diff --git a/NEWS.md b/NEWS.md
index 8895bcc8..9922e6b1 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -30,6 +30,9 @@
## Features and fixes
+* `pluck()` no longer replaces 0-length vectors with `default`; it now
+ only applies absent and `NULL` components.
+
* `lmap()` now always returns a list, even if `.x` is a data frame.
This makes it more consistent with other functions in the `map` family.
diff --git a/R/pluck.R b/R/pluck.R
index 4c4271fc..0aaed0ba 100644
--- a/R/pluck.R
+++ b/R/pluck.R
@@ -3,7 +3,7 @@
#' `pluck()` and `chuck()` implement a generalised form of `[[` that
#' allow you to index deeply and flexibly into data structures.
#' `pluck()` consistently returns `NULL` when an element does not
-#' exist, `chuck()` always throws (or chucks) an error in that case.
+#' exist while `chuck()` always throws (or chucks) an error.
#'
#' @param .x,x A vector or environment
#' @param ... A list of accessors for indexing into the object. Can be
@@ -15,7 +15,7 @@
#' [Dynamic dots][rlang::dyn-dots] are supported. In particular, if
#' your accessors are stored in a list, you can splice that in with
#' `!!!`.
-#' @param .default Value to use if target is empty or absent.
+#' @param .default Value to use if target is `NULL` or absent.
#'
#' @details
#' * You can pluck or chuck with standard accessors like integer
diff --git a/man/pluck.Rd b/man/pluck.Rd
index 97a4e297..cd4b5533 100644
--- a/man/pluck.Rd
+++ b/man/pluck.Rd
@@ -25,7 +25,7 @@ accessing it by name will return the corresponding slot.
your accessors are stored in a list, you can splice that in with
\verb{!!!}.}
-\item{.default}{Value to use if target is empty or absent.}
+\item{.default}{Value to use if target is \code{NULL} or absent.}
\item{value}{A value to replace in \code{.x} at the pluck location.}
}
@@ -33,7 +33,7 @@ your accessors are stored in a list, you can splice that in with
\code{pluck()} and \code{chuck()} implement a generalised form of \code{[[} that
allow you to index deeply and flexibly into data structures.
\code{pluck()} consistently returns \code{NULL} when an element does not
-exist, \code{chuck()} always throws (or chucks) an error in that case.
+exist while \code{chuck()} always throws (or chucks) an error.
}
\details{
\itemize{
diff --git a/revdep/README.md b/revdep/README.md
index 891eae5c..2ad46093 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -1,44 +1,27 @@
-# Platform
-
-|field |value |
-|:--------|:----------------------------|
-|version |R version 3.6.1 (2019-07-05) |
-|os |macOS Mojave 10.14 |
-|system |x86_64, darwin15.6.0 |
-|ui |X11 |
-|language |(EN) |
-|collate |en_US.UTF-8 |
-|ctype |en_US.UTF-8 |
-|tz |Europe/Brussels |
-|date |2019-10-16 |
-
-# Dependencies
-
-|package |old |new |Δ |
-|:--------|:-----|:----------|:--|
-|purrr |0.3.2 |0.3.2.9000 |* |
-|magrittr |1.5 |1.5 | |
-|rlang |0.4.0 |0.4.0 | |
-
# Revdeps
-## Failed to check (8)
-
-|package |version |error |warning |note |
-|:----------------|:-------|:-----|:-------|:----|
-|anomalyDetection |0.2.5 |1 | | |
-|circumplex |0.3.3 |1 | | |
-|clustermq |0.8.8 |1 | |1 |
-|codemetar |0.1.8 |1 | |1 |
-|colorednoise |1.0.5 |1 | | |
-|ELMER |2.8.3 |1 |1 |2 |
-|phenofit |0.2.5-2 |1 | | |
-|TCGAbiolinks |2.12.6 |1 | |3 |
-
-## New problems (2)
-
-|package |version |error |warning |note |
-|:--------------------------|:-------|:------|:-------|:------|
-|[arrow](problems.md#arrow) |0.15.0 |-1 | |__+1__ |
-|[nlrx](problems.md#nlrx) |0.3.0 |__+1__ | | |
+## Failed to check (3)
+
+|package |version |error |warning |note |
+|:------------|:-------|:-----|:-------|:----|
+|elbird |0.2.5 |1 | | |
+|ggPMX |? | | | |
+|ImputeRobust |? | | | |
+
+## New problems (12)
+
+|package |version |error |warning |note |
+|:------------------------------------------|:-------|:------|:-------|:--------|
+|[cattonum](problems.md#cattonum) |0.0.5 | | |1 __+1__ |
+|[dibble](problems.md#dibble) |0.2.1 |__+1__ | | |
+|[epitopR](problems.md#epitopr) |0.1.1 |__+1__ |1 |1 |
+|[gghighlight](problems.md#gghighlight) |0.3.3 | |__+1__ | |
+|[gratia](problems.md#gratia) |0.7.3 |__+1__ | | |
+|[grizbayr](problems.md#grizbayr) |1.3.2 |__+1__ | | |
+|[gwasrapidd](problems.md#gwasrapidd) |0.99.13 |__+1__ | | |
+|[partialised](problems.md#partialised) |0.1.0 |__+1__ | | |
+|[rATTAINS](problems.md#rattains) |0.1.3 |__+1__ |__+1__ | |
+|[ruta](problems.md#ruta) |1.1.0 |__+2__ |__+1__ |1 |
+|[sbm](problems.md#sbm) |0.4.4 |__+1__ | | |
+|[tidywikidatar](problems.md#tidywikidatar) |0.5.4 |__+1__ | | |
diff --git a/revdep/cran.md b/revdep/cran.md
new file mode 100644
index 00000000..5aae7582
--- /dev/null
+++ b/revdep/cran.md
@@ -0,0 +1,56 @@
+## revdepcheck results
+
+We checked 1345 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 12 new problems
+ * We failed to check 3 packages
+
+Issues with CRAN packages are summarised below.
