R package installation on windows considered harmful
Recently I have been getting this warning in R on windows while installing my penaltyLearning package for supervised changepoint detection:
** testing if installed package can be loaded from temporary location
WARNING: moving package to final location failed, copying instead
Warning in file.copy(instdir, dirname(final_instdir), recursive = TRUE, :
problem copying C:\Program Files\R\R-3.6.0\library\00LOCK-penaltyLearning\00new\penaltyLearning\libs\x64\penaltyLearning.dll to C:\Program Files\R\R-3.6.0\library\penaltyLearning\libs\x64\penaltyLearning.dll: Permission denied
** testing if installed package can be loaded from final location
This happens on Windows when the package is in use but you try to install it from source. It tries to copy the DLL but the copy fails with a warning because the DLL is in use, AND THEN PACKAGE INSTALLATION CONTINUES. This is a serious problem that could lead to hard to find bugs, because the old DLL file could be incompatible with the newly installed R code. I think the most obvious fix would be to stop package installation with an error rather than a warning.
Today I noticed one of my students was also having this issue, so I decided to investigate to see if there is a known solution. I’m not the first to have this issue.
- data.table had this issue, and they filed a base R bug which has not yet been addressed.
- remotes also had this issue. They filed a different bug in base R which was apparently addressed by this commit to R-3.5.1.
However I am having this issue now in R-3.6.0 – was there a regression? A reproducible example is below, but here is a summary:
- I start R with –vanilla and set options repos=cloud and warn=2 (which I expect should convert warnings to errors).
- In the first command line I install the penaltyLearning package from source, which results in a successful installation.
- In the second command line I first do library(penaltyLearning) and then install the package from source, which results in the warnings. I expected there should be an error.
- The third command line is the same as the first, and gives the same result.
UPDATE: this bug has been fixed as of R-3.6.1, i.e. R now stops with an error if the dll can not be installed. I highly recommend upgrading to R-3.6.1, because that also contains the updates for linear time regular expressions, as explained in my R journal submission.
th798@cmp2986 MINGW64 ~/R
$ R --vanilla -e "options(repos='https://cloud.r-project.org', warn=2);install.packages('penaltyLearning', type='source');getOption('warn');sessionInfo()"
R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> options(repos='https://cloud.r-project.org', warn=2);install.packages('penaltyLearning', type='source');getOption('warn');sessionInfo()
trying URL 'https://cloud.r-project.org/src/contrib/penaltyLearning_2018.09.04.tar.gz'
Content type 'application/x-gzip' length 2837289 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
* installing *source* package 'penaltyLearning' ...
** package 'penaltyLearning' successfully unpacked and MD5 sums checked
** using staged installation
** libs
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.0/include" -DNDEBUG -O2 -Wall -mtune=generic -c interface.cpp -o interface.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.0/include" -DNDEBUG -O2 -Wall -mtune=generic -c largestContinuousMinimum.cpp -o largestContinuousMinimum.o
largestContinuousMinimum.cpp: In function 'int largestContinuousMinimum(int, double*, double*, int*)':
largestContinuousMinimum.cpp:38:27: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
index_vec[0] = start;
^
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.0/include" -DNDEBUG -O2 -Wall -mtune=generic -c modelSelection.cpp -o modelSelection.o
/usr/bin/sed: -e expression #1, char 1: unknown command: `C'
c:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o penaltyLearning.dll tmp.def interface.o largestContinuousMinimum.o modelSelection.o -LC:/PROGRA~1/R/R-36~1.0/bin/x64 -lR
