substitute(expr), envir, enclos) : - no such table: warpbreaks -Calls: sqldf ... initialize -> initialize -> rsqlite_send_query -> .Call -Execution halted - checking whether package ‘sqldf’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available @@ -3096,7 +3067,7 @@ Warning: Named parameters not used in query: dname > closeDb(db) Warning: Named parameters not used in query: parent_id, name Warning: Named parameters not used in query: name, parent_id -Error in eval(substitute(expr), envir, enclos) : +Error in rsqlite_bind_rows(res@ptr, params) : Query requires 1 params; 2 supplied. Calls: closeDb ... -> db_bind -> rsqlite_bind_rows -> .Call Execution halted @@ -3172,24 +3143,24 @@ Maintainer: Paul Gilbert checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.util.Configuration init INFO: Configuration file: /home/muelleki/R/x86_64-pc-linux-gnu-library/3.3/RJSDMX/configuration.properties -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 25, 2016 12:03:42 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 25, 2016 12:03:43 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 25, 2016 12:03:43 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetData/QNA/CAN.B1_GE.CARSA.Q?format=compact_v2 ... 8 lines ... -Nov 18, 2016 3:53:59 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/data/ESTAT,ei_nama_q,1.0/Q.MIO-EUR.NSA.CP.NA-P72.IT -Nov 18, 2016 3:53:59 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData -INFO: The sdmx call returned messages in the footer: - Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]] +SEVERE: Connection failed. HTTP error code : 500, message: Internal Server Error +SDMX meaning: Error on the provider side. +Nov 25, 2016 12:03:44 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getDataFlowStructure +SEVERE: Exception caught parsing results from call to provider Eurostat Error: processing vignette 'Guide.Stex' failed with diagnostics: chunk 5 Error in .local(serIDs, con, ...) : - ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider. + ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: Exception. Class: it.bancaditalia.oss.sdmx.util.SdmxException .Message: Connection failed. HTTP error code : 500, message: Internal Server Error +SDMX meaning: Error on the provider side. Execution halted ``` @@ -3295,7 +3266,7 @@ Consider adding to your NAMESPACE file. ``` -## VariantFiltering (1.10.0) +## VariantFiltering (1.10.1) Maintainer: Robert Castelo Bug reports: https://github.com/rcastelo/VariantFiltering/issues diff --git a/revdep/checks.rds b/revdep/checks.rds index 1e7ba4499..fa647f5f3 100644 Binary files a/revdep/checks.rds and b/revdep/checks.rds differ diff --git a/revdep/diff.sh b/revdep/diff.sh index 91d68494f..843b5e59a 100755 --- a/revdep/diff.sh +++ b/revdep/diff.sh @@ -2,7 +2,7 @@ set -e -old_tag=v1.0.0 +old_tag= branch=$(git symbolic-ref --short HEAD) cd $(dirname $0)/.. diff --git a/revdep/problems-master.md b/revdep/problems-master.md deleted file mode 100644 index 72549dc84..000000000 --- a/revdep/problems-master.md +++ /dev/null @@ -1,1540 +0,0 @@ -# Setup - -## Platform - -|setting |value | -|:--------|:----------------------------| -|version |R version 3.3.1 (2016-06-21) | -|system |x86_64, linux-gnu | -|ui |X11 | -|language |(EN) | -|collate |en_US.UTF-8 | -|tz |Zulu | -|date |2016-10-19 | - -## Packages - -|package |* |version |date |source | -|:---------|:--|:----------|:----------|:----------------------------------| -|BH | |1.60.0-2 |2016-05-07 |cran (@1.60.0-) | -|DBI | |0.5-12 |2016-10-06 |Github (rstats-db/DBI@4f00863) | -|DBItest | |1.3-10 |2016-10-06 |Github (rstats-db/DBItest@9e87611) | -|knitr | |1.14 |2016-08-13 |cran (@1.14) | -|memoise | |1.0.0 |2016-01-29 |CRAN (R 3.3.1) | -|plogr | |0.1-1 |2016-09-24 |cran (@0.1-1) | -|Rcpp | |0.12.7 |2016-09-05 |cran (@0.12.7) | -|rmarkdown | |1.0 |2016-07-08 |cran (@1.0) | -|RSQLite | |1.0.0 |2014-10-25 |CRAN (R 3.3.1) | -|testthat | |1.0.2.9000 |2016-08-25 |Github (hadley/testthat@46d15da) | - -# Check results - -29 packages with problems - -|package |version | errors| warnings| notes| -|:------------------|:--------|------:|--------:|-----:| -|AnnotationDbi |1.36.0 | 0| 1| 5| -|AnnotationHubData |1.4.0 | 1| 0| 3| -|ChemmineR |2.26.0 | 1| 0| 0| -|clstutils |1.22.0 | 0| 2| 5| -|CNEr |1.10.0 | 0| 2| 2| -|ecd |0.8.2 | 1| 0| 0| -|filematrix |1.1.0 | 0| 1| 0| -|gcbd |0.2.6 | 0| 1| 1| -|GeneAnswers |2.16.0 | 1| 3| 6| -|maGUI |1.0 | 1| 0| 0| -|metagenomeFeatures |1.4.0 | 0| 2| 2| -|metaseqR |1.14.0 | 1| 1| 4| -|mgsa |1.22.0 | 0| 1| 5| -|oce |0.9-19 | 1| 0| 1| -|oligoClasses |1.36.0 | 0| 1| 4| -|oligo |1.38.0 | 1| 0| 9| -|PAnnBuilder |1.38.0 | 0| 3| 1| -|plethy |1.12.0 | 2| 1| 3| -|poplite |0.99.16 | 1| 0| 1| -|recoup |1.2.0 | 2| 0| 1| -|RImmPort |1.2.0 | 0| 1| 1| -|RQDA |0.2-7 | 1| 0| 1| -|specL |1.8.0 | 0| 1| 3| -|sqldf |0.4-10 | 1| 1| 2| -|TFBSTools |1.12.0 | 0| 1| 2| -|trackeR |0.0.3 | 0| 1| 0| -|TSdata |2016.8-1 | 0| 1| 0| -|VariantFiltering |1.10.0 | 0| 2| 4| -|vmsbase |2.1.3 | 1| 0| 0| - -## AnnotationDbi (1.36.0) -Maintainer: Bioconductor Package Maintainer - - -0 errors | 1 warning | 5 notes - -``` -checking for unstated dependencies in ‘tests’ ... WARNING -'library' or 'require' call not declared from: ‘org.testing.db’ - -checking installed package size ... NOTE - installed size is 8.6Mb - sub-directories of 1Mb or more: - extdata 6.0Mb - -checking DESCRIPTION meta-information ... NOTE -Packages listed in more than one of Depends, Imports, Suggests, Enhances: - ‘methods’ ‘utils’ ‘stats4’ ‘BiocGenerics’ ‘Biobase’ ‘IRanges’ ‘DBI’ ‘RSQLite’ -A package should be listed in only one of these fields. - -checking dependencies in R code ... NOTE -'library' or 'require' calls in package code: - ‘GO.db’ ‘KEGG.db’ ‘RSQLite’ ‘graph’ - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. -Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’ - See the note in ?`:::` about the use of this operator. - -checking R code for possible problems ... NOTE -.selectInp8: no visible global function definition for ‘.resort’ -annotMessage: no visible binding for global variable ‘pkgName’ -createORGANISMSeeds: no visible global function definition for - ‘makeAnnDbMapSeeds’ -makeGOGraph: no visible binding for global variable ‘GOBPPARENTS’ -makeGOGraph: no visible binding for global variable ‘GOMFPARENTS’ -makeGOGraph: no visible binding for global variable ‘GOCCPARENTS’ -makeGOGraph: no visible global function definition for ‘ftM2graphNEL’ -Undefined global functions or variables: - .resort GOBPPARENTS GOCCPARENTS GOMFPARENTS ftM2graphNEL - makeAnnDbMapSeeds pkgName - -checking Rd line widths ... NOTE -Rd file 'inpIDMapper.Rd': - \examples lines wider than 100 characters: - YeastUPSingles = inpIDMapper(ids, "HOMSA", "SACCE", destIDType="UNIPROT", keepMultDestIDMatches = FALSE) - -These lines will be truncated in the PDF manual. -``` - -## AnnotationHubData (1.4.0) -Maintainer: Bioconductor Package Maintainer - -1 error | 0 warnings | 3 notes - -``` -checking tests ... ERROR -Running the tests in ‘tests/AnnotationHubData_unit_tests.R’ failed. -Last 13 lines of output: - ERROR in test_UCSC2BitPreparer_recipe: Error in ahms[[1]] : subscript out of bounds - ERROR in test_UCSCChainPreparer_recipe: Error in ahms[[1]] : subscript out of bounds - - Test files with failing tests - - test_recipe.R - test_UCSC2BitPreparer_recipe - test_UCSCChainPreparer_recipe - - - Error in BiocGenerics:::testPackage("AnnotationHubData") : - unit tests failed for package AnnotationHubData - Execution halted - -checking top-level files ... NOTE -Non-standard file/directory found at top level: - ‘appveyor.yml’ - -checking dependencies in R code ... NOTE -Missing object imported by a ':::' call: ‘AnnotationHub:::.db_connection’ -Unexported object imported by a ':::' call: ‘OrganismDbi:::.packageTaxIds’ - See the note in ?`:::` about the use of this operator. - -checking R code for possible problems ... NOTE -.NCBIMetadataFromUrl: no visible binding for global variable ‘results’ -.NCBIMetadataFromUrl: no visible binding for global variable ‘specData’ -.makeComplexGR: no visible binding for global variable ‘seqname’ -jsonPath: no visible binding for global variable ‘SourceFile’ -jsonPath: no visible binding for global variable ‘HubRoot’ -makeAnnotationHubMetadata : : no visible binding for global - variable ‘Title’ -makeAnnotationHubMetadata : : no visible binding for global - variable ‘Description’ -... 52 lines ... - SourceFile SourceType SourceUrl SourceVersion Species TaxonomyId - Title ahroot bucket checkTrue read.csv results seqname specData - suppresWarnings -Consider adding - importFrom("utils", "read.csv") -to your NAMESPACE file. - -Found the following calls to data() loading into the global environment: -File ‘AnnotationHubData/R/makeNCBIToOrgDbs.R’: - data(specData, package = "GenomeInfoDb") -See section ‘Good practice’ in ‘?data’. -``` - -## ChemmineR (2.26.0) -Maintainer: Thomas Girke - -1 error | 0 warnings | 0 notes - -``` -checking whether package ‘ChemmineR’ can be installed ... ERROR -Installation failed. -See ‘/home/muelleki/git/R/RSQLite/revdep/checks/ChemmineR.Rcheck/00install.out’ for details. -``` - -## clstutils (1.22.0) -Maintainer: Noah Hoffman - -0 errors | 2 warnings | 5 notes - -``` -checking for GNU extensions in Makefiles ... WARNING -Found the following file(s) containing GNU extensions: - tests/unit/Makefile -Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), -$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in -the ‘Writing R Extensions’ manual. - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Loading required package: clst -Loading required package: rjson -Loading required package: ape -Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : - Running 'texi2dvi' on 'pplacerDemo.tex' failed. -LaTeX errors: -! Package auto-pst-pdf Error: - "shell escape" (or "write18") is not enabled: - auto-pst-pdf will not work! -. -Calls: buildVignettes -> texi2pdf -> texi2dvi -Execution halted - - -checking DESCRIPTION meta-information ... NOTE -Malformed Title field: should not end in a period. - -checking top-level files ... NOTE -Non-standard file/directory found at top level: - ‘devmakefile’ - -checking dependencies in R code ... NOTE -'library' or 'require' call to ‘rjson’ which was already attached by Depends. - Please remove these calls from your code. -'library' or 'require' call to ‘RSVGTipsDevice’ in package code. - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. -Packages in Depends field not imported from: - ‘ape’ ‘rjson’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - -checking foreign function calls ... NOTE -Foreign function call to a different package: - .Call("seq_root2tip", ..., PACKAGE = "ape") -See chapter ‘System and foreign language interfaces’ in the ‘Writing R -Extensions’ manual. - -checking R code for possible problems ... NOTE -edgeMap: no visible global function definition for ‘fromJSON’ -findOutliers: no visible global function definition for ‘quantile’ -findOutliers: no visible binding for global variable ‘median’ -maxDists: no visible binding for global variable ‘median’ -placeData: no visible global function definition for ‘read.table’ -prettyTree: no visible binding for global variable ‘par’ -prettyTree: no visible global function definition for ‘plot’ -prettyTree: no visible binding for global variable ‘.PlotPhyloEnv’ -prettyTree: no visible binding for global variable ‘points’ -... 