+
+### New problems
+(This reports the first line of each new failure)
+
+* cattonum
+ checking R code for possible problems ... NOTE
+
+* dibble
+ checking tests ... ERROR
+
+* epitopR
+ checking tests ... ERROR
+
+* gghighlight
+ checking re-building of vignette outputs ... WARNING
+
+* gratia
+ checking tests ... ERROR
+
+* grizbayr
+ checking tests ... ERROR
+
+* gwasrapidd
+ checking tests ... ERROR
+
+* partialised
+ checking tests ... ERROR
+
+* rATTAINS
+ checking tests ... ERROR
+ checking re-building of vignette outputs ... WARNING
+
+* ruta
+ checking examples ... ERROR
+ checking tests ... ERROR
+ checking re-building of vignette outputs ... WARNING
+
+* sbm
+ checking tests ... ERROR
+
+* tidywikidatar
+ checking examples ... ERROR
+
+### Failed to check
+
+* elbird (NA)
+* ggPMX (NA)
+* ImputeRobust (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
index 61f6a09e..943930aa 100644
--- a/revdep/failures.md
+++ b/revdep/failures.md
@@ -1,24 +1,23 @@
-# anomalyDetection
+# elbird
* Version: 0.2.5
-* Source code: https://github.com/cran/anomalyDetection
-* URL: https://github.com/koalaverse/anomalyDetection
-* BugReports: https://github.com/koalaverse/anomalyDetection/issues
-* Date/Publication: 2018-03-07 16:18:12 UTC
-* Number of recursive dependencies: 86
+* GitHub: https://github.com/mrchypark/elbird
+* Source code: https://github.com/cran/elbird
+* Date/Publication: 2022-08-12 15:50:02 UTC
+* Number of recursive dependencies: 54
-Run `revdep_details(,"anomalyDetection")` for more info
+Run `cloud_details(, "elbird")` for more info
## In both
-* checking whether package ‘anomalyDetection’ can be installed ... ERROR
+* checking whether package ‘elbird’ can be installed ... ERROR
```
Installation failed.
- See ‘/Users/lionel/Desktop/lowliner/revdep/checks.noindex/anomalyDetection/new/anomalyDetection.Rcheck/00install.out’ for details.
+ See ‘/tmp/workdir/elbird/new/elbird.Rcheck/00install.out’ for details.
```
## Installation
@@ -26,364 +25,182 @@ Run `revdep_details(,"anomalyDetection")` for more info
### Devel
```
-* installing *source* package ‘anomalyDetection’ ...
-** package ‘anomalyDetection’ successfully unpacked and MD5 sums checked
+* installing *source* package ‘elbird’ ...
+** package ‘elbird’ successfully unpacked and MD5 sums checked
** using staged installation
-** libs
-clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/anomalyDetection/Rcpp/include" -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/anomalyDetection/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -mtune=core2 -O3 -c RcppExports.cpp -o RcppExports.o
-clang: error: unsupported option '-fopenmp'
-make: *** [RcppExports.o] Error 1
-ERROR: compilation failed for package ‘anomalyDetection’
-* removing ‘/Users/lionel/Desktop/lowliner/revdep/checks.noindex/anomalyDetection/new/anomalyDetection.Rcheck/anomalyDetection’
+/usr/bin/uname
+Prior system libkiwi installation not found
+Preparing to download and build library from source...
+------------------------------[ ELBIRD ]------------------------------
+Configuration failed because 'git' was not found.
+If you want to kiwi build from source in package installation prosess,
+make sure git and cmake work in system.
+-------------------------------------------------------------------------
+ERROR: configuration failed for package ‘elbird’
+* removing ‘/tmp/workdir/elbird/new/elbird.Rcheck/elbird’
+
```
### CRAN
```
-* installing *source* package ‘anomalyDetection’ ...
-** package ‘anomalyDetection’ successfully unpacked and MD5 sums checked
+* installing *source* package ‘elbird’ ...
+** package ‘elbird’ successfully unpacked and MD5 sums checked
** using staged installation
-** libs
-clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/anomalyDetection/Rcpp/include" -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/anomalyDetection/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -mtune=core2 -O3 -c RcppExports.cpp -o RcppExports.o
-clang: error: unsupported option '-fopenmp'
-make: *** [RcppExports.o] Error 1
-ERROR: compilation failed for package ‘anomalyDetection’
-* removing ‘/Users/lionel/Desktop/lowliner/revdep/checks.noindex/anomalyDetection/old/anomalyDetection.Rcheck/anomalyDetection’
+/usr/bin/uname
+Prior system libkiwi installation not found
+Preparing to download and build library from source...
+------------------------------[ ELBIRD ]------------------------------
+Configuration failed because 'git' was not found.
+If you want to kiwi build from source in package installation prosess,
+make sure git and cmake work in system.