installing to C:/Program Files/R/R-3.6.0/library/00LOCK-penaltyLearning/00new/penaltyLearning/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'penaltyLearning'
finding HTML links ... done
GeomTallRect html
IntervalRegressionCV html
IntervalRegressionCVmargin html
IntervalRegressionInternal html
IntervalRegressionRegularized html
IntervalRegressionUnregularized html
ROChange html
change.colors html
change.labels html
changeLabel html
check_features_targets html
check_target_pred html
coef.IntervalRegression html
demo8 html
featureMatrix html
featureVector html
geom_tallrect html
labelError html
largestContinuousMinimumC html
largestContinuousMinimumR html
modelSelection html
modelSelectionC html
modelSelectionR html
neuroblastomaProcessed html
oneSkip html
plot.IntervalRegression html
predict.IntervalRegression html
print.IntervalRegression html
squared.hinge html
targetIntervalROC html
targetIntervalResidual html
targetIntervals html
theme_no_space html
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (penaltyLearning)
The downloaded source packages are in
'C:\Users\th798\AppData\Local\Temp\RtmpwDPOGo\downloaded_packages'
[1] 2
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.0 tools_3.6.0
>
>
]0;MINGW64:/c/Users/th798/R
th798@cmp2986 MINGW64 ~/R
$ R --vanilla -e "options(repos='https://cloud.r-project.org', warn=2);library(penaltyLearning);install.packages('penaltyLearning', type='source');getOption('warn');sessionInfo()"
R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> options(repos='https://cloud.r-project.org', warn=2);library(penaltyLearning);install.packages('penaltyLearning', type='source');getOption('warn');sessionInfo()
Loading required package: data.table
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
trying URL 'https://cloud.r-project.org/src/contrib/penaltyLearning_2018.09.04.tar.gz'
Content type 'application/x-gzip' length 2837289 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
* installing *source* package 'penaltyLearning' ...
** package 'penaltyLearning' successfully unpacked and MD5 sums checked
** using staged installation
** libs
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.0/include" -DNDEBUG -O2 -Wall -mtune=generic -c interface.cpp -o interface.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.0/include" -DNDEBUG -O2 -Wall -mtune=generic -c largestContinuousMinimum.cpp -o largestContinuousMinimum.o
largestContinuousMinimum.cpp: In function 'int largestContinuousMinimum(int, double*, double*, int*)':
largestContinuousMinimum.cpp:38:27: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
index_vec[0] = start;
^
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.0/include" -DNDEBUG -O2 -Wall -mtune=generic -c modelSelection.cpp -o modelSelection.o
/usr/bin/sed: -e expression #1, char 1: unknown command: `C'
c:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o penaltyLearning.dll tmp.def interface.o largestContinuousMinimum.o modelSelection.o -LC:/PROGRA~1/R/R-36~1.0/bin/x64 -lR
installing to C:/Program Files/R/R-3.6.0/library/00LOCK-penaltyLearning/00new/penaltyLearning/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'penaltyLearning'
finding HTML links ... done
GeomTallRect html
IntervalRegressionCV html
IntervalRegressionCVmargin html
IntervalRegressionInternal html
IntervalRegressionRegularized html
IntervalRegressionUnregularized html
ROChange html
change.colors html
change.labels html
changeLabel html
check_features_targets html
check_target_pred html
coef.IntervalRegression html
demo8 html
featureMatrix html
featureVector html
geom_tallrect html
labelError html
largestContinuousMinimumC html
largestContinuousMinimumR html
modelSelection html
modelSelectionC html
modelSelectionR html
neuroblastomaProcessed html
oneSkip html
plot.IntervalRegression html
predict.IntervalRegression html
print.IntervalRegression html
squared.hinge html
targetIntervalROC html
targetIntervalResidual html
targetIntervals html
theme_no_space html
