diff --git a/DESCRIPTION b/DESCRIPTION index 0582c8f25..282c09507 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: GGally -Version: 1.4.1 +Version: 1.5.0 License: GPL (>= 2.0) Title: Extension to 'ggplot2' Type: Package diff --git a/R/data-australia-pisa-2012.R b/R/data-australia-pisa-2012.R index 40bc53f79..85a0e6b08 100644 --- a/R/data-australia-pisa-2012.R +++ b/R/data-australia-pisa-2012.R @@ -1,4 +1,4 @@ -#' Programme for International Student Assesment (PISA) 2012 Data for Australia +#' Programme for International Student Assessment (PISA) 2012 Data for Australia #' #' About PISA #' diff --git a/R/ggnetworkmap.R b/R/ggnetworkmap.R index fd9845723..d65b500be 100644 --- a/R/ggnetworkmap.R +++ b/R/ggnetworkmap.R @@ -8,7 +8,7 @@ if(getRversion() >= "2.15.1") { #' ggnetworkmap - Plot a network with ggplot2 suitable for overlay on a ggmap:: map ggplot, or other ggplot #' -#' This is a descendent of the original \code{ggnet} function. \code{ggnet} added the innovation of plotting the network geographically. +#' This is a descendant of the original \code{ggnet} function. \code{ggnet} added the innovation of plotting the network geographically. #' However, \code{ggnet} needed to be the first object in the ggplot chain. \code{ggnetworkmap} does not. If passed a \code{ggplot} object as its first argument, #' such as output from \code{ggmap}, \code{ggnetworkmap} will plot on top of that chart, looking for vertex attributes \code{lon} and \code{lat} as coordinates. #' Otherwise, \code{ggnetworkmap} will generate coordinates using the Fruchterman-Reingold algorithm. diff --git a/cran-comments.md b/cran-comments.md index fee73dd7a..ab4895588 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,88 +1,65 @@ ## Comments -### 2017-5-17 +### 2020-3-19 -Altered test and added crosstalk as a suggests. Passes on travis, local mac, and against plotly (reason for test). +I've fixed the tests and the package now works with the latest (and prior) ggplot2 versions. -- Barret +Please let me know if there is anything else I can do. +Best, +Barret -### 2017-5-17 -$GGally -'::' or ':::' import not declared from: ‘crosstalk’ -'library' or 'require' call not declared from: ‘crosstalk’ +### 2020-3-6 -- Kurt +Dear maintainer, -### 2017-5-17 +Please see the problems shown on +. -Please let me know if there is anything else I can do! +Please correct before 2020-03-20 to safely retain your package on CRAN. -Thank you for your time. - -- Barret +Best, +-k #### Test environments and R CMD check results -* local OS X install - * R version 3.5.0 (2018-04-23) - Platform: system x86_64, darwin15.6.0 - Running under: macOS High ierra 10.13.4 - * 0 errors | 0 warnings | 0 notes - -* travis-ci - * Known travis issue of setting a _JAVA_OPTIONS value. **These _JAVA_OPTIONS notes are false positives** - - * R version 3.5.0 (2017-01-27) - Platform: x86_64-pc-linux-gnu (64-bit) - Running under: Ubuntu 14.04.5 LTS - * 0 errors | 0 warnings | 1 note - * checking dependencies in R code ... NOTE - Picked up _JAVA_OPTIONS: -Xmx2048m -Xms512m - - * R Under development (unstable) (2018-05-16 r74730) - Platform: x86_64-pc-linux-gnu (64-bit) - Running under: Ubuntu 14.04.5 LTS - * 0 errors | 0 warnings | 1 note - * checking dependencies in R code ... NOTE - Picked up _JAVA_OPTIONS: -Xmx2048m -Xms512m +* local macOS install 10.15.3 + * R 3.6.3 +* travis-ci ubuntu + * oldrelease, R version 3.5.3 (2017-01-27) + * release, R version 3.6.2 (2017-01-27) + * devel, R Under development (unstable) (2020-03-13 r77948) * rhub - * fedora-clang-devel - * http://builder.r-hub.io/status/GGally_1.3.3.tar.gz-9e96854baee648a5a65df453919ea45f - * 0 errors | 0 warnings | 1 note - * checking package dependencies ... NOTE - Package suggested but not available for checking: ‘scagnostics’ + * Windows Server 2008 R2 SP1, R-devel, 32/64 bit + * Ubuntu Linux 16.04 LTS, R-release, GCC + * Fedora Linux, R-devel, clang, gfortran +* win-builder + * oldrelease + * release + * devel -* win-builder (devel and release) - * R version 3.5.0 (2018-04-23) - * 0 errors | 0 warnings | 0 notes - * R Under development (unstable) (2018-05-15 r74727) - * 0 errors | 0 warnings | 0 notes -## Reverse dependencies +#### R CMD check results -### Checked on -|field |value | -|:--------|:----------------------------| -|version |R version 3.5.0 (2018-04-23) | -|os |macOS High Sierra 10.13.4 | -|system |x86_64, darwin15.6.0 | +rhub - Fedora R-devel +* 0 errors | 0 warnings | 1 note +* checking package dependencies ... NOTE + Package suggested but not available for checking: ‘scagnostics’ -No difference in test results from GGally upgrade: https://github.com/ggobi/ggally/blob/master/revdep/ +Everything else +* 0 errors | 0 warnings | 0 notes -### Couldn't check (1) -|package |version |error |warning |note | -|:--------------------------|:-------|:-----|:-------|:----| -|[LANDD](problems.md#landd) |1.1.0 |1 | | | +## revdepcheck results -### Revdep Maintainers +We checked 89 reverse dependencies (72 from CRAN + 17 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package. -Reverse dependency maintainers were not notified as no breaking changes occured. + * We saw 0 new problems + * We failed to check 0 packages diff --git a/man/australia_PISA2012.Rd b/man/australia_PISA2012.Rd index c91afdad2..eb9b9c6bf 100644 --- a/man/australia_PISA2012.Rd +++ b/man/australia_PISA2012.Rd @@ -3,7 +3,7 @@ \docType{data} \name{australia_PISA2012} \alias{australia_PISA2012} -\title{Programme for International Student Assesment (PISA) 2012 Data for Australia} +\title{Programme for International Student Assessment (PISA) 2012 Data for Australia} \format{ A data frame with 8247 rows and 32 variables } diff --git a/man/ggnetworkmap.Rd b/man/ggnetworkmap.Rd index 428d37cd2..f46294b06 100644 --- a/man/ggnetworkmap.Rd +++ b/man/ggnetworkmap.Rd @@ -67,7 +67,7 @@ it will be used to convert the object: see \item{...}{other arguments supplied to geom_text for the node labels. Arguments pertaining to the title or other items can be achieved through ggplot2 methods.} } \description{ -This is a descendent of the original \code{ggnet} function. \code{ggnet} added the innovation of plotting the network geographically. +This is a descendant of the original \code{ggnet} function. \code{ggnet} added the innovation of plotting the network geographically. However, \code{ggnet} needed to be the first object in the ggplot chain. \code{ggnetworkmap} does not. If passed a \code{ggplot} object as its first argument, such as output from \code{ggmap}, \code{ggnetworkmap} will plot on top of that chart, looking for vertex attributes \code{lon} and \code{lat} as coordinates. Otherwise, \code{ggnetworkmap} will generate coordinates using the Fruchterman-Reingold algorithm. diff --git a/revdep/.gitignore b/revdep/.gitignore index 4d56b08be..3965ee91c 100644 --- a/revdep/.gitignore +++ b/revdep/.gitignore @@ -6,3 +6,5 @@ data.sqlite *.html *.rds lib +*.nosync* +failures.md diff --git a/revdep/README.md b/revdep/README.md index 58df6d938..8039b7f87 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -2,88 +2,20 @@ |field |value | |:--------|:----------------------------| -|version |R version 3.5.0 (2018-04-23) | -|os |macOS High Sierra 10.13.4 | +|version |R version 3.6.3 (2020-02-29) | +|os |macOS Catalina 10.15.3 | |system |x86_64, darwin15.6.0 | |ui |X11 | |language |(EN) | |collate |en_US.UTF-8 | +|ctype |en_US.UTF-8 | |tz |America/New_York | -|date |2018-05-17 | +|date |2020-03-19 | # Dependencies |package |old |new |Δ | |:-------|:-----|:-----|:--| -|GGally |1.3.2 |1.3.3 |* | +|GGally |1.4.0 |1.5.0 |* | # Revdeps - -## Couldn't check (1) - -|package |version |error |warning |note | -|:--------------------------|:-------|:-----|:-------|:----| -|[LANDD](problems.md#landd) |1.1.0 |1 | | | - -## All (57) - -|package |version |error |warning |note | -|:----------------------------------------------------------|:-------|:-----|:-------|:----| -|[auditor](problems.md#auditor) |0.2.1 | | |1 | -|BAS |1.5.0 | | | | -|[CINNA](problems.md#cinna) |1.1.41 | | |1 | -|clustrd |1.2.2 | | | | -|DescribeDisplay |0.2.5 | | | | -|[eechidna](problems.md#eechidna) |1.1 | | |1 | -|egoTERGM |1.0.0 | | | | -|fingerPro |1.0 | | | | -|fpp2 |2.3 | | | | -|freqparcoord |1.0.1 | | | | -|[ggbio](problems.md#ggbio) |1.28.0 |1 |1 |3 | -|ggmcmc |1.1 | | | | -|[ggraptR](problems.md#ggraptr) |1.0 | | |2 | -|gsynth |1.0.6 | | | | -|[httk](problems.md#httk) |1.8 | | |1 | -|[ICtest](problems.md#ictest) |0.3 | | |1 | -|imageData |0.1-41 | | | | -|[isomiRs](problems.md#isomirs) |1.8.0 |1 | | | -|[ITNr](problems.md#itnr) |0.2.0 | | |1 | -|[jmv](problems.md#jmv) |0.8.6.2 | | |1 | -|[LANDD](problems.md#landd) |1.1.0 |1 | | | -|[MAST](problems.md#mast) |1.6.1 | |1 |4 | -|mbgraphic |1.0.0 | | | | -|[MCbiclust](problems.md#mcbiclust) |1.4.0 |1 | | | -|[MissingDataGUI](problems.md#missingdatagui) |0.2-5 |1 | | | -|mlrMBO |1.1.1 | | | | -|[NormalizeMets](problems.md#normalizemets) |0.25 | | |3 | -|[nzelect](problems.md#nzelect) |0.4.0 | | |2 | -|OutliersO3 |0.5.4 | | | | -|[ParamHelpers](problems.md#paramhelpers) |1.10 |1 | | | -|[Pi](problems.md#pi) |1.8.0 |1 | | | -|[plotly](problems.md#plotly) |4.7.1 | | |1 | -|[pmxTools](problems.md#pmxtools) |0.1.0 | | |1 | -|[PopGenReport](problems.md#popgenreport) |3.0.0 | | |1 | -|PPforest |0.1.0 | | | | -|qualvar |0.2.0 | | | | -|QuantNorm |1.0.3 | | | | -|[randomForestExplainer](problems.md#randomforestexplainer) |0.9 | | |1 | -|[robCompositions](problems.md#robcompositions) |2.0.7 | | |2 | -|[robustbase](problems.md#robustbase) |0.93-0 | | |1 | -|[rrr](problems.md#rrr) |1.0.0 | | |1 | -|rwty |1.0.1 | | | | -|[scPipe](problems.md#scpipe) |1.2.0 |1 | | | -|[SeqSQC](problems.md#seqsqc) |1.2.0 | | |1 | -|SHELF |1.3.0 | | | | -|[specmine](problems.md#specmine) |2.0.3 | | |1 | -|spup |1.2-1 | | | | -|[staRdom](problems.md#stardom) |1.0.5 | | |1 | -|[survivALL](problems.md#survivall) |0.9.3 | | |1 | -|svdvis |0.1 | | | | -|texmex |2.4 | | | | -|[toaster](problems.md#toaster) |0.5.5 | | |1 | -|[TVTB](problems.md#tvtb) |1.6.0 |1 |1 |2 | -|userfriendlyscience |0.7.1 | | | | -|[vdmR](problems.md#vdmr) |0.2.5 | | |1 | -|[vidger](problems.md#vidger) |1.0.0 | | |1 | -|vortexR |1.1.5 | | | | - diff --git a/revdep/email.md b/revdep/email.md deleted file mode 100644 index 25c57945c..000000000 --- a/revdep/email.md +++ /dev/null @@ -1,37 +0,0 @@ -Hi {{{your_package}}} Maintainer, - -This is an automated email to let you know about the upcoming release of {{{my_package}}} version {{{my_version}}}, which will be submitted to CRAN on {{{date}}}. - -To check for potential problems, I ran `R CMD check` on your package {{{your_package}}} (version {{{your_version}}}) with the development version of ggplot2 and plotly on my personal machine. I found {{{your_summary}}}. - -{{#you_have_problems}} -{{{your_results}}} - -{{#you_cant_install}}Looks like I couldn't install your package {{{your_package}}}, I'd recommend you check it yourself. Unfortunately I don't have the resources to manually fix installation failures. - -{{/you_cant_install}} -{{^you_cant_install}}Please submit an update of your package {{{your_package}}} to fix any ERRORs or WARNINGs. They may not be caused by the update to {{{my_package}}}, but it really makes life easier if you also fix any other problems that may have accumulated over time. Please also try to minimize the NOTEs. It's not essential you do this, but the fewer the false positives the more likely I am to detect a real problem with your package. - -{{/you_cant_install}} - -To get the development version of {{{my_package}}} so you can run the checks yourself, you can run: - - # install.packages("devtools") - - ## installs ggplot2 as well - devtools::install_github("{{my_github}}") - - ## and if you need plotly