+-------------------------------------------------------------------------
+ERROR: configuration failed for package ‘elbird’
+* removing ‘/tmp/workdir/elbird/old/elbird.Rcheck/elbird’
+
```
-# circumplex
+# ggPMX
-* Version: 0.3.3
-* Source code: https://github.com/cran/circumplex
-* URL: https://github.com/jmgirard/circumplex
-* BugReports: https://github.com/jmgirard/circumplex/issues
-* Date/Publication: 2019-09-26 08:30:15 UTC
-* Number of recursive dependencies: 95
+* Version: 1.2.8
+* GitHub: https://github.com/ggPMXdevelopment/ggPMX
+* Source code: https://github.com/cran/ggPMX
+* Date/Publication: 2022-06-17 23:10:02 UTC
+* Number of recursive dependencies: 175
-Run `revdep_details(,"circumplex")` for more info
+Run `cloud_details(, "ggPMX")` for more info
-## In both
-
-* checking whether package ‘circumplex’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/Users/lionel/Desktop/lowliner/revdep/checks.noindex/circumplex/new/circumplex.Rcheck/00install.out’ for details.
- ```
-
-## Installation
+## Error before installation
### Devel
```
-* installing *source* package ‘circumplex’ ...
-** package ‘circumplex’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-clang++ -std=gnu++11 -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/circumplex/Rcpp/include" -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/circumplex/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
-clang: error: unsupported option '-fopenmp'
-make: *** [RcppExports.o] Error 1
-ERROR: compilation failed for package ‘circumplex’
-* removing ‘/Users/lionel/Desktop/lowliner/revdep/checks.noindex/circumplex/new/circumplex.Rcheck/circumplex’
-
-```
-### CRAN
-
-```
-* installing *source* package ‘circumplex’ ...
-** package ‘circumplex’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-clang++ -std=gnu++11 -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/circumplex/Rcpp/include" -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/circumplex/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
-clang: error: unsupported option '-fopenmp'
-make: *** [RcppExports.o] Error 1
-ERROR: compilation failed for package ‘circumplex’
-* removing ‘/Users/lionel/Desktop/lowliner/revdep/checks.noindex/circumplex/old/circumplex.Rcheck/circumplex’
-
-```
-# clustermq
-
-
-
-* Version: 0.8.8
-* Source code: https://github.com/cran/clustermq
-* URL: https://github.com/mschubert/clustermq
-* BugReports: https://github.com/mschubert/clustermq/issues
-* Date/Publication: 2019-06-05 22:00:39 UTC
-* Number of recursive dependencies: 105
-
-Run `revdep_details(,"clustermq")` for more info
-
-
-
-## In both
+* using log directory ‘/tmp/workdir/ggPMX/new/ggPMX.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘ggPMX/DESCRIPTION’ ... OK
+* this is package ‘ggPMX’ version ‘1.2.8’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+...
+ [ FAIL 1 | WARN 10 | SKIP 8 | PASS 327 ]
+ Error: Test failures
+ Execution halted
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... NONE
+ ‘ggPMX-guide.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 1 ERROR, 2 NOTEs
-* R CMD check timed out
-
-* checking dependencies in R code ... NOTE
- ```
- Namespaces in Imports field not imported from:
- ‘purrr’ ‘R6’
- All declared Imports should be used.
- ```
-
-# codemetar
-
-
-
-* Version: 0.1.8
-* Source code: https://github.com/cran/codemetar
-* URL: https://github.com/ropensci/codemetar, https://ropensci.github.io/codemetar
-* BugReports: https://github.com/ropensci/codemetar/issues
-* Date/Publication: 2019-04-22 04:20:03 UTC
-* Number of recursive dependencies: 79
-
-Run `revdep_details(,"codemetar")` for more info
-
-
-
-## In both
-
-* R CMD check timed out
-
-
-* checking dependencies in R code ... NOTE
- ```
- Namespace in Imports field not imported from: ‘memoise’
- All declared Imports should be used.
- ```
-# colorednoise
-
-
-* Version: 1.0.5
-* Source code: https://github.com/cran/colorednoise
-* BugReports: http://github.com/japilo/colorednoise/issues
-* Date/Publication: 2019-09-27 13:10:02 UTC
-* Number of recursive dependencies: 79
-
-Run `revdep_details(,"colorednoise")` for more info
-
-
-
-## In both
-
-* checking whether package ‘colorednoise’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/Users/lionel/Desktop/lowliner/revdep/checks.noindex/colorednoise/new/colorednoise.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘colorednoise’ ...
-** package ‘colorednoise’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/colorednoise/Rcpp/include" -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/colorednoise/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -mtune=core2 -O3 -c RcppExports.cpp -o RcppExports.o
-clang: error: unsupported option '-fopenmp'
-make: *** [RcppExports.o] Error 1
-ERROR: compilation failed for package ‘colorednoise’
-* removing ‘/Users/lionel/Desktop/lowliner/revdep/checks.noindex/colorednoise/new/colorednoise.Rcheck/colorednoise’
```
### CRAN
```
-* installing *source* package ‘colorednoise’ ...
-** package ‘colorednoise’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/colorednoise/Rcpp/include" -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/colorednoise/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -mtune=core2 -O3 -c RcppExports.cpp -o RcppExports.o
-clang: error: unsupported option '-fopenmp'
-make: *** [RcppExports.o] Error 1
-ERROR: compilation failed for package ‘colorednoise’
-* removing ‘/Users/lionel/Desktop/lowliner/revdep/checks.noindex/colorednoise/old/colorednoise.Rcheck/colorednoise’
-
-```
-# ELMER
-
-
-
-* Version: 2.8.3
-* Source code: https://github.com/cran/ELMER
-* Date/Publication: 2019-09-06
-* Number of recursive dependencies: 205
+* using log directory ‘/tmp/workdir/ggPMX/old/ggPMX.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘ggPMX/DESCRIPTION’ ... OK
+* this is package ‘ggPMX’ version ‘1.2.8’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+...