19 lines ... -taxonomyFromRefpkg: no visible global function definition for - ‘read.csv’ -Undefined global functions or variables: - .PlotPhyloEnv dev.off devSVGTips fromJSON legend median par plot - points quantile read.csv read.table setSVGShapeToolTip text -Consider adding - importFrom("grDevices", "dev.off") - importFrom("graphics", "legend", "par", "plot", "points", "text") - importFrom("stats", "median", "quantile") - importFrom("utils", "read.csv", "read.table") -to your NAMESPACE file. -``` - -## CNEr (1.10.0) -Maintainer: Ge Tan -Bug reports: https://github.com/ge11232002/CNEr/issues - -0 errors | 2 warnings | 2 notes - -``` -checking compiled code ... WARNING -File ‘CNEr/libs/CNEr.so’: - Found ‘abort’, possibly from ‘abort’ (C) - Object: ‘ucsc/errabort.o’ - Found ‘exit’, possibly from ‘exit’ (C) - Objects: ‘ucsc/errabort.o’, ‘ucsc/pipeline.o’ - Found ‘printf’, possibly from ‘printf’ (C) - Objects: ‘ceScan.o’, ‘ucsc/pipeline.o’ - Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C) - Object: ‘ucsc/pipeline.o’ - Found ‘rand’, possibly from ‘rand’ (C) - Object: ‘ucsc/obscure.o’ - Found ‘stderr’, possibly from ‘stderr’ (C) - Objects: ‘ucsc/axt.o’, ‘ucsc/errabort.o’, ‘ucsc/obscure.o’, - ‘ucsc/verbose.o’, ‘ucsc/os.o’ - Found ‘stdout’, possibly from ‘stdout’ (C) - Objects: ‘ucsc/common.o’, ‘ucsc/errabort.o’, ‘ucsc/verbose.o’, - ‘ucsc/os.o’ - -Compiled code should not call entry points which might terminate R nor -write to stdout/stderr instead of to the console, nor the system RNG. - -See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because CNEr.Rmd appears to be an R Markdown v2 document. -Quitting from lines 2-15 (CNEr.Rmd) -Error: processing vignette 'CNEr.Rmd' failed with diagnostics: -could not find function "doc_date" -Execution halted - - -checking installed package size ... NOTE - installed size is 28.4Mb - sub-directories of 1Mb or more: - R 11.0Mb - extdata 15.9Mb - -checking dependencies in R code ... NOTE -Unexported objects imported by ':::' calls: - ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::make_zero_col_DataFrame’ - See the note in ?`:::` about the use of this operator. -``` - -## ecd (0.8.2) -Maintainer: Stephen H-T. Lihn - -1 error | 0 warnings | 0 notes - -``` -checking package dependencies ... ERROR -Package required and available but unsuitable version: ‘RSQLite’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -``` - -## filematrix (1.1.0) -Maintainer: Andrey A Shabalin -Bug reports: https://github.com/andreyshabalin/filematrix/issues - -0 errors | 1 warning | 0 notes - -``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because Best_Prectices.Rmd appears to be an R Markdown v2 document. -Quitting from lines 2-23 (Best_Prectices.Rmd) -Error: processing vignette 'Best_Prectices.Rmd' failed with diagnostics: -could not find function "doc_date" -Execution halted - -``` - -## gcbd (0.2.6) -Maintainer: Dirk Eddelbuettel - -0 errors | 1 warning | 1 note - -``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning in packageDescription("gputools") : - no package 'gputools' was found -Error: processing vignette 'gcbd.Rnw' failed with diagnostics: -at gcbd.Rnw:860, subscript out of bounds -Execution halted - - -checking package dependencies ... NOTE -Package suggested but not available for checking: ‘gputools’ -``` - -## GeneAnswers (2.16.0) -Maintainer: Lei Huang and Gang Feng - -1 error | 3 warnings | 6 notes - -``` -checking examples ... ERROR -Running examples in ‘GeneAnswers-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: chartPlots -> ### Title: Pie Chart and Bar Plots -> ### Aliases: chartPlots -> ### Keywords: methods -> -> ### ** Examples -> -> x <- matrix(c(6,9,3,30,13,2,15,20), nrow = 4, ncol=2, byrow=FALSE, -+ dimnames = list(c("group1", "group2", "group3", "group4"), -+ c("value1", "value2"))) -> chartPlots(x, chartType='all', specifiedCol = "value2", top = 3) -Error in x11() : screen devices should not be used in examples etc -Calls: chartPlots -> x11 -Execution halted - -checking whether package ‘GeneAnswers’ can be installed ... WARNING -Found the following significant warnings: - Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’ - Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’ -See ‘/home/muelleki/git/R/RSQLite/revdep/checks/GeneAnswers.Rcheck/00install.out’ for details. - -checking sizes of PDF files under ‘inst/doc’ ... WARNING - ‘gs+qpdf’ made some significant size reductions: - compacted ‘geneAnswers.pdf’ from 1373Kb to 600Kb - consider running tools::compactPDF(gs_quality = "ebook") on these files - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’ -Loading required package: org.Hs.eg.db - -Loading required package: GO.db - -Loading required package: KEGG.db - -... 8 lines ... -Loading required package: org.Mm.eg.db - -Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : - Running 'texi2dvi' on 'geneAnswers.tex' failed. -LaTeX errors: -! Package auto-pst-pdf Error: - "shell escape" (or "write18") is not enabled: - auto-pst-pdf will not work! -. -Calls: buildVignettes -> texi2pdf -> texi2dvi -Execution halted - -checking package dependencies ... NOTE -Depends: includes the non-default packages: - ‘igraph’ ‘RCurl’ ‘annotate’ ‘Biobase’ ‘XML’ ‘RSQLite’ ‘MASS’ - ‘Heatplus’ ‘RColorBrewer’ -Adding so many packages to the search path is excessive and importing -selectively is preferable. - -checking installed package size ... NOTE - installed size is 36.1Mb - sub-directories of 1Mb or more: - External 32.4Mb - data 1.1Mb - doc 1.6Mb - -checking DESCRIPTION meta-information ... NOTE -Package listed in more than one of Depends, Imports, Suggests, Enhances: - ‘annotate’ -A package should be listed in only one of these fields. - -checking dependencies in R code ... NOTE -'library' or 'require' calls to packages already attached by Depends: - ‘Biobase’ ‘Heatplus’ ‘MASS’ ‘RColorBrewer’ ‘XML’ ‘igraph’ - Please remove these calls from your code. -'library' or 'require' calls in package code: - ‘GO.db’ ‘KEGG.db’ ‘biomaRt’ ‘reactome.db’ - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. - -checking R code for possible problems ... NOTE -Found an obsolete/platform-specific call in the following functions: - ‘chartPlots’ ‘drawTable’ -Found the platform-specific device: - ‘x11’ -dev.new() is the preferred way to open a new device, in the unlikely -event one is needed. -File ‘GeneAnswers/R/zzz.R’: - .onLoad calls: - require(Biobase) -... 78 lines ... - data("DmIALite", package = "GeneAnswers") -File ‘GeneAnswers/R/getDOLiteTerms.R’: - data("DOLiteTerm", package = "GeneAnswers") -File ‘GeneAnswers/R/zzz.R’: - data("DOLite", package = "GeneAnswers") - data("DOLiteTerm", package = "GeneAnswers") - data("HsIALite", package = "GeneAnswers") - data("MmIALite", package = "GeneAnswers") - data("RnIALite", package = "GeneAnswers") - data("DmIALite", package = "GeneAnswers") -See section ‘Good practice’ in ‘?data’. - -checking Rd line widths ... NOTE -Rd file 'GeneAnswers-class.Rd': - \examples lines wider than 100 characters: - x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db', categoryType='GO.BP', testType='hyperG', pvalueT=0.01, FDR.correct=TRUE, geneEx ... [TRUNCATED] - -Rd file 'GeneAnswers-package.Rd': - \examples lines wider than 100 characters: - x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db', categoryType='GO.BP', testType='hyperG', pvalueT=0.01, FDR.correct=TRUE, geneEx ... [TRUNCATED] - -Rd file 'buildNet.Rd': -... 144 lines ... - ## Not run: topDOLITEGenes(x, geneSymbol=TRUE, orderby='pvalue', top=10, topGenes='ALL', genesOrderBy='pValue', file=TRUE) - -Rd file 'topPATHGenes.Rd': - \examples lines wider than 100 characters: - ## Not run: topPATHGenes(x, geneSymbol=TRUE, orderby='genenum', top=6, topGenes=8, genesOrderBy='foldChange') - -Rd file 'topREACTOME.PATHGenes.Rd': - \examples lines wider than 100 characters: - ## Not run: topREACTOME.PATHGenes(x, geneSymbol=TRUE, orderby='pvalue', top=10, topGenes='ALL', genesOrderBy='pValue', file=TRUE) - -These lines will be truncated in the PDF manual. -``` - -## maGUI (1.0) -Maintainer: Dhammapal Bharne - -1 error | 0 warnings | 0 notes - -``` -checking whether package ‘maGUI’ can be installed ... ERROR -Installation failed. -See ‘/home/muelleki/git/R/RSQLite/revdep/checks/maGUI.Rcheck/00install.out’ for details. -``` - -## metagenomeFeatures (1.4.0) -Maintainer: Nathan D. Olson -Bug reports: https://github.com/HCBravoLab/metagenomeFeatures/issues - -0 errors | 2 warnings | 2 notes - -``` -checking for missing documentation entries ... WARNING -Undocumented S4 methods: - generic 'taxa_columns' and siglist 'MgDb' - generic 'taxa_keys' and siglist 'MgDb' - generic 'taxa_keytypes' and siglist 'MgDb' -All user-level objects in a package (including S4 classes and methods) -should have documentation entries. -See chapter ‘Writing R documentation files’ in the ‘Writing R -Extensions’ manual. - -checking Rd \usage sections ... WARNING -Undocumented arguments in documentation object 'annotateFeatures' - ‘query_key’ -Documented arguments not in \usage in documentation object 'annotateFeatures': - ‘db_keys’ ‘query_df’ - -Functions with \usage entries need to have the appropriate \alias -entries, and all their arguments documented. -The \usage entries must correspond to syntactically valid R code. -See chapter ‘Writing R documentation files’ in the ‘Writing R -Extensions’ manual. - -checking installed package size ... NOTE - installed size is 6.3Mb - sub-directories of 1Mb or more: - R 1.1Mb - extdata 3.4Mb - -checking R code for possible problems ... NOTE -.mgDb_annotateFeatures: no visible binding for global variable - ‘db_keys’ -.select.taxa: no visible binding for global variable ‘Keys’ -.select.taxa: no visible binding for global variable ‘.’ -aggregate_taxa: no visible binding for global variable ‘.’ -aggregate_taxa: no visible binding for global variable ‘index’ -aggregate_taxa: no visible global function definition for - ‘newMRexperiment’ -vignette_pheno_data: no visible global function definition for - ‘read.csv’ -Undefined global functions or variables: - . Keys db_keys index newMRexperiment read.csv -Consider adding - importFrom("utils", "read.csv") -to your NAMESPACE file. -``` - -## metaseqR (1.14.0) -Maintainer: Panagiotis Moulos - -1 error | 1 warning | 4 notes - -``` -checking tests ... ERROR -Running the tests in ‘tests/runTests.R’ failed. -Last 13 lines of output: - - Test files with failing tests - - test_estimate_aufc_weights.R - test_estimate_aufc_weights - - test_metaseqr.R - test_metaseqr - - - Error in BiocGenerics:::testPackage("metaseqR") : - unit tests failed for package metaseqR - Execution halted - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... - -The following objects are masked from 'package:ShortRead': - - left, right - -Loading required package: lattice - Welcome to 'DESeq'. For improved performance, usability and -... 8 lines ... - plotMA - -The following object is masked from 'package:BiocGenerics': - - plotMA - -Loading required package: qvalue -Quitting from lines 119-159 (metaseqr-pdf.Rnw) -Error: processing vignette 'metaseqr-pdf.Rnw' failed with diagnostics: -13 simultaneous processes spawned -Execution halted - -checking package dependencies ... NOTE -Package which this enhances but not available for checking: ‘TCC’ - -checking DESCRIPTION meta-information ... NOTE -Malformed Title field: should not end in a period. - -checking dependencies in R code ... NOTE -'library' or 'require' calls in package code: - ‘BSgenome’ ‘BiocInstaller’ ‘GenomicRanges’ ‘RMySQL’ ‘RSQLite’ - ‘Rsamtools’ ‘TCC’ ‘VennDiagram’ ‘parallel’ ‘rtracklayer’ ‘survcomp’ - ‘zoo’ - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. - -checking R code for possible problems ... NOTE -biasPlotToJSON: no visible binding for global variable ‘nams’ -cddat: no visible global function definition for ‘assayData’ -cddat: no visible global function definition for ‘ks.test’ -cddat: no visible global function definition for ‘p.adjust’ -cdplot: no visible global function definition for ‘plot’ -cdplot: no visible global function definition for ‘lines’ -countsBioToJSON: no visible binding for global variable ‘nams’ -diagplot.avg.ftd : : no visible binding for global variable - ‘sd’ -... 246 lines ... - "dev.off", "jpeg", "pdf", "png", "postscript", "tiff") - importFrom("graphics", "abline", "arrows", "axis", "grid", "lines", - "mtext", "par", "plot", "plot.new", "plot.window", "points", - "text", "title") - importFrom("methods", "as", "new") - importFrom("stats", "as.dist", "cmdscale", "cor", "end", "ks.test", - "mad", "median", "model.matrix", "na.exclude", "optimize", - "p.adjust", "p.adjust.methods", "pchisq", "quantile", - "rexp", "rnbinom", "runif", "sd", "start", "var") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). -``` - -## mgsa (1.22.0) -Maintainer: Sebastian Bauer - -0 errors | 1 warning | 5 notes - -``` -checking for GNU extensions in Makefiles ... WARNING -Found the following file(s) containing GNU extensions: - src/Makevars - src/Makevars.in -Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), -$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in -the ‘Writing R Extensions’ manual. - -checking top-level files ... NOTE -Non-standard files/directories found at top level: - ‘acinclude.m4’ ‘aclocal.m4’ ‘script’ - -checking whether the namespace can be loaded with stated dependencies ... NOTE -Warning: no function found corresponding to methods exports from ‘mgsa’ for: ‘show’ - -A namespace must be able to be loaded with just the base namespace -loaded: otherwise if the namespace gets loaded by a saved object, the -session will be unable to start. - -Probably some imports need to be declared in the NAMESPACE file. - -checking dependencies in R code ... NOTE -'library' or 'require' call to ‘gplots’ which was already attached by Depends. - Please remove these calls from your code. -'library' or 'require' calls in package code: - ‘DBI’ ‘GO.db’ ‘RSQLite’ - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. -Packages in Depends field not imported from: - ‘gplots’ ‘methods’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - -checking R code for possible problems ... NOTE -createMgsaGoSets: no visible global function definition for ‘new’ -mcmcSummary: no visible binding for global variable ‘sd’ -mgsa.wrapper: no visible global function definition for ‘str’ -mgsa.wrapper: no visible global function definition for ‘new’ -readGAF: no visible global function definition for ‘read.delim’ -readGAF: no visible global function definition for ‘na.omit’ -readGAF: no visible global function definition for ‘new’ -initialize,MgsaSets: no visible global function definition for - ‘callNextMethod’ -... 10 lines ... - ‘close.screen’ -Undefined global functions or variables: - barplot2 callNextMethod close.screen na.omit new par read.delim - relist screen sd split.screen str -Consider adding - importFrom("graphics", "close.screen", "par", "screen", "split.screen") - importFrom("methods", "callNextMethod", "new") - importFrom("stats", "na.omit", "sd") - importFrom("utils", "read.delim", "relist", "str") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). - -checking compiled code ... NOTE -File ‘mgsa/libs/mgsa.so’: - Found ‘printf’, possibly from ‘printf’ (C) - Object: ‘mgsa.o’ - -Compiled code should not call entry points which might terminate R nor -write to stdout/stderr instead of to the console, nor the system RNG. - -See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. -``` - -## oce (0.9-19) -Maintainer: Dan Kelley -Bug reports: https://github.com/dankelley/oce/issues - -1 error | 0 warnings | 1 note - -``` -checking examples ... ERROR -Running examples in ‘oce-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: read.oce -> ### Title: Read an Oceanographic Data File -> ### Aliases: read.oce -> -> ### ** Examples -> -> -> library(oce) -> x <- read.oce(system.file("extdata", "ctd.cnv", package="oce")) -> plot(x) # summary with TS and profiles -Error in if (!is.null(x@metadata$startTime) && 4 < nchar(x@metadata$startTime, : - missing value where TRUE/FALSE needed -Calls: plot -> plot -> .local -Execution halted - -checking installed package size ... NOTE - installed size is 5.1Mb - sub-directories of 1Mb or more: - help 2.0Mb -``` - -## oligoClasses (1.36.0) -Maintainer: Benilton Carvalho and Robert Scharpf - -0 errors | 1 warning | 4 notes - -``` -checking for missing documentation entries ... WARNING -Undocumented S4 methods: - generic '[' and siglist 'CNSet,ANY,ANY,ANY' - generic '[' and siglist 'gSetList,ANY,ANY,ANY' -All user-level objects in a package (including S4 classes and methods) -should have documentation entries. -See chapter ‘Writing R documentation files’ in the ‘Writing R -Extensions’ manual. - -checking package dependencies ... NOTE -Packages which this enhances but not available for checking: - ‘doMC’ ‘doMPI’ ‘doSNOW’ ‘doRedis’ - -checking dependencies in R code ... NOTE -Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’ - See the note in ?`:::` about the use of this operator. - -checking R code for possible problems ... NOTE -getSequenceLengths: no visible binding for global variable ‘seqlengths’ -pdPkgFromBioC: no visible binding for global variable ‘contrib.url’ -pdPkgFromBioC: no visible global function definition for - ‘available.packages’ -pdPkgFromBioC: no visible global function definition for - ‘install.packages’ -chromosome,gSetList: no visible global function definition for - ‘chromosomeList’ -coerce,CNSet-CopyNumberSet: no visible global function definition for - ‘totalCopynumber’ -geometry,FeatureSet: no visible global function definition for ‘getPD’ -Undefined global functions or variables: - available.packages chromosomeList contrib.url getPD install.packages - seqlengths totalCopynumber -Consider adding - importFrom("utils", "available.packages", "contrib.url", - "install.packages") -to your NAMESPACE file. - -checking Rd line widths ... NOTE -Rd file 'AssayDataList.Rd': - \examples lines wider than 100 characters: - r <- lapply(r, function(x,dns) {dimnames(x) <- dns; return(x)}, dns=list(letters[1:5], LETTERS[1:5])) - -Rd file 'GenomeAnnotatedDataFrameFrom-methods.Rd': - \examples lines wider than 100 characters: - dimnames=list(c("rs10000092","rs1000055", "rs100016", "rs10003241", "rs10004197"), NULL)) - -Rd file 'largeObjects.Rd': - \usage lines wider than 90 characters: - initializeBigMatrix(name=basename(tempfile()), nr=0L, nc=0L, vmode = "integer", initdata = NA) - -Rd file 'oligoSetExample.Rd': - \examples lines wider than 100 characters: - copyNumber=integerMatrix(log2(locusLevelData[["copynumber"]]/100), 100), - -These lines will be truncated in the PDF manual. -``` - -## oligo (1.38.0) -Maintainer: Benilton Carvalho - -1 error | 0 warnings | 9 notes - -``` -checking examples ... ERROR -Running examples in ‘oligo-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: MAplot -> ### Title: MA plots -> ### Aliases: MAplot MAplot-methods MAplot,FeatureSet-method -> ### MAplot,TilingFeatureSet-method MAplot,PLMset-method -> ### MAplot,ExpressionSet-method MAplot,matrix-method -... 8 lines ... -+ groups <- factor(rep(c('brain', 'UnivRef'), each=3)) -+ data.frame(sampleNames(nimbleExpressionFS), groups) -+ MAplot(nimbleExpressionFS, pairs=TRUE, ylim=c(-.5, .5), groups=groups) -+ } -Loading required package: oligoData -Loading required package: pd.hg18.60mer.expr -Loading required package: RSQLite -Loading required package: DBI -Error in loadNamespace(name) : there is no package called ‘KernSmooth’ -Calls: MAplot ... tryCatch -> tryCatchList -> tryCatchOne -> -Execution halted - -checking package dependencies ... NOTE -Packages which this enhances but not available for checking: ‘doMC’ ‘doMPI’ - -checking installed package size ... NOTE - installed size is 30.2Mb - sub-directories of 1Mb or more: - R 1.2Mb - doc 12.9Mb - scripts 15.7Mb - -checking DESCRIPTION meta-information ... NOTE -Packages listed in more than one of Depends, Imports, Suggests, Enhances: - ‘biomaRt’ ‘AnnotationDbi’ ‘GenomeGraphs’ ‘RCurl’ ‘ff’ -A package should be listed in only one of these fields. - -checking top-level files ... NOTE -Non-standard file/directory found at top level: - ‘TODO.org’ - -checking whether the namespace can be loaded with stated dependencies ... NOTE -Warning: no function found corresponding to methods exports from ‘oligo’ for: ‘show’ - -A namespace must be able to be loaded with just the base namespace -loaded: otherwise if the namespace gets loaded by a saved object, the -session will be unable to start. - -Probably some imports need to be declared in the NAMESPACE file. - -checking dependencies in R code ... NOTE -Unexported object imported by a ':::' call: ‘Biobase:::annotatedDataFrameFromMatrix’ - See the note in ?