to work with ggplot2 - devtools::install_github("ropensci/plotly") - -To see what's changed visit . To see a list of all reverse dependency checks for {{{my_package}}} visit . - -{{/you_have_problems}} -{{^you_have_problems}}It looks like everything is ok, so you don't need to take any action, but you might want to read the NEWS, , to see what's changed. To see a list of all reverse dependency checks for {{{my_package}}} visit . - -{{/you_have_problems}} - -If you have any questions, please feel free to respond directly to this email. - -Best, -{{{ me }}} diff --git a/revdep/email.yml b/revdep/email.yml deleted file mode 100644 index 18c2a5975..000000000 --- a/revdep/email.yml +++ /dev/null @@ -1,4 +0,0 @@ -release_date: ??? -rel_release_date: ??? -my_news_url: ??? -release_version: ??? diff --git a/revdep/problems.md b/revdep/problems.md index 61527bcb0..9a2073633 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,724 +1 @@ -# auditor - -Version: 0.2.1 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘DALEX’ - ``` - -# CINNA - -Version: 1.1.41 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘circlize’ - All declared Imports should be used. - ``` - -# eechidna - -Version: 1.1 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.8Mb - sub-directories of 1Mb or more: - data 5.4Mb - doc 1.2Mb - ``` - -# ggbio - -Version: 1.28.0 - -## In both - -* checking examples ... ERROR - ``` - ... - > ################################################### - > p1 <- autoplot(xRleList, stat = "identity") - > p2 <- autoplot(xRleList, stat = "identity", geom = "point", color = "red") - > tracks('line' = p1, "point" = p2) - > - > - > ################################################### - > ### code chunk number 25: rlel-slice - > ################################################### - > p1 <- autoplot(xRleList, type = "viewMaxs", stat = "slice", lower = 5) - > p2 <- autoplot(xRleList, type = "viewMaxs", stat = "slice", lower = 5, geom = "heatmap") - > tracks('bar' = p1, "heatmap" = p2) - > - > - > ################################################### - > ### code chunk number 26: txdb - > ################################################### - > library(TxDb.Hsapiens.UCSC.hg19.knownGene) - Error in library(TxDb.Hsapiens.UCSC.hg19.knownGene) : - there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene' - Execution halted - ``` - -* checking whether package ‘ggbio’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: subclass "DoubleFilter" of class "AnnotationFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion() - See ‘/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/checks.noindex/ggbio/new/ggbio.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: - ‘BSgenome.Hsapiens.UCSC.hg19’ ‘Homo.sapiens’ - ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ - ‘TxDb.Mmusculus.UCSC.mm9.knownGene’ ‘EnsDb.Hsapiens.v75’ - ``` - -* checking dependencies in R code ... NOTE - ``` - Unexported objects imported by ':::' calls: - 'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion' - 'ggplot2:::rename_aes' 'ggplot2:::rescale01' - 'ggplot2:::set_last_plot' - See the note in ?`:::` about the use of this operator. - ``` - -* checking R code for possible problems ... NOTE - ``` - ... - layout_karyogram,GRanges: no visible binding for global variable 'xend' - layout_karyogram,GRanges: no visible binding for global variable 'yend' - layout_karyogram,GRanges: no visible binding for global variable 'y2' - layout_karyogram,GRanges: no visible binding for global variable - 'yend2' - layout_karyogram,GRanges: no visible binding for global variable 'name' - plotFragLength,character-GRanges: no visible binding for global - variable '.fragLength' - plotSpliceSum,character-EnsDb: possible error in GRangesFilter(which, - condition = "overlapping"): unused argument (condition = - "overlapping") - stat_mismatch,GRanges: no visible binding for global variable 'sts' - stat_mismatch,GRanges: no visible binding for global variable 'eds' - stat_mismatch,GRanges: no visible binding for global variable 'read' - Undefined global functions or variables: - .fragLength .layout_circle.stats .x breaks coefs data eds fe fl - gieStain ideoCyto indexProbesProcessed midpoint mt name read se - stepping sts value variable x xend y y.text y2 yend yend2 - Consider adding - importFrom("utils", "data") - to your NAMESPACE file. - ``` - -# ggraptR - -Version: 1.0 - -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘RSelenium’ - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘DBI’ ‘GGally’ ‘RColorBrewer’ ‘Rcpp’ ‘assertthat’ ‘backports’ - ‘colorspace’ ‘colourpicker’ ‘evaluate’ ‘futile.options’ ‘gdtools’ - ‘gtable’ ‘htmltools’ ‘htmlwidgets’ ‘httpuv’ ‘labeling’ ‘lambda.r’ - ‘lazyeval’ ‘magrittr’ ‘miniUI’ ‘munsell’ ‘plyr’ ‘reshape’ ‘rprojroot’ - ‘scales’ ‘stringi’ ‘stringr’ ‘svglite’ ‘tibble’ ‘xtable’ ‘yaml’ - All declared Imports should be used. - ``` - -# httk - -Version: 1.8 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 15.0Mb - sub-directories of 1Mb or more: - data 13.1Mb - doc 1.3Mb - ``` - -# ICtest - -Version: 0.3 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘fICA’ - ``` - -# isomiRs - -Version: 1.8.0 - -## In both - -* checking package dependencies ... ERROR - ``` - Package required but not available: ‘targetscan.Hs.eg.db’ - - Package suggested but not available for checking: ‘org.Mm.eg.db’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# ITNr - -Version: 0.2.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘Matrix’ ‘animation’ ‘comtradr’ ‘ndtv’ ‘statnet’ ‘xergm’ - All declared Imports should be used. - ``` - -# jmv - -Version: 0.8.6.2 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’ - ‘afex’ ‘car’ ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’ - ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’ - All declared Imports should be used. - ``` - -# LANDD - -Version: 1.1.0 - -## In both - -* checking whether package ‘LANDD’ can be installed ... ERROR - ``` - Installation failed. - See ‘/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/checks.noindex/LANDD/new/LANDD.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘LANDD’ ... -** package ‘LANDD’ successfully unpacked and MD5 sums checked -** libs -/usr/local/clang4/bin/clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/Rcpp/include" -I"/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -/usr/local/clang4/bin/clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/Rcpp/include" -I"/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c normalize.cpp -o normalize.o -In file included from normalize.cpp:4: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/math/distributions/normal.hpp:19: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/math/special_functions/erf.hpp:15: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/math/special_functions/gamma.hpp:24: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/math/constants/constants.hpp:13: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/math/tools/convert_from_string.hpp:15: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/lexical_cast.hpp:32: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/lexical_cast/try_lexical_convert.hpp:42: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/container/container_fwd.hpp:61: -/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] -BOOST_MOVE_STD_NS_BEG -^ -/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG' - #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD - ^ -/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD' -#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE { - ^ -1 warning generated. -/usr/local/clang4/bin/clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o LANDD.so RcppExports.o normalize.