+ [ FAIL 1 | WARN 10 | SKIP 8 | PASS 327 ]
+ Error: Test failures
+ Execution halted
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... NONE
+ ‘ggPMX-guide.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 1 ERROR, 2 NOTEs
-Run `revdep_details(,"ELMER")` for more info
-
-## In both
-* R CMD check timed out
-
-* checking Rd \usage sections ... WARNING
- ```
- Undocumented arguments in documentation object 'heatmapGene'
- ‘correlation.method’ ‘scatter.plot.width’ ‘scatter.plot.height’
-
- 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 75.8Mb
- sub-directories of 1Mb or more:
- doc 75.1Mb
- ```
-
-* checking R code for possible problems ... NOTE
- ```
- ...
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/ELMER/new/ELMER.Rcheck/00_pkg_src/ELMER/R/GetNearbyGenes.R:538-539)
- getRegionNearGenes: no visible binding for global variable 'ID'
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/ELMER/new/ELMER.Rcheck/00_pkg_src/ELMER/R/GetNearbyGenes.R:551)
- getTFtargets: no visible binding for global variable 'TF'
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/ELMER/new/ELMER.Rcheck/00_pkg_src/ELMER/R/Main_function.R:1620)
- getTFtargets: no visible binding for global variable 'TF'
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/ELMER/new/ELMER.Rcheck/00_pkg_src/ELMER/R/Main_function.R:1622)
- heatmapGene: no visible global function definition for 'melt'
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/ELMER/new/ELMER.Rcheck/00_pkg_src/ELMER/R/plots.R:590)
- heatmapGene: no visible binding for global variable 'mae'
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/ELMER/new/ELMER.Rcheck/00_pkg_src/ELMER/R/plots.R:590)
- heatmapGene: no visible binding for global variable 'mae'
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/ELMER/new/ELMER.Rcheck/00_pkg_src/ELMER/R/plots.R:592)
- heatmapGene: no visible global function definition for 'melt'
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/ELMER/new/ELMER.Rcheck/00_pkg_src/ELMER/R/plots.R:593)
- heatmapGene: no visible binding for global variable 'mae'
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/ELMER/new/ELMER.Rcheck/00_pkg_src/ELMER/R/plots.R:593)
- heatmapGene: no visible global function definition for 'stat_cor'
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/ELMER/new/ELMER.Rcheck/00_pkg_src/ELMER/R/plots.R:597-613)
- Undefined global functions or variables:
- DistanceTSS Hugo_Symbol ID mae melt Side stat_cor TF
- ```
-
-# phenofit
+```
+# ImputeRobust
-* Version: 0.2.5-2
-* Source code: https://github.com/cran/phenofit
-* URL: https://github.com/kongdd/phenofit
-* BugReports: https://github.com/kongdd/phenofit/issues
-* Date/Publication: 2019-06-07 08:00:08 UTC
-* Number of recursive dependencies: 78
+* Version: 1.3-1
+* GitHub: NA
+* Source code: https://github.com/cran/ImputeRobust
+* Date/Publication: 2018-11-30 12:10:03 UTC
+* Number of recursive dependencies: 52
-Run `revdep_details(,"phenofit")` for more info
+Run `cloud_details(, "ImputeRobust")` for more info
-## In both
-
-* checking whether package ‘phenofit’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/Users/lionel/Desktop/lowliner/revdep/checks.noindex/phenofit/new/phenofit.Rcheck/00install.out’ for details.
- ```
-
-## Installation
+## Error before installation
### Devel
```
-* installing *source* package ‘phenofit’ ...
-** package ‘phenofit’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-clang++ -std=gnu++11 -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/phenofit/Rcpp/include" -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/phenofit/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
-clang: error: unsupported option '-fopenmp'
-make: *** [RcppExports.o] Error 1
-ERROR: compilation failed for package ‘phenofit’
-* removing ‘/Users/lionel/Desktop/lowliner/revdep/checks.noindex/phenofit/new/phenofit.Rcheck/phenofit’
+* using log directory ‘/tmp/workdir/ImputeRobust/new/ImputeRobust.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘ImputeRobust/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘ImputeRobust’ version ‘1.3-1’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘extremevalues’
-```
-### CRAN
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
-```
-* installing *source* package ‘phenofit’ ...
-** package ‘phenofit’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-clang++ -std=gnu++11 -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/phenofit/Rcpp/include" -I"/Users/lionel/Desktop/lowliner/revdep/library.noindex/phenofit/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
-clang: error: unsupported option '-fopenmp'
-make: *** [RcppExports.o] Error 1
-ERROR: compilation failed for package ‘phenofit’
-* removing ‘/Users/lionel/Desktop/lowliner/revdep/checks.noindex/phenofit/old/phenofit.Rcheck/phenofit’
-```
-# TCGAbiolinks
-
-* Version: 2.12.6
-* Source code: https://github.com/cran/TCGAbiolinks
-* URL: https://github.com/BioinformaticsFMRP/TCGAbiolinks
-* BugReports: https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues
-* Date/Publication: 2019-09-05
-* Number of recursive dependencies: 266
-Run `revdep_details(,"TCGAbiolinks")` for more info
+```
+### CRAN
-
+```
+* using log directory ‘/tmp/workdir/ImputeRobust/old/ImputeRobust.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘ImputeRobust/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘ImputeRobust’ version ‘1.3-1’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘extremevalues’
-## In both
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
-* R CMD check timed out
-
-* checking installed package size ... NOTE
- ```
- installed size is 97.2Mb
- sub-directories of 1Mb or more:
- data 4.2Mb
- doc 90.1Mb
- R 2.7Mb
- ```
-* 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:
- ‘move’
- ```
-* checking R code for possible problems ... NOTE
- ```
- ...