`:::` about the use of this operator. - -checking foreign function calls ... NOTE -Foreign function calls to a different package: - .Call("ReadHeader", ..., PACKAGE = "affyio") - .Call("read_abatch", ..., PACKAGE = "affyio") -See chapter ‘System and foreign language interfaces’ in the ‘Writing R -Extensions’ manual. - -checking R code for possible problems ... NOTE -image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]): - partial argument match of 'nr' to 'nrow' -image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]): - partial argument match of 'nc' to 'ncol' -NUSE: no visible global function definition for ‘abline’ -RLE: no visible global function definition for ‘abline’ -basicMvApairsPlot: no visible binding for global variable - ‘smoothScatter’ -basicMvApairsPlot: no visible global function definition for ‘frame’ -... 36 lines ... -Undefined global functions or variables: - IQR abline aggregate approx complete.cases data frame intensities - loess man_fsetid mtext predict rnorm smooth.spline smoothScatter - splinefun text -Consider adding - importFrom("graphics", "abline", "frame", "mtext", "smoothScatter", - "text") - importFrom("stats", "IQR", "aggregate", "approx", "complete.cases", - "loess", "predict", "rnorm", "smooth.spline", "splinefun") - importFrom("utils", "data") -to your NAMESPACE file. - -checking Rd line widths ... NOTE -Rd file 'basicRMA.Rd': - \usage lines wider than 90 characters: - basicRMA(pmMat, pnVec, normalize = TRUE, background = TRUE, bgversion = 2, destructive = FALSE, verbose = TRUE, ...) - -Rd file 'fitProbeLevelModel.Rd': - \usage lines wider than 90 characters: - fitProbeLevelModel(object, background=TRUE, normalize=TRUE, target="core", method="plm", verbose=TRUE, S4=TRUE, ...) - -Rd file 'getProbeInfo.Rd': - \usage lines wider than 90 characters: - getProbeInfo(object, field, probeType = "pm", target = "core", sortBy = c("fid", "man_fsetid", "none"), ...) - \examples lines wider than 100 characters: - agenGene <- getProbeInfo(affyGeneFS, field=c('fid', 'fsetid', 'type'), target='probeset', subset= type == 'control->bgp->antigenomic ... [TRUNCATED] - -Rd file 'preprocessTools.Rd': - \usage lines wider than 90 characters: - backgroundCorrect(object, method=backgroundCorrectionMethods(), copy=TRUE, extra, subset=NULL, target='core', verbose=TRUE) - normalize(object, method=normalizationMethods(), copy=TRUE, subset=NULL,target='core', verbose=TRUE, ...) - -These lines will be truncated in the PDF manual. -``` - -## PAnnBuilder (1.38.0) -Maintainer: Li Hong - -0 errors | 3 warnings | 1 note - -``` -checking dependencies in R code ... WARNING -'library' or 'require' call to ‘Biobase’ which was already attached by Depends. - Please remove these calls from your code. -':::' calls which should be '::': - ‘AnnotationDbi:::as.list’ ‘base:::get’ ‘tools:::list_files_with_type’ - See the note in ?`:::` about the use of this operator. -Unexported objects imported by ':::' calls: - ‘AnnotationDbi:::createAnnDbBimaps’ - ‘AnnotationDbi:::prefixAnnObjNames’ ‘tools:::makeLazyLoadDB’ - See the note in ?`:::` about the use of this operator. - Including base/recommended package(s): - ‘tools’ -There are ::: calls to the package's namespace in its code. A package - almost never needs to use ::: for its own objects: - ‘getShortSciName’ ‘twoStepSplit’ - -checking R code for possible problems ... WARNING -Found an obsolete/platform-specific call in the following function: - ‘makeLLDB’ -Found the defunct/removed function: - ‘.saveRDS’ - -In addition to the above warning(s), found the following notes: - -File ‘PAnnBuilder/R/zzz.R’: - .onLoad calls: - require(Biobase) - -Package startup functions should not change the search path. -See section ‘Good practice’ in '?.onAttach'. - -Found the following calls to data() loading into the global environment: -File ‘PAnnBuilder/R/writeManPage.R’: - data("descriptionInfo") - data("descriptionInfo") -See section ‘Good practice’ in ‘?data’. - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... - } - - -trying URL 'http://gpcr2.biocomp.unibo.it/bacello/dataset.htm' -Content type 'text/html; charset=iso-8859-1' length 5062 bytes -================================================== -downloaded 5062 bytes -... 8 lines ... -Warning in rsqlite_disconnect(conn@ptr) : - There are 1 result in use. The connection will be released when they are closed -Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : - Running 'texi2dvi' on 'PAnnBuilder.tex' failed. -LaTeX errors: -! Package auto-pst-pdf Error: - "shell escape" (or "write18") is not enabled: - auto-pst-pdf will not work! -. -Calls: buildVignettes -> texi2pdf -> texi2dvi -Execution halted - -checking DESCRIPTION meta-information ... NOTE -Packages listed in more than one of Depends, Imports, Suggests, Enhances: - ‘methods’ ‘utils’ ‘Biobase’ ‘RSQLite’ ‘AnnotationDbi’ -A package should be listed in only one of these fields. -``` - -## plethy (1.12.0) -Maintainer: Daniel Bottomly - -2 errors | 1 warning | 3 notes - -``` -checking examples ... ERROR -Running examples in ‘plethy-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: BuxcoDB-class -> ### Title: Class '"BuxcoDB"' -> ### Aliases: BuxcoDB-class BuxcoDB addAnnotation,BuxcoDB-method -> ### addAnnotation annoTable,BuxcoDB-method annoTable -> ### annoCols,BuxcoDB-method annoCols annoLevels,BuxcoDB-method annoLevels -... 53 lines ... -> -> tables(bux.db) -[1] "WBPth" -> -> variables(bux.db) - [1] "f" "TVb" "MVb" "Penh" "PAU" "Rpef" "Comp" "PIFb" "PEFb" -[10] "Ti" "Te" "EF50" "Tr" "Tbody" "Tc" "RH" "Rinx" -> -> addAnnotation(bux.db, query=day.infer.query, index=FALSE) -Error: is.null(dbGetQuery(db.con, i)) is not TRUE -Execution halted - -checking tests ... ERROR -Running the tests in ‘tests/runTests.R’ failed. -Last 13 lines of output: - test.db.insert.autoincrement - test.dbImport - test.examine.table.lines - test.get.err.breaks - test.parse.buxco - test.retrieveData - test.summaryMeasures - test.write.sample.db - - - Error in BiocGenerics:::testPackage("plethy") : - unit tests failed for package plethy - Execution halted - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... - - IQR, mad, xtabs - -The following objects are masked from ‘package:base’: - - Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, - cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, -... 8 lines ... -Attaching package: ‘S4Vectors’ - -The following objects are masked from ‘package:base’: - - colMeans, colSums, expand.grid, rowMeans, rowSums - - -Error: processing vignette 'plethy.Rnw' failed with diagnostics: - chunk 3 -Error : is.null(dbGetQuery(db.con, query.list[[i]])) is not TRUE -Execution halted - -checking dependencies in R code ... NOTE -There are ::: calls to the package's namespace in its code. A package - almost never needs to use ::: for its own objects: - ‘csv.to.table’ ‘find.break.ranges.integer’ ‘fix.time’ ‘multi.grep’ - -checking R code for possible problems ... NOTE -generate.sample.buxco : : : : - : no visible global function definition for ‘rnorm’ -make.db.package: no visible global function definition for - ‘packageDescription’ -mvtsplot.data.frame: no visible global function definition for ‘colors’ -mvtsplot.data.frame: no visible global function definition for ‘par’ -mvtsplot.data.frame: no visible global function definition for ‘layout’ -mvtsplot.data.frame: no visible global function definition for - ‘strwidth’ -... 14 lines ... -tsplot,BuxcoDB: no visible binding for global variable ‘Sample_Name’ -Undefined global functions or variables: - Axis Days Sample_Name Value abline bxp colors layout legend lines - median mtext packageDescription par plot rnorm strwidth terms -Consider adding - importFrom("grDevices", "colors") - importFrom("graphics", "Axis", "abline", "bxp", "layout", "legend", - "lines", "mtext", "par", "plot", "strwidth") - importFrom("stats", "median", "rnorm", "terms") - importFrom("utils", "packageDescription") -to your NAMESPACE file. - -checking Rd line widths ... NOTE -Rd file 'parsing.Rd': - \usage lines wider than 90 characters: - parse.buxco(file.name = NULL, table.delim = "Table", burn.in.lines = c("Measurement", "Create measurement", "Waiting for", "Site Acknow ... [TRUNCATED] - chunk.size = 500, db.name = "bux_test.db", max.run.time.minutes = 60, overwrite = TRUE, verbose=TRUE, make.package = F, author = NULL ... [TRUNCATED] - parse.buxco.basic(file.name=NULL, table.delim="Table", burn.in.lines=c("Measurement", "Create measurement", "Waiting for", "Site Acknow ... [TRUNCATED] - -Rd file 'utilities.Rd': - \usage lines wider than 90 characters: - get.err.breaks(bux.db, max.exp.count=150, max.acc.count=900, vary.perc=.1, label.val="ERR") - proc.sanity(bux.db, max.exp.time=300, max.acc.time=1800, max.exp.count=150, max.acc.count=900) - \examples lines wider than 100 characters: - err.dta <- data.frame(samples=samples, count=count, measure_break=measure_break, table_break=table_break, phase=phase, stringsAsFactors ... [TRUNCATED] - sample.labels <- data.frame(samples=c("sample_1","sample_3"), response_type=c("high", "low"),stringsAsFactors=FALSE) - -These lines will be truncated in the PDF manual. -``` - -## poplite (0.99.16) -Maintainer: Daniel Bottomly - -1 error | 0 warnings | 1 note - -``` -checking tests ... ERROR -Running the tests in ‘tests/testthat.R’ failed. -Last 13 lines of output: - 1. Failure: createTable (@test-poplite.R#252) - 2. Failure: createTable (@test-poplite.R#252) - 3. Failure: createTable (@test-poplite.R#252) - 4. Failure: createTable (@test-poplite.R#252) - 5. Failure: insertStatement (@test-poplite.R#330) - 6. Failure: insertStatement (@test-poplite.R#350) - 7. Failure: insertStatement (@test-poplite.R#330) - 8. Failure: insertStatement (@test-poplite.R#350) - 9. Failure: insertStatement (@test-poplite.R#330) - 1. ... - - Error: testthat unit tests failed - Execution halted - -checking R code for possible problems ... NOTE -filter_.Database: no visible global function definition for ‘stack’ -get.starting.point : : no visible global function definition - for ‘na.omit’ -select_.Database: no visible global function definition for ‘stack’ -tsl.to.graph: no visible global function definition for ‘stack’ -join,Database: no visible global function definition for ‘stack’ -join,Database : .get.select.cols: no visible global function definition - for ‘setNames’ -join,Database: no visible binding for global variable ‘new.ancil’ -join,Database: no visible global function definition for ‘setNames’ -Undefined global functions or variables: - na.omit new.ancil setNames stack -Consider adding - importFrom("stats", "na.omit", "setNames") - importFrom("utils", "stack") -to your NAMESPACE file. -``` - -## recoup (1.2.0) -Maintainer: Panagiotis Moulos - -2 errors | 0 warnings | 1 note - -``` -checking examples ... ERROR -Running examples in ‘recoup-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: calcCoverage -> ### Title: Calculate coverages over a genomic region -> ### Aliases: calcCoverage -> -> ### ** Examples -> -> # Load some data -> data("recoup_test_data",package="recoup") -> -> # Calculate coverage Rle -> mask <- makeGRangesFromDataFrame(df=test.genome, -+ keep.extra.columns=TRUE) -> small.cov <- calcCoverage(test.input[[1]]$ranges,mask) -Error in .check_ncores(cores) : 16 simultaneous processes spawned -Calls: calcCoverage ... splitBySeqname -> cmclapply -> mclapply -> .check_ncores -Execution halted -** found \donttest examples: check also with --run-donttest - -checking tests ... ERROR -Running the tests in ‘tests/runTests.R’ failed. -Last 13 lines of output: - 1 Test Suite : - recoup RUnit Tests - 1 test function, 1 error, 0 failures - ERROR in test_recoup: Error in .check_ncores(cores) : 16 simultaneous processes spawned - - Test files with failing tests - - test_recoup.R - test_recoup - - - Error in BiocGenerics:::testPackage("recoup") : - unit tests failed for package recoup - Execution halted - -checking R code for possible problems ... NOTE -areColors : : no visible global function definition for - ‘col2rgb’ -buildAnnotationStore: no visible global function definition for - ‘Seqinfo’ -calcCoverage: no visible global function definition for ‘is’ -calcDesignPlotProfiles : : no visible global function - definition for ‘smooth.spline’ -calcPlotProfiles : : no visible global function definition - for ‘smooth.spline’ -... 94 lines ... -Consider adding - importFrom("grDevices", "bmp", "col2rgb", "dev.new", "dev.off", "jpeg", - "pdf", "png", "postscript", "tiff") - importFrom("graphics", "plot") - importFrom("methods", "as", "is") - importFrom("stats", "approx", "kmeans", "lowess", "quantile", - "smooth.spline", "spline", "var") - importFrom("utils", "download.file", "packageVersion", "read.delim", - "unzip") -to your NAMESPACE file (and ensure that your DESCRIPTION Imports field -contains 'methods'). -``` - -## RImmPort (1.2.0) -Maintainer: Ravi Shankar - -0 errors | 1 warning | 1 note - -``` -checking sizes of PDF files under ‘inst/doc’ ... WARNING - ‘gs+qpdf’ made some significant size reductions: - compacted ‘RImmPort_Article.pdf’ from 731Kb to 336Kb - consider running tools::compactPDF(gs_quality = "ebook") on these files - -checking R code for possible problems ... NOTE -getCellularQuantification: no visible binding for global variable - ‘experiment_sample_accession’ -getCellularQuantification: no visible binding for global variable - ‘control_files_names’ -getCellularQuantification: no visible binding for global variable - ‘ZBREFIDP’ -getGeneticsFindings: no visible binding for global variable - ‘experiment_sample_accession’ -getNucleicAcidQuantification: no visible binding for global variable - ‘experiment_sample_accession’ -getProteinQuantification: no visible binding for global variable - ‘experiment_sample_accession’ -getTiterAssayResults: no visible binding for global variable - ‘experiment_sample_accession’ -Undefined global functions or variables: - ZBREFIDP control_files_names experiment_sample_accession -``` - -## RQDA (0.2-7) -Maintainer: HUANG Ronggui - -1 error | 0 warnings | 1 note - -``` -checking whether package ‘RQDA’ can be installed ... ERROR -Installation failed. -See ‘/home/muelleki/git/R/RSQLite/revdep/checks/RQDA.Rcheck/00install.out’ for details. - -checking package dependencies ... NOTE -Packages which this enhances but not available for checking: - ‘rjpod’ ‘d3Network’ -``` - -## specL (1.8.0) -Maintainer: Christian Panse , Witold E. Wolski -Bug reports: https://github.com/fgcz/specL/issues - -0 errors | 1 warning | 3 notes - -``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because cdsw.Rmd appears to be an R Markdown v2 document. -Quitting from lines 2-25 (cdsw.Rmd) -Error: processing vignette 'cdsw.Rmd' failed with diagnostics: -could not find function "doc_date" -Execution halted - - -checking S3 generic/method consistency ... NOTE -Found the following apparent S3 methods exported but not registered: - merge.specLSet plot.psm plot.psmSet summary.psmSet -See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ -manual. - -checking R code for possible problems ... NOTE -.onAttach: no visible global function definition for ‘packageVersion’ -plot,specLSet: no visible global function definition for ‘draw.circle’ -summary,specLSet : : no visible binding for global variable - ‘iRTpeptides’ -Undefined global functions or variables: - draw.circle iRTpeptides packageVersion -Consider adding - importFrom("utils", "packageVersion") -to your NAMESPACE file. - -checking Rd files ... NOTE -prepare_Rd: ms1.p2069.Rd:28-32: Dropping empty section \references -prepare_Rd: ms1.p2069.Rd:23-26: Dropping empty section \examples -``` - -## sqldf (0.4-10) -Maintainer: G. Grothendieck -Bug reports: http://groups.google.com/group/sqldf - -1 error | 1 warning | 2 notes - -``` -checking examples ... ERROR -Running examples in ‘sqldf-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: sqldf -> ### Title: SQL select on data frames -> ### Aliases: sqldf -> ### Keywords: manip -> -... 6 lines ... -> # in R without SQL and then again with SQL -> # -> -> # head -> a1r <- head(warpbreaks) -> a1s <- sqldf("select * from warpbreaks limit 6") -Loading required package: tcltk -Error in eval(substitute(expr), envir, enclos) : - no such table: warpbreaks -Calls: sqldf ... initialize -> initialize -> rsqlite_send_query -> .Call -Execution halted - -checking whether package ‘sqldf’ can be installed ... WARNING -Found the following significant warnings: - Warning: no DISPLAY variable so Tk is not available -See ‘/home/muelleki/git/R/RSQLite/revdep/checks/sqldf.Rcheck/00install.out’ for details. - -checking dependencies in R code ... NOTE -'library' or 'require' call to ‘tcltk’ in package code. - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. - -checking R code for possible problems ... NOTE -read.csv.sql: no visible global function definition for ‘download.file’ -sqldf: no visible global function definition for ‘modifyList’ -sqldf: no visible global function definition for ‘head’ -Undefined global functions or variables: - download.file head modifyList -Consider adding - importFrom("utils", "download.file", "head", "modifyList") -to your NAMESPACE file. -``` - -## TFBSTools (1.12.0) -Maintainer: Ge Tan -Bug reports: https://github.com/ge11232002/TFBSTools/issues - -0 errors | 1 warning | 2 notes - -``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because TFBSTools.Rmd appears to be an R Markdown v2 document. -Quitting from lines 2-16 (TFBSTools.Rmd) -Error: processing vignette 'TFBSTools.Rmd' failed with diagnostics: -could not find function "doc_date" -Execution halted - - -checking installed package size ... NOTE - installed size is 12.1Mb - sub-directories of 1Mb or more: - R 11.3Mb - -checking dependencies in R code ... NOTE -Unexported objects imported by ':::' calls: - ‘S4Vectors:::new_SimpleList_from_list’ ‘seqLogo:::pwm2ic’ - See the note in ?`:::` about the use of this operator. -``` - -## trackeR (0.0.3) -Maintainer: Hannah Frick - -0 errors | 1 warning | 0 notes - -``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Warning in readLines(con) : - incomplete final line found on 'TourDetrackeR.Rmd' -Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because TourDetrackeR.Rmd appears to be an R Markdown v2 document. -Loading required package: zoo - -Attaching package: 'zoo' - -... 7 lines ... -Attaching package: 'trackeR' - -The following object is masked from 'package:base': - - append - -Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&sensor=false -Quitting from lines 96-97 (TourDetrackeR.Rmd) -Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics: -there is no package called 'webshot' -Execution halted -``` - -## TSdata (2016.8-1) -Maintainer: Paul Gilbert - -0 errors | 1 warning | 0 notes - -``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Oct 19, 2016 3:29:25 PM it.bancaditalia.oss.sdmx.util.Configuration init -INFO: Configuration file: /home/muelleki/R/x86_64-pc-linux-gnu-library/3.3/RJSDMX/configuration.properties -Oct 19, 2016 3:29:25 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Oct 19, 2016 3:29:25 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Oct 19, 2016 3:29:26 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -... 8 lines ... -Oct 19, 2016 3:29:27 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/data/ESTAT,ei_nama_q,1.0/Q.MIO-EUR.NSA.CP.NA-P72.IT -Oct 19, 2016 3:29:27 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData -INFO: The sdmx call returned messages in the footer: - Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]] - -Error: processing vignette 'Guide.Stex' failed with diagnostics: - chunk 5 -Error in .local(serIDs, con, ...) : - ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider. -Execution halted -``` - -## VariantFiltering (1.10.0) -Maintainer: Robert Castelo -Bug reports: https://github.com/rcastelo/VariantFiltering/issues - -0 errors | 2 warnings | 4 notes - -``` -checking sizes of PDF files under ‘inst/doc’ ... WARNING - ‘gs+qpdf’ made some significant size reductions: - compacted ‘usingVariantFiltering.pdf’ from 415Kb to 153Kb - consider running tools::compactPDF(gs_quality = "ebook") on these files - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Loading required package: Biostrings -Loading required package: XVector - -Attaching package: ‘VariantAnnotation’ - -The following object is masked from ‘package:base’: - -... 