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -installing to /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/checks.noindex/LANDD/new/LANDD.Rcheck/LANDD/libs -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘GO.db’ -ERROR: lazy loading failed for package ‘LANDD’ -* removing ‘/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/checks.noindex/LANDD/new/LANDD.Rcheck/LANDD’ - -``` -### CRAN - -``` -* installing *source* package ‘LANDD’ ... -** package ‘LANDD’ successfully unpacked and MD5 sums checked -** libs -/usr/local/clang4/bin/clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/Rcpp/include" -I"/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -/usr/local/clang4/bin/clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/Rcpp/include" -I"/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c normalize.cpp -o normalize.o -In file included from normalize.cpp:4: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/math/distributions/normal.hpp:19: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/math/special_functions/erf.hpp:15: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/math/special_functions/gamma.hpp:24: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/math/constants/constants.hpp:13: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/math/tools/convert_from_string.hpp:15: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/lexical_cast.hpp:32: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/lexical_cast/try_lexical_convert.hpp:42: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: -In file included from /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/container/container_fwd.hpp:61: -/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] -BOOST_MOVE_STD_NS_BEG -^ -/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/library.noindex/LANDD/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG' - #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD - ^ -/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD' -#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE { - ^ -1 warning generated. -/usr/local/clang4/bin/clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o LANDD.so RcppExports.o normalize.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -installing to /Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/checks.noindex/LANDD/old/LANDD.Rcheck/LANDD/libs -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘GO.db’ -ERROR: lazy loading failed for package ‘LANDD’ -* removing ‘/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/checks.noindex/LANDD/old/LANDD.Rcheck/LANDD’ - -``` -# MAST - -Version: 1.6.1 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Quitting from lines 36-54 (MAITAnalysis.Rmd) - Error: processing vignette 'MAITAnalysis.Rmd' failed with diagnostics: - there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene' - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ - ``` - -* 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 installed package size ... NOTE - ``` - installed size is 8.7Mb - sub-directories of 1Mb or more: - R 1.0Mb - data 3.7Mb - doc 3.7Mb - ``` - -* checking R code for possible problems ... NOTE - ``` - assay_idx: no visible global function definition for ‘assayNames’ - collectResiduals: no visible global function definition for - ‘assayNames’ - collectResiduals: no visible global function definition for ‘assay<-’ - collectResiduals: no visible global function definition for - ‘assayNames<-’ - primerAverage: no visible global function definition for ‘assay<-’ - primerAverage: no visible global function definition for ‘rowData<-’ - assay<-,SingleCellAssay-missing: no visible global function definition - for ‘assay<-’ - assayNames<-,SingleCellAssay-character: no visible global function - definition for ‘assayNames’ - assayNames<-,SingleCellAssay-character: no visible global function - definition for ‘assays<-’ - exprs<-,SingleCellAssay-ANY: no visible global function definition for - ‘assay<-’ - Undefined global functions or variables: - assay<- assayNames assayNames<- assays<- rowData<- - ``` - -# MCbiclust - -Version: 1.4.0 - -## In both - -* checking package dependencies ... ERROR - ``` - Packages required but not available: ‘GO.db’ ‘org.Hs.eg.db’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# MissingDataGUI - -Version: 0.2-5 - -## In both - -* checking package dependencies ... ERROR - ``` - Packages required but not available: ‘gWidgetsRGtk2’ ‘cairoDevice’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# NormalizeMets - -Version: 0.25 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 9.3Mb - sub-directories of 1Mb or more: - doc 8.6Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘knitr’ - All declared Imports should be used. - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘DiffCorr’ - ``` - -# nzelect - -Version: 0.4.0 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.3Mb - sub-directories of 1Mb or more: - data 5.0Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 6409 marked UTF-8 strings - ``` - -# ParamHelpers - -Version: 1.10 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/run-all.R’ failed. - Last 13 lines of output: - -2.53545942614891, 0.422975436239536, -2.47230070010972, -1.46055918222656), .algo = structure(c(1L, - 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L - ), .Label = c("algo1", "algo2", "algo3"), class = "factor"), .repl = c(1L, 1L, 1L, - 1L, 1L, 2L, 2L, 2L, 2L, 2L, 3L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L)), row.names = c("5", - "7", "12", "15", "19", "2", "51", "6", "151", "20", "8", "22", "52", "21", "3", "11", - "17", "18", "1", "71", "81", "181"), class = "data.frame"), groups = .algo, maximise = c(y1 = FALSE, - y2 = FALSE)) - 5: stop("formula missing") - - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 1036 SKIPPED: 1 FAILED: 1 - 1. Error: plotEAF works (@test_plotEAF.R#27) - - Error: testthat unit tests failed - Execution halted - ``` - -# Pi - -Version: 1.8.0 - -## In both - -* checking package dependencies ... ERROR - ``` - Package required but not available: ‘XGR’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# plotly - -Version: 4.7.1 - -## In both - -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: ‘sf’ ‘RSelenium’ - ``` - -# pmxTools - -Version: 0.1.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘GGally’ ‘PKNCA’ ‘grid’ ‘magrittr’ ‘plyr’ ‘xpose’ - All declared Imports should be used. - ``` - -# PopGenReport - -Version: 3.0.0 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘ecodist’ - ``` - -# randomForestExplainer - -Version: 0.9 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘MASS’ ‘dtplyr’ - All declared Imports should be used. - ``` - -# robCompositions - -Version: 2.0.7 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘mvoutlier’, ‘StatDA’ - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 5701 marked UTF-8 strings - ``` - -# robustbase - -Version: 0.93-0 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘matrixStats’, ‘robustX’ - ``` - -# rrr - -Version: 1.0.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘Rcpp’ - All declared Imports should be used. - ``` - -# scPipe - -Version: 1.2.0 - -## In both - -* checking package dependencies ... ERROR - ``` - Packages required but not available: ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# SeqSQC - -Version: 1.2.0 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.6Mb - sub-directories of 1Mb or more: - doc 1.9Mb - extdata 3.3Mb - ``` - -# specmine - -Version: 2.0.3 - -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘rcytoscapejs’ - ``` - -# staRdom - -Version: 1.0.5 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘readr’ ‘tools’ - All declared Imports should be used. - ``` - -# survivALL - -Version: 0.9.3 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘cowplot’ - All declared Imports should be used. - ``` - -# toaster - -Version: 0.5.5 