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/clinical.R:712)
- TCGAtumor_purity: no visible binding for global variable ‘Tumor.purity’
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/clinical.R:723-724)
- TCGAvisualize_oncoprint: no visible binding for global variable ‘value’
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/visualize.R:932)
- TCGAvisualize_SurvivalCoxNET: no visible global function definition for
- ‘dNetInduce’
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/visualize.R:156-157)
- TCGAvisualize_SurvivalCoxNET: no visible global function definition for
- ‘dNetPipeline’
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/visualize.R:161-162)
- TCGAvisualize_SurvivalCoxNET: no visible global function definition for
- ‘dCommSignif’
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/visualize.R:174)
- TCGAvisualize_SurvivalCoxNET: no visible global function definition for
- ‘visNet’
- (/Users/lionel/Desktop/lowliner/revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/visualize.R:184-189)
- Undefined global functions or variables:
- barcode c3net clinical coordinates dCommSignif dNetInduce
- dNetPipeline exon knnmi.cross limmacontrasts.fit limmamakeContrasts
- minet openSesame portions rse_gene Tumor.purity value visNet
- ```
+```
diff --git a/revdep/problems.md b/revdep/problems.md
index 03e6837f..699b342f 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -1,48 +1,400 @@
-# arrow
+# cattonum
-* Version: 0.15.0
-* Source code: https://github.com/cran/arrow
-* URL: https://github.com/apache/arrow/, https://arrow.apache.org/docs/r
-* BugReports: https://issues.apache.org/jira/projects/ARROW/issues
-* Date/Publication: 2019-10-07 19:00:02 UTC
+* Version: 0.0.5
+* GitHub: https://github.com/bfgray3/cattonum
+* Source code: https://github.com/cran/cattonum
+* Date/Publication: 2020-06-15 04:50:06 UTC
+* Number of recursive dependencies: 78
+
+Run `cloud_details(, "cattonum")` for more info
+
+
+
+## Newly broken
+
+* checking R code for possible problems ... NOTE
+ ```
+ catto_median.data.frame : : no visible global function
+ definition for ‘median’
+ Undefined global functions or variables:
+ median
+ Consider adding
+ importFrom("stats", "median")
+ to your NAMESPACE file.
+ ```
+
+## In both
+
+* checking LazyData ... NOTE
+ ```
+ 'LazyData' is specified without a 'data' directory
+ ```
+
+# dibble
+
+
+
+* Version: 0.2.1
+* GitHub: https://github.com/UchidaMizuki/dibble
+* Source code: https://github.com/cran/dibble
+* Date/Publication: 2022-08-07 14:20:02 UTC
* Number of recursive dependencies: 50
-Run `revdep_details(,"arrow")` for more info
+Run `cloud_details(, "dibble")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Last 13 lines of output:
+ 7. ├─dibble (local) Ops.ddf_col(x, y)
+ 8. │ └─dibble:::broadcast_dim_names_warn(old_dim_names_e2, new_dim_names)
+ 9. │ ├─dibble:::broadcast_dim_names_message(...)
+ 10. │ │ ├─base::withVisible(eval(mc, parent.frame()))
+ 11. │ │ └─base::eval(mc, parent.frame())
+ 12. │ │ └─base::eval(mc, parent.frame())
+ 13. │ └─dibble (local) ``(...)
+ 14. │ └─purrr::map2(...)
+ 15. └─vctrs:::stop_recycle_incompatible_size(...)
+ 16. └─vctrs:::stop_vctrs(...)
+ 17. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
+
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 61 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# epitopR
+
+
+
+* Version: 0.1.1
+* GitHub: NA
+* Source code: https://github.com/cran/epitopR
+* Date/Publication: 2022-08-19 13:00:06 UTC
+* Number of recursive dependencies: 164
+
+Run `cloud_details(, "epitopR")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Last 13 lines of output:
+ 10. ├─dplyr:::mutate.data.frame(., antigen = str_remove(gsub(".*/", "", id), paste0("_", nm_method, ".txt")))
+ 11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
+ 12. │ ├─base::withCallingHandlers(...)
+ 13. │ └─mask$eval_all_mutate(quo)
+ 14. ├─stringr::str_remove(...)
+ 15. │ └─stringr::str_replace(string, pattern, "")
+ 16. │ └─stringi::stri_replace_first_regex(...)
+ 17. ├─base::gsub(".*/", "", id)
+ 18. └─base::.handleSimpleError(...)
+ 19. └─dplyr (local) h(simpleError(msg, call))
+ 20. └─rlang::abort(...)
+
+ [ FAIL 1 | WARN 0 | SKIP 2 | PASS 0 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+## In both
+
+* checking re-building of vignette outputs ... WARNING
+ ```
+ Error(s) in re-building vignettes:
+ --- re-building ‘mhcII-hu.Rmd’ using rmarkdown
+ ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
+ ✔ ggplot2 3.3.6 ✔ purrr 0.3.4.9000
+ ✔ tibble 3.1.8 ✔ dplyr 1.0.9
+ ✔ tidyr 1.2.0 ✔ stringr 1.4.1
+ ✔ readr 2.1.2 ✔ forcats 0.5.2
+ ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
+ ✖ dplyr::filter() masks stats::filter()
+ ✖ dplyr::lag() masks stats::lag()
+ ...