8 lines ... -Error in eval(expr, envir, enclos) : database disk image is malformed -Error in eval(expr, envir, enclos) : database disk image is malformed -Error : .onLoad failed in loadNamespace() for 'MafDb.1Kgenomes.phase3.hs37d5', details: - call: eval(expr, envir, enclos) - error: database disk image is malformed - -Error: processing vignette 'usingVariantFiltering.Rnw' failed with diagnostics: - chunk 3 -Error in VariantFilteringParam(vcfFilenames = CEUvcf) : - package MafDb.1Kgenomes.phase3.hs37d5 could not be loaded. -Execution halted - -checking installed package size ... NOTE - installed size is 7.8Mb - sub-directories of 1Mb or more: - R 3.5Mb - extdata 3.5Mb - -checking dependencies in R code ... NOTE -Unexported objects imported by ':::' calls: - 'S4Vectors:::labeledLine' 'VariantAnnotation:::.checkArgs' - 'VariantAnnotation:::.consolidateHits' - 'VariantAnnotation:::.returnEmpty' - See the note in ?`:::` about the use of this operator. -There are ::: calls to the package's namespace in its code. A package - almost never needs to use ::: for its own objects: - '.adjustForStrandSense' - -checking Rd line widths ... NOTE -Rd file 'MafDb-class.Rd': - \examples lines wider than 100 characters: - ## founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression. - -Rd file 'MafDb2-class.Rd': - \examples lines wider than 100 characters: - ## founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression. - -Rd file 'VariantFilteringParam-class.Rd': -... 19 lines ... - -Rd file 'autosomalRecessiveHeterozygous.Rd': - \usage lines wider than 90 characters: - BPPARAM=bpparam("SerialParam")) - -Rd file 'autosomalRecessiveHomozygous.Rd': - \usage lines wider than 90 characters: - use=c("everything", "complete.obs", "all.obs"), - BPPARAM=bpparam("SerialParam")) - -These lines will be truncated in the PDF manual. - -checking Rd cross-references ... NOTE -Package unavailable to check Rd xrefs: ‘phastCons100way.UCSC.hg38’ -``` - -## vmsbase (2.1.3) -Maintainer: Lorenzo D'Andrea - -1 error | 0 warnings | 0 notes - -``` -checking whether package ‘vmsbase’ can be installed ... ERROR -Installation failed. -See ‘/home/muelleki/git/R/RSQLite/revdep/checks/vmsbase.Rcheck/00install.out’ for details. -``` - diff --git a/revdep/problems-f-revdep.md b/revdep/problems-r-1.1.md similarity index 94% rename from revdep/problems-f-revdep.md rename to revdep/problems-r-1.1.md index 74eb2df66..4c0070a97 100644 --- a/revdep/problems-f-revdep.md +++ b/revdep/problems-r-1.1.md @@ -10,32 +10,31 @@ |language |(EN) | |collate |en_US.UTF-8 | |tz |Universal | -|date |2016-11-18 | +|date |2016-11-25 | ## Packages |package |* |version |date |source | |:---------|:--|:----------|:----------|:----------------------------------| -|BH | |1.60.0-2 |2016-05-07 |cran (@1.60.0-) | +|BH | |1.62.0-1 |2016-11-19 |cran (@1.62.0-) | |DBI | |0.5-12 |2016-10-06 |Github (rstats-db/DBI@4f00863) | |DBItest | |1.3-10 |2016-10-06 |Github (rstats-db/DBItest@9e87611) | -|knitr | |1.15 |2016-11-09 |cran (@1.15) | +|knitr | |1.15.1 |2016-11-22 |cran (@1.15.1) | |memoise | |1.0.0 |2016-01-29 |CRAN (R 3.3.1) | |plogr | |0.1-1 |2016-09-24 |cran (@0.1-1) | -|Rcpp | |0.12.7 |2016-09-05 |cran (@0.12.7) | -|rmarkdown | |1.1 |2016-10-16 |cran (@1.1) | +|Rcpp | |0.12.8 |2016-11-17 |cran (@0.12.8) | +|rmarkdown | |1.2 |2016-11-21 |cran (@1.2) | |RSQLite | |1.0.0 |2014-10-25 |CRAN (R 3.3.1) | |testthat | |1.0.2.9000 |2016-08-25 |Github (hadley/testthat@46d15da) | # Check results -32 packages with problems +31 packages with problems |package |version | errors| warnings| notes| |:------------------|:--------|------:|--------:|-----:| |AnnotationDbi |1.36.0 | 0| 1| 5| |AnnotationHubData |1.4.0 | 1| 0| 3| -|archivist |2.1 | 1| 0| 2| |ChemmineR |2.26.0 | 1| 0| 0| |clstutils |1.22.0 | 0| 2| 5| |CNEr |1.10.1 | 0| 2| 2| @@ -48,7 +47,7 @@ |metagenomeFeatures |1.4.0 | 0| 2| 2| |metaseqR |1.14.0 | 1| 1| 4| |mgsa |1.22.0 | 0| 1| 4| -|oce |0.9-19 | 1| 0| 1| +|oce |0.9-20 | 1| 0| 1| |oligoClasses |1.36.0 | 0| 1| 4| |oligo |1.38.0 | 1| 0| 9| |PAnnBuilder |1.38.0 | 0| 3| 1| @@ -58,12 +57,12 @@ |RImmPort |1.2.0 | 0| 1| 1| |RQDA |0.2-7 | 1| 0| 1| |specL |1.8.0 | 0| 1| 3| -|sqldf |0.4-10 | 1| 1| 2| +|sqldf |0.4-10 | 0| 1| 2| |TFBSTools |1.12.1 | 0| 1| 2| |tigreBrowserWriter |0.1.2 | 1| 0| 0| |trackeR |0.0.4 | 0| 1| 0| |TSdata |2016.8-1 | 0| 1| 0| -|VariantFiltering |1.10.0 | 0| 1| 4| +|VariantFiltering |1.10.1 | 0| 1| 4| |vmsbase |2.1.3 | 1| 0| 0| ## AnnotationDbi (1.36.0) @@ -171,40 +170,6 @@ File ‘AnnotationHubData/R/makeNCBIToOrgDbs.R’: See section ‘Good practice’ in ‘?data’. ``` -## archivist (2.1) -Maintainer: Przemyslaw Biecek -Bug reports: https://github.com/pbiecek/archivist/issues - -1 error | 0 warnings | 2 notes - -``` -checking examples ... ERROR -Running examples in ‘archivist-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: aread -> ### Title: Read Artifacts Given as md5hashes from the Repository -> ### Aliases: aread -> -> ### ** Examples -> -> # read the object from local directory -> setLocalRepo(system.file("graphGallery", package = "archivist")) -> pl <- aread("f05f0ed0662fe01850ec1b928830ef32") -> # plot it -> pl -Error: ScalesList was built with an incompatible version of ggproto. -Please reinstall the package that provides this extension. -Execution halted - -checking package dependencies ... NOTE -Package which this enhances but not available for checking: ‘archivist.github’ - -checking Rd cross-references ... NOTE -Package unavailable to check Rd xrefs: ‘archivist.github’ -``` - ## ChemmineR (2.26.0) Maintainer: Thomas Girke @@ -783,7 +748,7 @@ to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). ``` -## oce (0.9-19) +## oce (0.9-20) Maintainer: Dan Kelley Bug reports: https://github.com/dankelley/oce/issues @@ -811,9 +776,9 @@ Calls: plot -> plot -> .local Execution halted checking installed package size ... NOTE - installed size is 5.3Mb + installed size is 5.4Mb sub-directories of 1Mb or more: - help 2.0Mb + help 2.1Mb ``` ## oligoClasses (1.36.0) @@ -1381,32 +1346,9 @@ prepare_Rd: ms1.p2069.Rd:23-26: Dropping empty section \examples Maintainer: G. Grothendieck Bug reports: http://groups.google.com/group/sqldf -1 error | 1 warning | 2 notes +0 errors | 1 warning | 2 notes ``` -checking examples ... ERROR -Running examples in ‘sqldf-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: sqldf -> ### Title: SQL select on data frames -> ### Aliases: sqldf -> ### Keywords: manip -> -... 6 lines ... -> # in R without SQL and then again with SQL -> # -> -> # head -> a1r <- head(warpbreaks) -> a1s <- sqldf("select * from warpbreaks limit 6") -Loading required package: tcltk -Error in eval(substitute(expr), envir, enclos) : - no such table: warpbreaks -Calls: sqldf ... initialize -> initialize -> rsqlite_send_query -> .Call -Execution halted - checking whether package ‘sqldf’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available @@ -1483,7 +1425,7 @@ Warning: Named parameters not used in query: dname > closeDb(db) Warning: Named parameters not used in query: parent_id, name Warning: Named parameters not used in query: name, parent_id -Error in eval(substitute(expr), envir, enclos) : +Error in rsqlite_bind_rows(res@ptr, params) : Query requires 1 params; 2 supplied. Calls: closeDb ... -> db_bind -> rsqlite_bind_rows -> .Call Execution halted @@ -1529,28 +1471,28 @@ Maintainer: Paul Gilbert checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.util.Configuration init INFO: Configuration file: /home/muelleki/R/x86_64-pc-linux-gnu-library/3.3/RJSDMX/configuration.properties -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 25, 2016 12:03:42 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 25, 2016 12:03:43 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 25, 2016 12:03:43 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetData/QNA/CAN.B1_GE.CARSA.Q?format=compact_v2 ... 8 lines ... -Nov 18, 2016 3:53:59 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/data/ESTAT,ei_nama_q,1.0/Q.MIO-EUR.NSA.CP.NA-P72.IT -Nov 18, 2016 3:53:59 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData -INFO: The sdmx call returned messages in the footer: - Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]] +SEVERE: Connection failed. HTTP error code : 500, message: Internal Server Error +SDMX meaning: Error on the provider side. +Nov 25, 2016 12:03:44 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getDataFlowStructure +SEVERE: Exception caught parsing results from call to provider Eurostat Error: processing vignette 'Guide.Stex' failed with diagnostics: chunk 5 Error in .local(serIDs, con, ...) : - ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider. + ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: Exception. Class: it.bancaditalia.oss.sdmx.util.SdmxException .Message: Connection failed. HTTP error code : 500, message: Internal Server Error +SDMX meaning: Error on the provider side. Execution halted ``` -## VariantFiltering (1.10.0) +## VariantFiltering (1.10.1) Maintainer: Robert Castelo Bug reports: https://github.com/rcastelo/VariantFiltering/issues diff --git a/revdep/problems-v1.0.0.md b/revdep/problems-v1.0.0.md index 6b8b5f402..5d40e3e30 100644 --- a/revdep/problems-v1.0.0.md +++ b/revdep/problems-v1.0.0.md @@ -10,7 +10,7 @@ |language |(EN) | |collate |en_US.UTF-8 | |tz |Universal | -|date |2016-11-18 | +|date |2016-11-24 | ## Packages @@ -22,13 +22,12 @@ # Check results -30 packages with problems +28 packages with problems |package |version | errors| warnings| notes| |:------------------|:--------|------:|--------:|-----:| |AnnotationDbi |1.36.0 | 0| 1| 5| |AnnotationHubData |1.4.0 | 1| 0| 3| -|archivist |2.1 | 1| 0| 2| |ChemmineR |2.26.0 | 1| 0| 0| |clstutils |1.22.0 | 0| 2| 5| |CNEr |1.10.1 | 0| 2| 2| @@ -40,7 +39,7 @@ |metagenomeFeatures |1.4.0 | 0| 2| 2| |metaseqR |1.14.0 | 1| 1| 4| |mgsa |1.22.0 | 0| 1| 4| -|oce |0.9-19 | 1| 0| 1| +|oce |0.9-20 | 1| 0| 1| |oligoClasses |1.36.0 | 0| 1| 4| |oligo |1.38.0 | 1| 0| 9| |PAnnBuilder |1.38.0 | 0| 3| 1| @@ -53,8 +52,7 @@ |TFBSTools |1.12.1 | 0| 1| 2| |trackeR |0.0.4 | 0| 1| 0| |TSdata |2016.8-1 | 0| 1| 0| -|UniProt.ws |2.14.0 | 1| 0| 1| -|VariantFiltering |1.10.0 | 0| 1| 4| +|VariantFiltering |1.10.1 | 0| 1| 4| |vmsbase |2.1.3 | 1| 0| 