** building package indices
** testing if installed package can be loaded from temporary location
WARNING: moving package to final location failed, copying instead
Warning in file.copy(instdir, dirname(final_instdir), recursive = TRUE, :
problem copying C:\Program Files\R\R-3.6.0\library\00LOCK-penaltyLearning\00new\penaltyLearning\libs\x64\penaltyLearning.dll to C:\Program Files\R\R-3.6.0\library\penaltyLearning\libs\x64\penaltyLearning.dll: Permission denied
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (penaltyLearning)
The downloaded source packages are in
'C:\Users\th798\AppData\Local\Temp\RtmpUrOoFE\downloaded_packages'
[1] 2
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] penaltyLearning_2018.09.04 data.table_1.12.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 assertthat_0.2.1 dplyr_0.8.1 crayon_1.3.4
[5] R6_2.4.0 grid_3.6.0 plyr_1.8.4 magic_1.5-9
[9] gtable_0.3.0 magrittr_1.5 scales_1.0.0 ggplot2_3.1.1
[13] pillar_1.4.0 rlang_0.3.4 lazyeval_0.2.2 geometry_0.4.1
[17] tools_3.6.0 glue_1.3.1 purrr_0.3.2 munsell_0.5.0
[21] abind_1.4-7 compiler_3.6.0 pkgconfig_2.0.2 colorspace_1.4-1
[25] tidyselect_0.2.5 tibble_2.1.1
>
>
]0;MINGW64:/c/Users/th798/R
th798@cmp2986 MINGW64 ~/R
$ R --vanilla -e "options(repos='https://cloud.r-project.org', warn=2);install.packages('penaltyLearning', type='source');getOption('warn');sessionInfo()"
R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> options(repos='https://cloud.r-project.org', warn=2);install.packages('penaltyLearning', type='source');getOption('warn');sessionInfo()
trying URL 'https://cloud.r-project.org/src/contrib/penaltyLearning_2018.09.04.tar.gz'
Content type 'application/x-gzip' length 2837289 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
* installing *source* package 'penaltyLearning' ...
** package 'penaltyLearning' successfully unpacked and MD5 sums checked
** using staged installation
** libs
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.0/include" -DNDEBUG -O2 -Wall -mtune=generic -c interface.cpp -o interface.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.0/include" -DNDEBUG -O2 -Wall -mtune=generic -c largestContinuousMinimum.cpp -o largestContinuousMinimum.o
largestContinuousMinimum.cpp: In function 'int largestContinuousMinimum(int, double*, double*, int*)':
largestContinuousMinimum.cpp:38:27: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
index_vec[0] = start;
^
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.0/include" -DNDEBUG -O2 -Wall -mtune=generic -c modelSelection.cpp -o modelSelection.o
/usr/bin/sed: -e expression #1, char 1: unknown command: `C'
c:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o penaltyLearning.dll tmp.def interface.o largestContinuousMinimum.o modelSelection.o -LC:/PROGRA~1/R/R-36~1.0/bin/x64 -lR
installing to C:/Program Files/R/R-3.6.0/library/00LOCK-penaltyLearning/00new/penaltyLearning/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'penaltyLearning'
finding HTML links ... done
GeomTallRect html
IntervalRegressionCV html
IntervalRegressionCVmargin html
IntervalRegressionInternal html
IntervalRegressionRegularized html
IntervalRegressionUnregularized html
ROChange html
change.colors html
change.labels html
changeLabel html
check_features_targets html
check_target_pred html
coef.IntervalRegression html
demo8 html
featureMatrix html
featureVector html
geom_tallrect html
labelError html
largestContinuousMinimumC html
largestContinuousMinimumR html
modelSelection html
modelSelectionC html
modelSelectionR html
neuroblastomaProcessed html
oneSkip html
plot.IntervalRegression html
predict.IntervalRegression html
print.IntervalRegression html
squared.hinge html
targetIntervalROC html
targetIntervalResidual html
targetIntervals html
theme_no_space html
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (penaltyLearning)
The downloaded source packages are in
'C:\Users\th798\AppData\Local\Temp\RtmpCeEYVI\downloaded_packages'
[1] 2
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.0 tools_3.6.0
>
>
]0;MINGW64:/c/Users/th798/R
th798@cmp2986 MINGW64 ~/R
$