+ paste0("_", nm_method, ".txt"))`.
+ Caused by error in `as.character()`:
+ ! cannot coerce type 'closure' to vector of type 'character'
+ --- failed re-building ‘mhcII-hu.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘mhcII-hu.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+* checking dependencies in R code ... NOTE
+ ```
+ Namespaces in Imports field not imported from:
+ ‘devtools’ ‘ggseqlogo’ ‘rstudioapi’ ‘usethis’
+ All declared Imports should be used.
+ ```
+
+# gghighlight
+
+
+
+* Version: 0.3.3
+* GitHub: https://github.com/yutannihilation/gghighlight
+* Source code: https://github.com/cran/gghighlight
+* Date/Publication: 2022-06-06 20:10:11 UTC
+* Number of recursive dependencies: 82
+
+Run `cloud_details(, "gghighlight")` for more info
+
+
+
+## Newly broken
+
+* checking re-building of vignette outputs ... WARNING
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘gghighlight.Rmd’ using rmarkdown
+ Quitting from lines 245-251 (gghighlight.Rmd)
+ Error: processing vignette 'gghighlight.Rmd' failed with diagnostics:
+ geom_label_repel requires the following missing aesthetics: label
+ --- failed re-building ‘gghighlight.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘gghighlight.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# gratia
+
+
+
+* Version: 0.7.3
+* GitHub: https://github.com/gavinsimpson/gratia
+* Source code: https://github.com/cran/gratia
+* Date/Publication: 2022-05-09 11:20:03 UTC
+* Number of recursive dependencies: 83
+
+Run `cloud_details(, "gratia")` for more info
## Newly broken
-* checking installed package size ... NOTE
+* checking tests ... ERROR
```
- installed size is 10.9Mb
- sub-directories of 1Mb or more:
- libs 7.7Mb
- R 3.0Mb
+ Running ‘test-all.R’
+ Running the tests in ‘tests/test-all.R’ failed.
+ Last 13 lines of output:
+ • hgam-paper/hgam-paper-bird-move-model-1.svg
+ • hgam-paper/hgam-paper-bird-move-model-2.svg
+ • hgam-paper/hgam-paper-bird-move-model-3.svg
+ • hgam-paper/hgam-paper-bird-move-model-5.svg
+ • hgam-paper/hgam-paper-co2-model-1.svg
+ • hgam-paper/hgam-paper-co2-model-2.svg
+ • hgam-paper/hgam-paper-co2-model-3.svg
+ • hgam-paper/hgam-paper-co2-model-4.svg
+ • hgam-paper/hgam-paper-co2-model-5.svg
+ • hgam-paper/hgam-paper-zoop-model-4.svg
+ • hgam-paper/hgam-paper-zoop-model-5.svg
+ • rootograms/draw-gaussian-rootogram.svg
+ • rootograms/draw-neg-bin-rootogram.svg
+ Error: Test failures
+ Execution halted
```
-## Newly fixed
+# grizbayr
-* checking whether package ‘arrow’ can be installed ... ERROR
+
+
+* Version: 1.3.2
+* GitHub: NA
+* Source code: https://github.com/cran/grizbayr
+* Date/Publication: 2022-08-15 18:30:02 UTC
+* Number of recursive dependencies: 59
+
+Run `cloud_details(, "grizbayr")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
```
- Installation failed.
- See ‘/Users/lionel/Desktop/lowliner/revdep/checks.noindex/arrow/old/arrow.Rcheck/00install.out’ for details.
+ Running ‘spelling.R’
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Last 13 lines of output:
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ── Error (test-sample_from_posterior.R:45:3): sample_from_posterior returns correct dataframe shape for all types ──
+ Error in `.p(.x[[i]], ...)`: Predicate functions must return a single `TRUE` or `FALSE`, not a logical vector of length 3.
+ Backtrace:
+ ▆
+ 1. ├─testthat::expect_true(purrr::every(output, ~colnames(.x) == expected_col_names)) at test-sample_from_posterior.R:45:2
+ 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
+ 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
+ 4. └─purrr::every(output, ~colnames(.x) == expected_col_names)
+ 5. └─purrr (local) .p(.x[[i]], ...)
+ 6. └─rlang::abort(...)
+
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 245 ]
+ Error: Test failures
+ Execution halted
```
-# nlrx
+# gwasrapidd
-* Version: 0.3.0
-* Source code: https://github.com/cran/nlrx
-* URL: https://github.com/nldoc/nlrx/
-* BugReports: https://github.com/nldoc/nlrx/issues/
-* Date/Publication: 2019-09-26 12:50:02 UTC
-* Number of recursive dependencies: 90
+* Version: 0.99.13
+* GitHub: https://github.com/ramiromagno/gwasrapidd
+* Source code: https://github.com/cran/gwasrapidd
+* Date/Publication: 2022-08-11 22:20:02 UTC
+* Number of recursive dependencies: 79
-Run `revdep_details(,"nlrx")` for more info
+Run `cloud_details(, "gwasrapidd")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘spelling.R’
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Last 13 lines of output:
+ 3. │ ├─testthat (local) .capture(...)
+ 4. │ │ └─base::withCallingHandlers(...)