0| ## AnnotationDbi (1.36.0) @@ -115,15 +113,15 @@ Maintainer: Bioconductor Package Maintainer checking tests ... ERROR Running the tests in ‘tests/AnnotationHubData_unit_tests.R’ failed. Last 13 lines of output: + ERROR in test_UCSCChainPreparer_recipe: Error : 1: Unknown IO error2: failed to load external entity "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=&retmax=0" + + Test files with failing tests test_recipe.R test_UCSC2BitPreparer_recipe test_UCSCChainPreparer_recipe - test_webAccessFunctions.R - test_listRemoteFiles - Error in BiocGenerics:::testPackage("AnnotationHubData") : unit tests failed for package AnnotationHubData @@ -162,40 +160,6 @@ File ‘AnnotationHubData/R/makeNCBIToOrgDbs.R’: See section ‘Good practice’ in ‘?data’. ``` -## archivist (2.1) -Maintainer: Przemyslaw Biecek -Bug reports: https://github.com/pbiecek/archivist/issues - -1 error | 0 warnings | 2 notes - -``` -checking examples ... ERROR -Running examples in ‘archivist-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: aread -> ### Title: Read Artifacts Given as md5hashes from the Repository -> ### Aliases: aread -> -> ### ** Examples -> -> # read the object from local directory -> setLocalRepo(system.file("graphGallery", package = "archivist")) -> pl <- aread("f05f0ed0662fe01850ec1b928830ef32") -> # plot it -> pl -Error: ScalesList was built with an incompatible version of ggproto. -Please reinstall the package that provides this extension. -Execution halted - -checking package dependencies ... NOTE -Package which this enhances but not available for checking: ‘archivist.github’ - -checking Rd cross-references ... NOTE -Package unavailable to check Rd xrefs: ‘archivist.github’ -``` - ## ChemmineR (2.26.0) Maintainer: Thomas Girke @@ -761,7 +725,7 @@ to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). ``` -## oce (0.9-19) +## oce (0.9-20) Maintainer: Dan Kelley Bug reports: https://github.com/dankelley/oce/issues @@ -789,9 +753,9 @@ Calls: plot -> plot -> .local Execution halted checking installed package size ... NOTE - installed size is 5.3Mb + installed size is 5.4Mb sub-directories of 1Mb or more: - help 2.0Mb + help 2.1Mb ``` ## oligoClasses (1.36.0) @@ -1063,7 +1027,7 @@ The error most likely occurred in: > temp.db.file <- tempfile() > write(sim.bux.lines, file=temp.file) > test.bux.db <- parse.buxco(file.name=temp.file, db.name=temp.db.file, chunk.size=10000) -Processing /tmp/RtmpUmYjPW/filed52c298e3ea2 in chunks of 10000 +Processing /tmp/RtmpcwL4RG/filee779641e173e in chunks of 10000 Starting chunk 1 Reached breakpoint change Processing breakpoint 1 @@ -1086,7 +1050,7 @@ Last 13 lines of output: Error in BiocGenerics:::testPackage("plethy") : unit tests failed for package plethy In addition: Warning message: - closing unused connection 3 (/tmp/RtmpmtQQ3m/filed6117e71fb4f) + closing unused connection 3 (/tmp/RtmppOK3Wi/filee8f02e70ec78) Execution halted checking dependencies in R code ... NOTE @@ -1387,69 +1351,28 @@ Maintainer: Paul Gilbert checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... -Nov 18, 2016 3:21:19 PM it.bancaditalia.oss.sdmx.util.Configuration init +Loading required package: TSdbi +Nov 24, 2016 3:15:47 PM it.bancaditalia.oss.sdmx.util.Configuration init INFO: Configuration file: /home/muelleki/R/x86_64-pc-linux-gnu-library/3.3/RJSDMX/configuration.properties -Nov 18, 2016 3:21:19 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 24, 2016 3:15:47 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Nov 18, 2016 3:21:20 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 24, 2016 3:15:48 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Nov 18, 2016 3:21:20 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -... 8 lines ... -Nov 18, 2016 3:21:22 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/data/ESTAT,ei_nama_q,1.0/Q.MIO-EUR.NSA.CP.NA-P72.IT -Nov 18, 2016 3:21:22 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData -INFO: The sdmx call returned messages in the footer: - Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]] +... 6 lines ... +INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest +Nov 24, 2016 3:18:01 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +SEVERE: Exception. Class: java.net.ConnectException .Message: Connection timed out (Connection timed out) +Nov 24, 2016 3:18:01 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient getDataflow +SEVERE: Exception caught parsing results from call to provider Eurostat Error: processing vignette 'Guide.Stex' failed with diagnostics: chunk 5 Error in .local(serIDs, con, ...) : - ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider. + ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: Exception. Class: it.bancaditalia.oss.sdmx.util.SdmxException .Message: Exception. Class: java.net.ConnectException .Message: Connection timed out (Connection timed out) Execution halted ``` -## UniProt.ws (2.14.0) -Maintainer: Bioconductor Package Maintainer - -1 error | 0 warnings | 1 note - -``` -checking tests ... ERROR -Running the tests in ‘tests/UniProt.ws_unit_tests.R’ failed. -Last 13 lines of output: - UniProt.ws RUnit Tests - 14 test functions, 0 errors, 1 failure - FAILURE in test_mapUniprot: Error in checkTrue(res[1, 1] == "1") : Test not TRUE - - - Test files with failing tests - - test_serviceAccessors.R - test_mapUniprot - - - Error in BiocGenerics:::testPackage("UniProt.ws") : - unit tests failed for package UniProt.ws - Execution halted - -checking R code for possible problems ... NOTE -.getSomeUniprotGoodies: no visible global function definition for - ‘head’ -.tryReadResult: no visible global function definition for ‘read.delim’ -.tryReadResult: no visible global function definition for ‘URLencode’ -availableUniprotSpecies: no visible global function definition for - ‘read.delim’ -availableUniprotSpecies: no visible global function definition for - ‘head’ -lookupUniprotSpeciesFromTaxId: no visible global function definition - for ‘read.delim’ -Undefined global functions or variables: - URLencode head read.delim -Consider adding - importFrom("utils", "URLencode", "head", "read.delim") -to your NAMESPACE file. -``` - -## VariantFiltering (1.10.0) +## VariantFiltering (1.10.1) Maintainer: Robert Castelo Bug reports: https://github.com/rcastelo/VariantFiltering/issues diff --git a/revdep/problems.md b/revdep/problems.md index 74eb2df66..4c0070a97 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -10,32 +10,31 @@ |language |(EN) | |collate |en_US.UTF-8 | |tz |Universal | -|date |2016-11-18 | +|date |2016-11-25 | ## Packages |package |* |version |date |source | |:---------|:--|:----------|:----------|:----------------------------------| -|BH | |1.60.0-2 |2016-05-07 |cran (@1.60.0-) | +|BH | |1.62.0-1 |2016-11-19 |cran (@1.62.0-) | |DBI | |0.5-12 |2016-10-06 |Github (rstats-db/DBI@4f00863) | |DBItest | |1.3-10 |2016-10-06 |Github (rstats-db/DBItest@9e87611) | -|knitr | |1.15 |2016-11-09 |cran (@1.15) | +|knitr | |1.15.1 |2016-11-22 |cran (@1.15.1) | |memoise | |1.0.0 |2016-01-29 |CRAN (R 3.3.1) | |plogr | |0.1-1 |2016-09-24 |cran (@0.1-1) | -|Rcpp | |0.12.7 |2016-09-05 |cran (@0.12.7) | -|rmarkdown | |1.1 |2016-10-16 |cran (@1.1) | +|Rcpp | |0.12.8 |2016-11-17 |cran (@0.12.8) | +|rmarkdown | |1.2 |2016-11-21 |cran (@1.2) | |RSQLite | |1.0.0 |2014-10-25 |CRAN (R 3.3.1) | |testthat | |1.0.2.9000 |2016-08-25 |Github (hadley/testthat@46d15da) | # Check results -32 packages with problems +31 packages with problems |package |version | errors| warnings| notes| |:------------------|:--------|------:|--------:|-----:| |AnnotationDbi |1.36.0 | 0| 1| 5| |AnnotationHubData |1.4.0 | 1| 0| 3| -|archivist |2.1 | 1| 0| 2| |ChemmineR |2.26.0 | 1| 0| 0| |clstutils |1.22.0 | 0| 2| 5| |CNEr |1.10.1 | 0| 2| 2| @@ -48,7 +47,7 @@ |metagenomeFeatures |1.4.0 | 0| 2| 2| |metaseqR |1.14.0 | 1| 1| 4| |mgsa |1.22.0 | 0| 1| 4| -|oce |0.9-19 | 1| 0| 1| +|oce |0.9-20 | 1| 0| 1| |oligoClasses |1.36.0 | 0| 1| 4| |oligo |1.38.0 | 1| 0| 9| |PAnnBuilder |1.38.0 | 0| 3| 1| @@ -58,12 +57,12 @@ |RImmPort |1.2.0 | 0| 1| 1| |RQDA |0.2-7 | 1| 0| 1| |specL |1.8.0 | 0| 1| 3| -|sqldf |0.4-10 | 1| 1| 2| +|sqldf |0.4-10 | 0| 1| 2| |TFBSTools |1.12.1 | 0| 1| 2| |tigreBrowserWriter |0.1.2 | 1| 0| 0| |trackeR |0.0.4 | 0| 1| 0| |TSdata |2016.8-1 | 0| 1| 0| -|VariantFiltering |1.10.0 | 0| 1| 4| +|VariantFiltering |1.10.1 | 0| 1| 4| |vmsbase |2.1.3 | 1| 0| 0| ## AnnotationDbi (1.36.0) @@ -171,40 +170,6 @@ File ‘AnnotationHubData/R/makeNCBIToOrgDbs.R’: See section ‘Good practice’ in ‘?data’. ``` -## archivist (2.1) -Maintainer: Przemyslaw Biecek -Bug reports: https://github.com/pbiecek/archivist/issues - -1 error | 0 warnings | 2 notes - -``` -checking examples ... ERROR -Running examples in ‘archivist-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: aread -> ### Title: Read Artifacts Given as md5hashes from the Repository -> ### Aliases: aread -> -> ### ** Examples -> -> # read the object from local directory -> setLocalRepo(system.file("graphGallery", package = "archivist")) -> pl <- aread("f05f0ed0662fe01850ec1b928830ef32") -> # plot it -> pl -Error: ScalesList was built with an incompatible version of ggproto. -Please reinstall the package that provides this extension. -Execution halted - -checking package dependencies ... NOTE -Package which this enhances but not available for checking: ‘archivist.github’ - -checking Rd cross-references ... NOTE -Package unavailable to check Rd xrefs: ‘archivist.github’ -``` - ## ChemmineR (2.26.0) Maintainer: Thomas Girke @@ -783,7 +748,7 @@ to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). ``` -## oce (0.9-19) +## oce (0.9-20) Maintainer: Dan Kelley Bug reports: https://github.com/dankelley/oce/issues @@ -811,9 +776,9 @@ Calls: plot -> plot -> .local Execution halted checking installed package size ... NOTE - installed size is 5.3Mb + installed size is 5.4Mb sub-directories of 1Mb or more: - help 2.0Mb + help 2.1Mb ``` ## oligoClasses (1.36.0) @@ -1381,32 +1346,9 @@ prepare_Rd: ms1.p2069.Rd:23-26: Dropping empty section \examples Maintainer: G. Grothendieck Bug reports: http://groups.google.com/group/sqldf -1 error | 1 warning | 2 notes +0 errors | 1 warning | 2 notes ``` -checking examples ... ERROR -Running examples in ‘sqldf-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: sqldf -> ### Title: SQL select on data frames -> ### Aliases: sqldf -> ### Keywords: manip -> -... 