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘igraph’ - ``` - -# TVTB - -Version: 1.6.0 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672 - TRUE TRUE FALSE FALSE TRUE FALSE - rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382 - TRUE FALSE TRUE TRUE FALSE FALSE - rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600 - FALSE FALSE FALSE FALSE FALSE FALSE - rs550201688 rs565338261 rs201239799 rs200461129 rs146726548 - FALSE FALSE FALSE FALSE TRUE - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 225 SKIPPED: 2 FAILED: 2 - 1. Error: all signatures work to completion (@test_plotInfo-methods.R#25) - 2. Error: invalid metric/phenotype combination is detected (@test_plotInfo-methods.R#50) - - Error: testthat unit tests failed - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Overwriting INFO keys in data: - - REF - - HET - - ALT - - AAF - - MAF - Overwriting INFO keys in header: - - REF - - HET - - ALT - - AAF - - MAF - Quitting from lines 574-581 (Introduction.Rmd) - Error: processing vignette 'Introduction.Rmd' failed with diagnostics: - there is no package called 'EnsDb.Hsapiens.v75' - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’ - ``` - -* checking installed package size ... NOTE - ``` - installed size is 5.2Mb - sub-directories of 1Mb or more: - R 2.1Mb - doc 2.2Mb - ``` - -# vdmR - -Version: 0.2.5 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘Rdpack’ ‘maptools’ ‘rgeos’ - All declared Imports should be used. - ``` - -# vidger - -Version: 1.0.0 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.0Mb - sub-directories of 1Mb or more: - data 4.0Mb - doc 1.7Mb - ``` - +*Wow, no problems at all. :)* \ No newline at end of file diff --git a/revdep/timing.md b/revdep/timing.md deleted file mode 100644 index 13279d570..000000000 --- a/revdep/timing.md +++ /dev/null @@ -1,50 +0,0 @@ -# Check times - -| |package |version | check_time| -|:--|:---------------------|:-------|----------:| -|25 |Pi |1.4.0 | 15545.1| -|8 |ggbio |1.24.1 | 433.1| -|18 |MAST |1.2.1 | 320.9| -|20 |MCbiclust |1.0.1 | 319| -|37 |spup |0.1-1 | 284.8| -|15 |isomiRs |1.4.0 | 253.4| -|41 |TVTB |1.2.0 | 234.7| -|32 |robustbase |0.92-7 | 144.4| -|19 |mbgraphic |1.0.0 | 124.4| -|27 |PopGenReport |3.0.0 | 108.6| -|31 |robCompositions |2.0.5 | 106.2| -|42 |userfriendlyscience |0.6-1 | 106| -|22 |mlrMBO |1.1.0 | 97.4| -|17 |LANDD |1.1.0 | 88.8| -|13 |ICtest |0.3 | 88.5| -|3 |CINNA |1.0.0 | 87.2| -|12 |httk |1.7 | 83.4| -|10 |ggmcmc |1.1 | 80| -|6 |eechidna |1.1 | 67.9| -|2 |BAS |1.4.6 | 65.9| -|44 |vortexR |1.1.4 | 62| -|14 |imageData |0.1-26 | 61.5| -|34 |rwty |1.0.1 | 60.1| -|30 |randomForestExplainer |0.9 | 56| -|9 |ggCompNet |0.1.0 | 52.2| -|4 |clustrd |1.2.0 | 50.8| -|43 |vdmR |0.2.4 | 47.5| -|26 |plotly |4.7.1 | 46| -|39 |texmex |2.3 | 45.7| -|38 |svdvis |0.1 | 44.6| -|16 |jmv |0.7.3.5 | 44.1| -|33 |rrr |1.0.0 | 41.5| -|35 |SHELF |1.2.3 | 41.2| -|1 |BANFF |2.0 | 40.8| -|24 |ParamHelpers |1.10 | 32| -|40 |toaster |0.5.5 | 32| -|11 |gsynth |1.0.3 | 30.3| -|23 |nzelect |0.3.3 | 28.3| -|5 |DescribeDisplay |0.2.5 | 25.2| -|7 |freqparcoord |1.0.1 | 24.9| -|29 |qualvar |0.1.0 | 19.8| -|28 |POUMM |1.3.2 | 2.8| -|21 |MissingDataGUI |0.2-5 | 1.4| -|36 |specmine |1.0 | 1.4| - - diff --git a/vignettes/docs.Rmd b/vignettes/docs.Rmd index 53bb71175..f49980541 100644 --- a/vignettes/docs.Rmd +++ b/vignettes/docs.Rmd @@ -82,7 +82,7 @@ ggcoef(log.reg, exponentiate = TRUE) ## Customizing the plot -You can use `conf.int`, `vline` and `exclude_intercept` to display or not confidence intervals as error bars, a vertical line for `x = 0` (or `x = 1` if coeffcients are exponentiated) and the intercept. +You can use `conf.int`, `vline` and `exclude_intercept` to display or not confidence intervals as error bars, a vertical line for `x = 0` (or `x = 1` if coefficients are exponentiated) and the intercept. ```{r ggcoef-reg-custom} ggcoef(reg, vline = FALSE, conf.int = FALSE, exclude_intercept = TRUE)