+ 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
+ 6. └─gwasrapidd::trait_to_variant(c("EFO_0000000"), warnings = TRUE)
+ 7. └─purrr::map_dfr(...)
+ 8. └─purrr::map(.x, .f, ...)
+ 9. └─gwasrapidd (local) .f(.x[[i]], ...)
+ 10. └─gwasrapidd::get_variants(efo_id = .x, verbose = verbose, warnings = warnings)
+ 11. └─gwasrapidd:::get_variants_by_efo_id(...)
+ 12. └─gwasrapidd:::get_variants_by_efo_trait(...)
+ 13. └─assertthat::assert_that(...)
+
+ [ FAIL 1 | WARN 2 | SKIP 1 | PASS 720 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# partialised
+
+
+
+* Version: 0.1.0
+* GitHub: https://github.com/UchidaMizuki/partialised
+* Source code: https://github.com/cran/partialised
+* Date/Publication: 2022-05-04 12:20:02 UTC
+* Number of recursive dependencies: 32
+
+Run `cloud_details(, "partialised")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Last 13 lines of output:
+ fn <- new_function(pairlist2(... = ), body, env = env)
+ }
+ structure(fn, class = c("purrr_function_partial", "function"),
+ body = call)
+ })(.Primitive("quote")(.fn), x = 6)`: `.f` must be a function, not a symbol
+ Backtrace:
+ ▆
+ 1. └─partialised::`arguments<-`(`*tmp*`, value = ``) at test-partialised.R:12:2
+ 2. ├─rlang::exec(purrr::partial, partialised_fn(x), !!!value)
+ 3. └─purrr (local) ``(``(.fn), x = 6)
+ 4. └─rlang::abort(sprintf("`.f` must be a function, not %s", friendly_type_of(.f)))
+
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# rATTAINS
+
+
+
+* Version: 0.1.3
+* GitHub: https://github.com/mps9506/rATTAINS
+* Source code: https://github.com/cran/rATTAINS
+* Date/Publication: 2021-11-03 14:10:02 UTC
+* Number of recursive dependencies: 80
+
+Run `cloud_details(, "rATTAINS")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Last 13 lines of output:
+ no files found
+ no files found
+ no files found
+ no files found
+ no files found
+ [ FAIL 2 | WARN 0 | SKIP 17 | PASS 33 ]
+
+ ══ Skipped tests ═══════════════════════════════════════════════════════════════
+ • On CRAN (17)
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ Error in `$<-.data.frame`(`*tmp*`, "call_text", value = c("vcr::use_cassette(...)", :
+ replacement has 25 rows, data has 24
+ Calls: test_check ... trace_format -> trace_as_tree -> $<- -> $<-.data.frame
+ Execution halted
+ ```
+
+* checking re-building of vignette outputs ... WARNING
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘Introduction.Rmd’ using rmarkdown
+ Quitting from lines 42-46 (Introduction.Rmd)
+ Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
+ Result 1 must be a single string, not a list of length 0
+ --- failed re-building ‘Introduction.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘Introduction.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# ruta
+
+
+
+* Version: 1.1.0
+* GitHub: https://github.com/fdavidcl/ruta
+* Source code: https://github.com/cran/ruta
+* Date/Publication: 2019-03-18 13:10:02 UTC
+* Number of recursive dependencies: 70
+
+Run `cloud_details(, "ruta")` for more info
@@ -50,27 +402,157 @@ Run `revdep_details(,"nlrx")` for more info
* checking examples ... ERROR
```
+ Running examples in ‘ruta-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: as_network
+ > ### Title: Coercion to ruta_network
+ > ### Aliases: as_network as_network.ruta_layer as_network.ruta_network
+ > ### as_network.numeric as_network.integer
+ >
+ > ### ** Examples
+ >
...
+ 11. └─ruta (local) .f(.x[[i]], ...)
+ 12. └─ruta:::make_atomic_network(ruta_layer_dense, units = units, activation = activation)
+ 13. ├─ruta::as_network(new_layer(cl, ...))
+ 14. └─ruta:::as_network.ruta_layer(new_layer(cl, ...))
+ 15. └─ruta::new_network(x)
+ 16. ├─base::stopifnot(every(args, ~class(.) == ruta_layer))
+ 17. └─purrr::every(args, ~class(.) == ruta_layer)
+ 18. └─purrr (local) .p(.x[[i]], ...)
+ 19. └─rlang::abort(...)
+ Execution halted
+ ```
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Last 13 lines of output:
+ 12. │ └─rlang::is_empty(x)
+ 13. └─purrr::map(., dense)
+ 14. └─ruta (local) .f(.x[[i]], ...)
+ 15. └─ruta:::make_atomic_network(ruta_layer_dense, units = units, activation = activation)
+ 16. ├─ruta::as_network(new_layer(cl, ...))
+ 17. └─ruta:::as_network.ruta_layer(new_layer(cl, ...))
+ 18. └─ruta::new_network(x)
+ 19. ├─base::stopifnot(every(args, ~class(.) == ruta_layer))
+ 20. └─purrr::every(args, ~class(.) == ruta_layer)
+ 21. └─purrr (local) .p(.x[[i]], ...)
+ 22. └─rlang::abort(...)
+
+ [ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+* checking re-building of vignette outputs ... WARNING
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘architectures.Rmd’ using rmarkdown
+ Quitting from lines 23-28 (architectures.Rmd)
+ Error: processing vignette 'architectures.Rmd' failed with diagnostics:
+ Predicate functions must return a single `TRUE` or `FALSE`, not a logical vector of length 2.