6 lines ... -> # in R without SQL and then again with SQL -> # -> -> # head -> a1r <- head(warpbreaks) -> a1s <- sqldf("select * from warpbreaks limit 6") -Loading required package: tcltk -Error in eval(substitute(expr), envir, enclos) : - no such table: warpbreaks -Calls: sqldf ... initialize -> initialize -> rsqlite_send_query -> .Call -Execution halted - checking whether package ‘sqldf’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available @@ -1483,7 +1425,7 @@ Warning: Named parameters not used in query: dname > closeDb(db) Warning: Named parameters not used in query: parent_id, name Warning: Named parameters not used in query: name, parent_id -Error in eval(substitute(expr), envir, enclos) : +Error in rsqlite_bind_rows(res@ptr, params) : Query requires 1 params; 2 supplied. Calls: closeDb ... -> db_bind -> rsqlite_bind_rows -> .Call Execution halted @@ -1529,28 +1471,28 @@ Maintainer: Paul Gilbert checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.util.Configuration init INFO: Configuration file: /home/muelleki/R/x86_64-pc-linux-gnu-library/3.3/RJSDMX/configuration.properties -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 25, 2016 12:03:42 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 25, 2016 12:03:43 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA -Nov 18, 2016 3:53:58 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +Nov 25, 2016 12:03:43 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery +INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetData/QNA/CAN.B1_GE.CARSA.Q?format=compact_v2 ... 8 lines ... -Nov 18, 2016 3:53:59 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery -INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/data/ESTAT,ei_nama_q,1.0/Q.MIO-EUR.NSA.CP.NA-P72.IT -Nov 18, 2016 3:53:59 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData -INFO: The sdmx call returned messages in the footer: - Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]] +SEVERE: Connection failed. HTTP error code : 500, message: Internal Server Error +SDMX meaning: Error on the provider side. +Nov 25, 2016 12:03:44 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getDataFlowStructure +SEVERE: Exception caught parsing results from call to provider Eurostat Error: processing vignette 'Guide.Stex' failed with diagnostics: chunk 5 Error in .local(serIDs, con, ...) : - ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider. + ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: Exception. Class: it.bancaditalia.oss.sdmx.util.SdmxException .Message: Connection failed. HTTP error code : 500, message: Internal Server Error +SDMX meaning: Error on the provider side. Execution halted ``` -## VariantFiltering (1.10.0) +## VariantFiltering (1.10.1) Maintainer: Robert Castelo Bug reports: https://github.com/rcastelo/VariantFiltering/issues diff --git a/revdep/timing.md b/revdep/timing.md index 6081c0be8..81fcefe57 100644 --- a/revdep/timing.md +++ b/revdep/timing.md @@ -2,121 +2,122 @@ | |package |version | check_time| |:---|:------------------|:---------|----------:| -|4 |AnnotationHubData |1.4.0 | 1628.1| -|64 |OrganismDbi |1.16.0 | 903.4| -|38 |GenomicFeatures |1.26.0 | 888.6| -|23 |customProDB |1.14.0 | 656.5| -|94 |SRAdb |1.32.0 | 605.7| -|22 |cummeRbund |2.16.0 | 591.8| -|114 |VariantFiltering |1.10.0 | 578.3| -|111 |UniProt.ws |2.14.0 | 557.8| -|67 |PGA |1.4.0 | 544.5| -|1 |affycoretools |1.46.1 | 456| -|44 |lumi |2.26.3 | 442.1| -|102 |TFBSTools |1.12.1 | 434.3| -|20 |CNEr |1.10.1 | 421.5| -|39 |Genominator |1.28.0 | 392.8| -|52 |metaseqR |1.14.0 | 381.8| -|30 |ensembldb |1.6.2 | 367.8| -|41 |GWASTools |1.20.0 | 347| -|37 |GeneAnswers |2.16.0 | 324.9| -|63 |oligo |1.38.0 | 310.9| -|25 |DECIPHER |2.2.0 | 294.7| -|75 |recoup |1.2.0 | 294.5| -|87 |seqplots |1.12.0 | 282.4| -|29 |emuR |0.2.0 | 278.4| -|2 |AnnotationDbi |1.36.0 | 258.5| -|15 |Category |2.40.0 | 252.8| -|3 |AnnotationForge |1.16.0 | 248.6| -|50 |metagenomeFeatures |1.4.0 | 216.7| -|62 |oligoClasses |1.36.0 | 208.1| -|5 |AnnotationHub |2.6.2 | 207.5| -|66 |pdInfoBuilder |1.38.0 | 171.2| -|99 |survey |3.31-2 | 169.3| -|73 |rangeMapper |0.3-0 | 162.5| -|88 |SGP |1.5-0.0 | 149.6| -|61 |oce |0.9-19 | 146.5| -|40 |GEOmetadb |1.34.0 | 137| -|104 |tigre |1.28.0 | 131.6| -|74 |RecordLinkage |0.4-10 | 129| -|9 |BatchJobs |1.6 | 125.7| -|112 |Uniquorn |1.2.0 | 119.9| -|47 |manta |1.20.0 | 118.5| -|48 |marmap |0.9.5 | 116.6| -|51 |MetaIntegrator |1.0.3 | 113.1| -|56 |MonetDBLite |0.3.1 | 111.7| -|12 |bioassayR |1.12.1 | 110| -|83 |rTRM |1.12.0 | 104.2| -|96 |SSN |1.1.8 | 102.5| -|105 |trackeR |0.0.4 | 100.9| -|54 |miRNAtap |1.8.0 | 96.6| -|98 |stream |1.2-3 | 94.9| -|89 |smnet |2.1 | 90.8| -|69 |plethy |1.12.0 | 88.2| -|90 |snplist |0.16 | 87.3| -|109 |tweet2r |1.0 | 87| -|86 |SEERaBomb |2016.2 | 81.9| -|8 |BatchExperiments |1.4.1 | 79| -|65 |PAnnBuilder |1.38.0 | 77.5| -|18 |CITAN |2015.12-2 | 75| -|26 |diffrprojects |0.1.14 | 72.8| -|55 |MmPalateMiRNA |1.24.0 | 72.1| -|101 |tcpl |1.2.2 | 71.6| -|27 |dplyr |0.5.0 | 70| -|7 |archivist |2.1 | 68.8| -|6 |APSIM |0.9.1 | 68.7| -|49 |MeSHDbi |1.10.0 | 66.5| -|79 |RObsDat |16.03 | 62.2| -|19 |clstutils |1.22.0 | 62.1| -|68 |pitchRx |1.8.2 | 60.1| -|76 |refGenome |1.7.0 | 60.1| -|72 |quantmod |0.4-7 | 46.4| -|21 |CollapsABEL |0.10.8 | 45.7| -|70 |poplite |0.99.16 | 44.7| -|36 |gcbd |0.2.6 | 44.4| -|80 |rplexos |1.1.8 | 41.6| -|78 |RImmPort |1.2.0 | 40.8| -|82 |rtext |0.1.20 | 40.4| -|107 |TSSQLite |2015.4-1 | 40.2| -|53 |mgsa |1.22.0 | 38.4| -|95 |srvyr |0.2.0 | 38| -|57 |MUCflights |0.0-3 | 37.5| -|45 |macleish |0.3.0 | 35.7| -|108 |TSsql |2015.1-2 | 34.4| -|115 |vegdata |0.9 | 34.4| -|43 |iontree |1.20.0 | 34.2| -|35 |freqweights |1.0.2 | 32.6| -|91 |specL |1.8.0 | 31| -|31 |etl |0.3.4 | 27.6| -|77 |rgrass7 |0.1-9 | 25| -|84 |rvertnet |0.5.0 | 24| -|13 |BoSSA |2.0 | 21.8| -|17 |chunked |0.3 | 21.1| -|110 |twitteR |1.1.9 | 20.3| -|34 |filematrix |1.1.0 | 19.5| -|59 |nutshell |2.0 | 19.2| -|113 |UPMASK |1.0 | 19.2| -|92 |sqldf |0.4-10 | 18.6| -|24 |DBI |0.5-1 | 17.4| -|85 |scrime |1.3.3 | 17.3| -|97 |storr |1.0.1 | 17.2| -|60 |oai |0.2.0 | 16.5| -|33 |filehashSQLite |0.2-4 | 16.3| -|100 |taRifx |1.0.6 | 15.6| -|32 |ETLUtils |1.3 | 15.5| -|10 |bibliospec |0.0.4 | 15.3| -|42 |imputeMulti |0.6.3 | 14.9| -|46 |maGUI |1.0 | 14.9| -|14 |caroline |0.7.6 | 14.4| -|103 |tigreBrowserWriter |0.1.2 | 13.4| -|93 |sqliter |0.1.0 | 13| -|71 |ProjectTemplate |0.7 | 12.4| -|11 |biglm |0.9-1 | 12.1| -|106 |TSdata |2016.8-1 | 9.1| -|58 |nutshell.bbdb |1.0 | 5.6| -|16 |ChemmineR |2.26.0 | 4.7| -|116 |vmsbase |2.1.3 | 4.2| -|81 |RQDA |0.2-7 | 2.8| -|28 |ecd |0.8.2 | 1.3| +|115 |VariantFiltering |1.10.1 | 966.7| +|38 |GenomicFeatures |1.26.0 | 932.8| +|95 |SRAdb |1.32.0 | 781.2| +|65 |OrganismDbi |1.16.0 | 734.5| +|4 |AnnotationHubData |1.4.0 | 695.5| +|23 |customProDB |1.14.0 | 649.7| +|22 |cummeRbund |2.16.0 | 622.5| +|68 |PGA |1.4.0 | 547.5| +|30 |ensembldb |1.6.2 | 489.9| +|1 |affycoretools |1.46.1 | 471.4| +|20 |CNEr |1.10.1 | 468.6| +|2 |AnnotationDbi |1.36.0 | 456.9| +|103 |TFBSTools |1.12.1 | 453.2| +|45 |lumi |2.26.3 | 447.6| +|39 |Genominator |1.28.0 | 412.2| +|53 |metaseqR |1.14.0 | 392.2| +|41 |GWASTools |1.20.0 | 375.2| +|64 |oligo |1.38.0 | 364.5| +|37 |GeneAnswers |2.16.0 | 331.8| +|76 |recoup |1.2.0 | 301.9| +|25 |DECIPHER |2.2.0 | 300.8| +|88 |seqplots |1.12.0 | 287.9| +|55 |miRNAtap |1.8.0 | 276.1| +|29 |emuR |0.2.0 | 271.7| +|3 |AnnotationForge |1.16.0 | 267.6| +|15 |Category |2.40.0 | 263.4| +|112 |UniProt.ws |2.14.0 | 237.7| +|5 |AnnotationHub |2.6.4 | 223.4| +|63 |oligoClasses |1.36.0 | 222.2| +|51 |metagenomeFeatures |1.4.0 | 219| +|40 |GEOmetadb |1.34.0 | 207.6| +|67 |pdInfoBuilder |1.38.0 | 177.7| +|100 |survey |3.31-2 | 169.9| +|74 |rangeMapper |0.3-0 | 168.3| +|89 |SGP |1.5-0.0 | 154.5| +|62 |oce |0.9-20 | 153| +|105 |tigre |1.28.0 | 136.3| +|49 |marmap |0.9.5 | 134.6| +|75 |RecordLinkage |0.4-10 | 131.9| +|84 |rTRM |1.12.0 | 131.3| +|9 |BatchJobs |1.6 | 130| +|12 |bioassayR |1.12.1 | 123.7| +|113 |Uniquorn |1.2.0 | 122.6| +|48 |manta |1.20.0 | 115.8| +|52 |MetaIntegrator |1.0.3 | 115.4| +|57 |MonetDBLite |0.3.1 | 115.1| +|97 |SSN |1.1.8 | 103.3| +|106 |trackeR |0.0.4 | 103.2| +|99 |stream |1.2-3 | 96.7| +|90 |smnet |2.1 | 94.3| +|70 |plethy |1.12.0 | 92.3| +|110 |tweet2r |1.0 | 92.3| +|91 |snplist |0.16 | 90.6| +|8 |BatchExperiments |1.4.1 | 87.4| +|87 |SEERaBomb |2016.2 | 85.6| +|66 |PAnnBuilder |1.38.0 | 80.8| +|56 |MmPalateMiRNA |1.24.0 | 79.5| +|18 |CITAN |2015.12-2 | 78.5| +|7 |archivist |2.1.1 | 78.4| +|27 |dplyr |0.5.0 | 74.6| +|26 |diffrprojects |0.1.14 | 74.2| +|6 |APSIM |0.9.1 | 72.9| +|19 |clstutils |1.22.0 | 72.8| +|102 |tcpl |1.2.2 | 71.7| +|80 |RObsDat |16.03 | 66.6| +|50 |MeSHDbi |1.10.0 | 66.2| +|77 |refGenome |1.7.0 | 63.7| +|69 |pitchRx |1.8.2 | 62.8| +|36 |gcbd |0.2.6 | 49.9| +|73 |quantmod |0.4-7 | 49.4| +|71 |poplite |0.99.16 | 48.8| +|21 |CollapsABEL |0.10.8 | 48.6| +|81 |rplexos |1.1.8 | 44.7| +|79 |RImmPort |1.2.0 | 43.5| +|46 |macleish |0.3.0 | 42.7| +|83 |rtext |0.1.20 | 41.2| +|108 |TSSQLite |2015.4-1 | 41.1| +|47 |maGUI |1.0 | 40.2| +|54 |mgsa |1.22.0 | 39.8| +|96 |srvyr |0.2.0 | 37.9| +|116 |vegdata |0.9 | 37.9| +|58 |MUCflights |0.0-3 | 37.8| +|35 |freqweights |1.0.2 | 36.3| +|44 |KoNLP |0.80.0 | 36.2| +|109 |TSsql |2015.1-2 | 34.9| +|43 |iontree |1.20.0 | 33.6| +|92 |specL |1.8.0 | 32.6| +|31 |etl |0.3.4 | 29.9| +|78 |rgrass7 |0.1-9 | 25.6| +|85 |rvertnet |0.5.0 | 25.5| +|13 |BoSSA |2.0 | 23.5| +|17 |chunked |0.3 | 21.2| +|93 |sqldf |0.4-10 | 20.9| +|111 |twitteR |1.1.9 | 20.8| +|34 |filematrix |1.1.0 | 20| +|114 |UPMASK |1.0 | 19.9| +|60 |nutshell |2.0 | 19.7| +|86 |scrime |1.3.3 | 18.1| +|10 |bibliospec |0.0.4 | 17.9| +|24 |DBI |0.5-1 | 17.3| +|33 |filehashSQLite |0.2-4 | 17| +|61 |oai |0.2.2 | 16.3| +|98 |storr |1.0.1 | 16.3| +|14 |caroline |0.7.6 | 15.9| +|32 |ETLUtils |1.3 | 15.8| +|11 |biglm |0.9-1 | 15.7| +|72 |ProjectTemplate |0.7 | 15.5| +|101 |taRifx |1.0.6 | 15| +|42 |imputeMulti |0.6.3 | 14.3| +|94 |sqliter |0.1.0 | 13.7| +|104 |tigreBrowserWriter |0.1.2 | 13.3| +|107 |TSdata |2016.8-1 | 12.1| +|16 |ChemmineR |2.26.0 | 7.9| +|59 |nutshell.bbdb |1.0 | 4.9| +|117 |vmsbase |2.1.3 | 4.5| +|82 |RQDA |0.2-7 | 3.1| +|28 |ecd |0.8.2 | 1.2| diff --git a/src/Makevars b/src/Makevars index 16fc4c74a..7de739c74 100644 --- a/src/Makevars +++ b/src/Makevars @@ -11,6 +11,9 @@ PKG_LIBS = sqlite3/extension-functions.o sqlite3/sqlite3.o $(SHLIB): ${PKG_LIBS} +clean: + rm -f Makevars.local + # This file exists only for R CMD INSTALL, is created as empty file # for building from source archive Makevars.local: