Toby Hocking
2019-May-30 23:31 UTC
[Rd] R pkg install should fail for unsuccessful DLL copy on windows?
thanks for the tip Jan.
However it would be nice if I didn't have to handle this myself for all of
my packages. (and teach my students how to do that)
BTW I tried to disable staged installation, and the issue still happens:
th798 at cmp2986 MINGW64 ~/projects/max-generalized-auc (master)
$ R_INSTALL_STAGED=FALSE R --vanilla -e
".libPaths('~/R/library');.libPaths();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.
> .libPaths('~/R/library');.libPaths();options(repos='
https://cloud.r-project.org',
warn=2);library(penaltyLearning);install.packages('penaltyLearning',
type='source');getOption('warn');sessionInfo()
[1] "C:/Users/th798/R/library" "C:/Program
Files/R/R-3.6.0/library"
Loading required package: data.table
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Installing package into 'C:/Users/th798/R/library'
(as 'lib' is unspecified)
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 non-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:/Users/th798/R/library/penaltyLearning/libs/x64
Warning in file.copy(files, dest, overwrite = TRUE) :
problem copying .\penaltyLearning.dll to
C:\Users\th798\R\library\penaltyLearning\libs\x64\penaltyLearning.dll:
Permission denied
** 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
* DONE (penaltyLearning)
The downloaded source packages are in
'C:\Users\th798\AppData\Local\Temp\RtmpkVV0sH\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/projects/max-generalized-auc
th798 at cmp2986 MINGW64 ~/projects/max-generalized-auc (master)
$
On Wed, May 29, 2019 at 8:15 PM Jan Gorecki <j.gorecki at wit.edu.pl>
wrote:
> Hi Toby,
> AFAIK it has not been addressed in R. You can handle the problem on
> your package side, see
> https://github.com/Rdatatable/data.table/pull/3237
> Regards,
> Jan
>
>
> On Thu, May 30, 2019 at 4:46 AM Toby Hocking <tdhock5 at gmail.com>
wrote:
> >
> > Hi all,
> >
> > I am having an issue related to installing packages on windows with
> > R-3.6.0. When installing a package that is in use, I expected R to
stop
> > with an error. However I am getting a warning that the DLL copy was
not
> > successful, but the overall package installation IS successful. This
is
> > quite dangerous because the old DLL and the new R code could be
> > incompatible.
> >
> > I am definitely not the first person to have this issue.
> > * Matt Dowle reported
> > https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17478 which was
> never
> > addressed.
> > * Jim Hester reported
> > https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17453 which was
> > apparently addressed in R-3.5.1, via
> >
>
https://github.com/wch/r-source/commit/828a04f9c428403e476620b1905a1d8ca41d0bcd
> >
> > But I am now having the same issue in R-3.6.0 -- is this a regression
in
> R?
> > or is there another fix that I can use?
> >
> > Below is the minimal R code that I used to reproduce the issue.
> Essentially,
> > * I start R with --vanilla and set options repos=cloud and warn=2
(which
> I
> > expect should convert warnings to errors).
> > * I do library(penaltyLearning) and then install the package from
source,
> > which results in the
> > warnings. I expected there should be an error.
> >
> > th798 at 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 at cmp2986 MINGW64 ~/R
> > $
> >
> > related blog post: https://tdhock.github.io/blog/2019/windows-dll/
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
[[alternative HTML version deleted]]
Pages, Herve
2019-May-30 23:50 UTC
[Rd] R pkg install should fail for unsuccessful DLL copy on windows?
Also note that this can lead to people not being able to load the package if the set of .Call entry points has changed between the old and new versions of the package. We strongly suspect that this is what happened to this Bioconductor user: https://support.bioconductor.org/p/121228/ Note that she's installing the binary and in this case no warning is issued. All we see is: package ?S4Vectors? successfully unpacked and MD5 sums checked but the old DLL apparently didn't get replaced with the new one. Hence the error: "make_RAW_from_NA_LLINT" not available for .Call() for package "S4Vectors" later on when trying to load the package. Cheers, H. On 5/30/19 16:31, Toby Hocking wrote:> thanks for the tip Jan. > > However it would be nice if I didn't have to handle this myself for all of > my packages. (and teach my students how to do that) > > BTW I tried to disable staged installation, and the issue still happens: > > th798 at cmp2986 MINGW64 ~/projects/max-generalized-auc (master) > $ R_INSTALL_STAGED=FALSE R --vanilla -e > ".libPaths('~/R/library');.libPaths();options(repos=' > https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=7X00xNRObhT9O68YU8m-IBkt38N5p_GP-UV77XEnKZw&e= ', > 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. > >> .libPaths('~/R/library');.libPaths();options(repos=' > https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=7X00xNRObhT9O68YU8m-IBkt38N5p_GP-UV77XEnKZw&e= ', > warn=2);library(penaltyLearning);install.packages('penaltyLearning', > type='source');getOption('warn');sessionInfo() > [1] "C:/Users/th798/R/library" "C:/Program > Files/R/R-3.6.0/library" > Loading required package: data.table > Registered S3 methods overwritten by 'ggplot2': > method from > [.quosures rlang > c.quosures rlang > print.quosures rlang > Installing package into 'C:/Users/th798/R/library' > (as 'lib' is unspecified) > trying URL ' > https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org_src_contrib_penaltyLearning-5F2018.09.04.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=o34c6BnD4LvJv-00tYn5M2TqO_IjH5qtaKnnhI4ph50&e= ' > 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 non-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:/Users/th798/R/library/penaltyLearning/libs/x64 > Warning in file.copy(files, dest, overwrite = TRUE) : > problem copying .\penaltyLearning.dll to > C:\Users\th798\R\library\penaltyLearning\libs\x64\penaltyLearning.dll: > Permission denied > ** 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 > * DONE (penaltyLearning) > > The downloaded source packages are in > 'C:\Users\th798\AppData\Local\Temp\RtmpkVV0sH\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/projects/max-generalized-auc > th798 at cmp2986 MINGW64 ~/projects/max-generalized-auc (master) > $ > > > > On Wed, May 29, 2019 at 8:15 PM Jan Gorecki <j.gorecki at wit.edu.pl> wrote: > >> Hi Toby, >> AFAIK it has not been addressed in R. You can handle the problem on >> your package side, see >> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Rdatatable_data.table_pull_3237&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=rI7qS9klz5h9_Cxq2381FT730_fIJS2eYuO7zfoFuOQ&e>> Regards, >> Jan >> >> >> On Thu, May 30, 2019 at 4:46 AM Toby Hocking <tdhock5 at gmail.com> wrote: >>> >>> Hi all, >>> >>> I am having an issue related to installing packages on windows with >>> R-3.6.0. When installing a package that is in use, I expected R to stop >>> with an error. However I am getting a warning that the DLL copy was not >>> successful, but the overall package installation IS successful. This is >>> quite dangerous because the old DLL and the new R code could be >>> incompatible. >>> >>> I am definitely not the first person to have this issue. >>> * Matt Dowle reported >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__bugs.r-2Dproject.org_bugzilla_show-5Fbug.cgi-3Fid-3D17478&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=IJuOtHB4O_KwvegXltTlKm91bD5nu9Ltdcyi2xBqurA&e= which was >> never >>> addressed. >>> * Jim Hester reported >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__bugs.r-2Dproject.org_bugzilla_show-5Fbug.cgi-3Fid-3D17453&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=j0nlC7mk5y3nA30dLMfkiYhsgFRsexMMfWoLgOVIO6w&e= which was >>> apparently addressed in R-3.5.1, via >>> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_wch_r-2Dsource_commit_828a04f9c428403e476620b1905a1d8ca41d0bcd&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=92B6JnxdBpF06tY0vcrp4SJ2avJA6t68xlDGF7cWFfk&e>>> >>> But I am now having the same issue in R-3.6.0 -- is this a regression in >> R? >>> or is there another fix that I can use? >>> >>> Below is the minimal R code that I used to reproduce the issue. >> Essentially, >>> * I start R with --vanilla and set options repos=cloud and warn=2 (which >> I >>> expect should convert warnings to errors). >>> * I do library(penaltyLearning) and then install the package from source, >>> which results in the >>> warnings. I expected there should be an error. >>> >>> th798 at cmp2986 MINGW64 ~/R >>> $ R --vanilla -e "options(repos='https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=7X00xNRObhT9O68YU8m-IBkt38N5p_GP-UV77XEnKZw&e= ', >>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=7X00xNRObhT9O68YU8m-IBkt38N5p_GP-UV77XEnKZw&e= ', >>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org_src_contrib_penaltyLearning-5F2018.09.04.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=o34c6BnD4LvJv-00tYn5M2TqO_IjH5qtaKnnhI4ph50&e= ' >>> 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 at cmp2986 MINGW64 ~/R >>> $ >>> >>> related blog post: https://urldefense.proofpoint.com/v2/url?u=https-3A__tdhock.github.io_blog_2019_windows-2Ddll_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=966ZHBqmdlD56fg01o9FZKpQYT07ZL3dzmZt3cEWgaQ&e>>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-devel at r-project.org mailing list >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=8Tg6DVEkxJdPCYGLbPDOm7UQuVwBJS_ezJksvJkECNM&e>> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=8Tg6DVEkxJdPCYGLbPDOm7UQuVwBJS_ezJksvJkECNM&e>-- Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319
Toby Hocking
2019-May-31 15:41 UTC
[Rd] R pkg install should fail for unsuccessful DLL copy on windows?
thanks for your input Herv?. Glad to hear I'm not the only one still having this issue. In my opinion install.packages should stop with an error (instead of a warning) if this happens. However even if you want to keep the warning, at least make it so that users can set options(warn=2) to get an error if they want one. I tried setting options(warn=2) but for some reason I still get a warning. I believe that is a bug in install.packages -- if I specify options(warn=2) it should convert that warning to an error (but it currently does not). Toby On Thu, May 30, 2019 at 4:50 PM Pages, Herve <hpages at fredhutch.org> wrote:> Also note that this can lead to people not being able to load the > package if the set of .Call entry points has changed between the old > and new versions of the package. We strongly suspect that this is what > happened to this Bioconductor user: > > https://support.bioconductor.org/p/121228/ > > Note that she's installing the binary and in this case no warning > is issued. All we see is: > > package ?S4Vectors? successfully unpacked and MD5 sums checked > > but the old DLL apparently didn't get replaced with the new one. > Hence the > > error: "make_RAW_from_NA_LLINT" not available for .Call() for package > "S4Vectors" > > later on when trying to load the package. > > Cheers, > H. > > > On 5/30/19 16:31, Toby Hocking wrote: > > thanks for the tip Jan. > > > > However it would be nice if I didn't have to handle this myself for all > of > > my packages. (and teach my students how to do that) > > > > BTW I tried to disable staged installation, and the issue still happens: > > > > th798 at cmp2986 MINGW64 ~/projects/max-generalized-auc (master) > > $ R_INSTALL_STAGED=FALSE R --vanilla -e > > ".libPaths('~/R/library');.libPaths();options(repos=' > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=7X00xNRObhT9O68YU8m-IBkt38N5p_GP-UV77XEnKZw&e> ', > > 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. > > > >> .libPaths('~/R/library');.libPaths();options(repos=' > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=7X00xNRObhT9O68YU8m-IBkt38N5p_GP-UV77XEnKZw&e> ', > > warn=2);library(penaltyLearning);install.packages('penaltyLearning', > > type='source');getOption('warn');sessionInfo() > > [1] "C:/Users/th798/R/library" "C:/Program > > Files/R/R-3.6.0/library" > > Loading required package: data.table > > Registered S3 methods overwritten by 'ggplot2': > > method from > > [.quosures rlang > > c.quosures rlang > > print.quosures rlang > > Installing package into 'C:/Users/th798/R/library' > > (as 'lib' is unspecified) > > trying URL ' > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org_src_contrib_penaltyLearning-5F2018.09.04.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=o34c6BnD4LvJv-00tYn5M2TqO_IjH5qtaKnnhI4ph50&e> ' > > 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 non-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:/Users/th798/R/library/penaltyLearning/libs/x64 > > Warning in file.copy(files, dest, overwrite = TRUE) : > > problem copying .\penaltyLearning.dll to > > C:\Users\th798\R\library\penaltyLearning\libs\x64\penaltyLearning.dll: > > Permission denied > > ** 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 > > * DONE (penaltyLearning) > > > > The downloaded source packages are in > > 'C:\Users\th798\AppData\Local\Temp\RtmpkVV0sH\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/projects/max-generalized-auc > > th798 at cmp2986 MINGW64 ~/projects/max-generalized-auc (master) > > $ > > > > > > > > On Wed, May 29, 2019 at 8:15 PM Jan Gorecki <j.gorecki at wit.edu.pl> > wrote: > > > >> Hi Toby, > >> AFAIK it has not been addressed in R. You can handle the problem on > >> your package side, see > >> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Rdatatable_data.table_pull_3237&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=rI7qS9klz5h9_Cxq2381FT730_fIJS2eYuO7zfoFuOQ&e> >> Regards, > >> Jan > >> > >> > >> On Thu, May 30, 2019 at 4:46 AM Toby Hocking <tdhock5 at gmail.com> wrote: > >>> > >>> Hi all, > >>> > >>> I am having an issue related to installing packages on windows with > >>> R-3.6.0. When installing a package that is in use, I expected R to stop > >>> with an error. However I am getting a warning that the DLL copy was not > >>> successful, but the overall package installation IS successful. This is > >>> quite dangerous because the old DLL and the new R code could be > >>> incompatible. > >>> > >>> I am definitely not the first person to have this issue. > >>> * Matt Dowle reported > >>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__bugs.r-2Dproject.org_bugzilla_show-5Fbug.cgi-3Fid-3D17478&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=IJuOtHB4O_KwvegXltTlKm91bD5nu9Ltdcyi2xBqurA&e> which was > >> never > >>> addressed. > >>> * Jim Hester reported > >>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__bugs.r-2Dproject.org_bugzilla_show-5Fbug.cgi-3Fid-3D17453&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=j0nlC7mk5y3nA30dLMfkiYhsgFRsexMMfWoLgOVIO6w&e> which was > >>> apparently addressed in R-3.5.1, via > >>> > >> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_wch_r-2Dsource_commit_828a04f9c428403e476620b1905a1d8ca41d0bcd&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=92B6JnxdBpF06tY0vcrp4SJ2avJA6t68xlDGF7cWFfk&e> >>> > >>> But I am now having the same issue in R-3.6.0 -- is this a regression > in > >> R? > >>> or is there another fix that I can use? > >>> > >>> Below is the minimal R code that I used to reproduce the issue. > >> Essentially, > >>> * I start R with --vanilla and set options repos=cloud and warn=2 > (which > >> I > >>> expect should convert warnings to errors). > >>> * I do library(penaltyLearning) and then install the package from > source, > >>> which results in the > >>> warnings. I expected there should be an error. > >>> > >>> th798 at cmp2986 MINGW64 ~/R > >>> $ R --vanilla -e "options(repos=' > https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=7X00xNRObhT9O68YU8m-IBkt38N5p_GP-UV77XEnKZw&e> ', > >>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=7X00xNRObhT9O68YU8m-IBkt38N5p_GP-UV77XEnKZw&e> ', > >>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org_src_contrib_penaltyLearning-5F2018.09.04.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=o34c6BnD4LvJv-00tYn5M2TqO_IjH5qtaKnnhI4ph50&e> ' > >>> 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 at cmp2986 MINGW64 ~/R > >>> $ > >>> > >>> related blog post: > https://urldefense.proofpoint.com/v2/url?u=https-3A__tdhock.github.io_blog_2019_windows-2Ddll_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=966ZHBqmdlD56fg01o9FZKpQYT07ZL3dzmZt3cEWgaQ&e> >>> > >>> [[alternative HTML version deleted]] > >>> > >>> ______________________________________________ > >>> R-devel at r-project.org mailing list > >>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=8Tg6DVEkxJdPCYGLbPDOm7UQuVwBJS_ezJksvJkECNM&e> >> > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-devel at r-project.org mailing list > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zldJhdavBFtHDHr08_HFRAi9MY2WBkTiDn1ggbog4cA&s=8Tg6DVEkxJdPCYGLbPDOm7UQuVwBJS_ezJksvJkECNM&e> > > > -- > Herv? Pag?s > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 >[[alternative HTML version deleted]]
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