+ --- failed re-building ‘architectures.Rmd’
+
+ --- re-building ‘troubleshooting.Rmd’ using rmarkdown
+ --- finished re-building ‘troubleshooting.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘architectures.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+## In both
+
+* checking LazyData ... NOTE
+ ```
+ 'LazyData' is specified without a 'data' directory
+ ```
+
+# sbm
+
+
+
+* Version: 0.4.4
+* GitHub: https://github.com/GrossSBM/sbm
+* Source code: https://github.com/cran/sbm
+* Date/Publication: 2022-08-24 17:40:02 UTC
+* Number of recursive dependencies: 104
+
+Run `cloud_details(, "sbm")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘spelling.R’
+ Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...6c6
+ < NULL
+ ---
+ > All Done!
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Last 13 lines of output:
+
+
+ ...
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1050 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ── Failure (test-MultipartiteSBM.R:35:5): initializing Multipartite SBM works ──
+ myMBM$blockProp not equivalent to list(NULL, list(numeric(0), numeric(0))).
+ Component 1: target is numeric, current is NULL
+
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1050 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# tidywikidatar
+
+
+
+* Version: 0.5.4
+* GitHub: NA
+* Source code: https://github.com/cran/tidywikidatar
+* Date/Publication: 2022-08-06 14:00:02 UTC
+* Number of recursive dependencies: 135
+
+Run `cloud_details(, "tidywikidatar")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘tidywikidatar-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: tw_filter
+ > ### Title: Filter search result and keep only items with matching property
+ > ### and Q identifier
+ > ### Aliases: tw_filter
>
- > # Define output directory:
- > outdir <- tempdir() # adjust path to your needs
+ > ### ** Examples
>
- > # Create documentation:
- > nldoc(modelfiles = modelfiles,
- + infotab=TRUE,
- + gui=TRUE,
- + bs=TRUE,
- + outpath = outdir,
- + output_format = "html",
- + number_sections = TRUE,
- + theme = "cosmo",
- + date = date(),
- + toc = TRUE)
- Warning in file(con, "r") :
- URL 'https://raw.githubusercontent.com/nldoc/nldoc_pg/master/WSP.nlogo': status was 'Couldn't connect to server'
- Error in file(con, "r") :
- cannot open the connection to 'https://raw.githubusercontent.com/nldoc/nldoc_pg/master/WSP.nlogo'
- Calls: nldoc -> nldoc_read_nlogo -> readLines -> file
+ ...
+ 15. │ └─dplyr:::filter_rows(.data, ..., caller_env = caller_env())
+ 16. │ └─dplyr:::filter_eval(dots, mask = mask, error_call = error_call)
+ 17. │ ├─base::withCallingHandlers(...)
+ 18. │ └─mask$eval_all_filter(dots, env_filter)
+ 19. ├─property
+ 20. ├─rlang:::`$.rlang_data_pronoun`(.data, property)
+ 21. │ └─rlang:::data_pronoun_get(...)
+ 22. └─rlang:::abort_data_pronoun(x, call = y)
+ 23. └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
Execution halted
```
diff --git a/src/pluck.c b/src/pluck.c
index d9aa7c48..1f9a85d5 100644
--- a/src/pluck.c
+++ b/src/pluck.c
@@ -256,7 +256,7 @@ SEXP pluck_impl(SEXP x, SEXP index, SEXP missing, SEXP strict_arg) {
end:
UNPROTECT(1);
- return (Rf_length(x) == 0) ? missing : x;
+ return x == R_NilValue ? missing : x;
}
diff --git a/tests/testthat/test-as-mapper.R b/tests/testthat/test-as-mapper.R
index 50a4732f..7a458d8b 100644
--- a/tests/testthat/test-as-mapper.R
+++ b/tests/testthat/test-as-mapper.R
@@ -28,13 +28,14 @@ test_that(".default replaces absent values", {
expect_equal(map_dbl(x, "b", .default = NA), c(2, NA, NA))
})
-test_that(".default replaces elements with length 0", {
+test_that(".default only replaces NULL elements", {
x <- list(
list(a = 1),
+ list(a = numeric()),
list(a = NULL),
- list(a = numeric())
+ list()
)
- expect_equal(map_dbl(x, "a", .default = NA), c(1, NA, NA))
+ expect_equal(map(x, "a", .default = NA), list(1, numeric(), NA, NA))
})
test_that("Additional arguments are ignored", {
@@ -75,3 +76,4 @@ test_that("complex types aren't supported for indexing", {
test_that("raw vectors are supported for indexing", {
expect_equal( as_mapper(1)(raw(2)), raw(1) )
})
+
diff --git a/tests/testthat/test-pluck.R b/tests/testthat/test-pluck.R
index aeff40cc..d2ab2e90 100644
--- a/tests/testthat/test-pluck.R
+++ b/tests/testthat/test-pluck.R
@@ -59,15 +59,17 @@ test_that("special indexes never match", {
})
test_that("special values return NULL", {
- # unnamed input
+ # absent name
expect_null(pluck(list(1, 2), "a"))
+ expect_null(pluck(list(a = 1, b = 2), "c"))
- # zero length input
- expect_null(pluck(integer(), 1))
-
- # past end
+ # outside of range
+ expect_null(pluck(1:4, 0))
expect_null(pluck(1:4, 10))
- expect_null(pluck(1:4, 10L))
+})
+
+test_that("can pluck 0-length object", {
+ expect_equal(pluck(list(integer()), 1), integer())
})
test_that("handles weird names", {