Re: [Rd] R pkg install should fail for unsuccessful DLL copy on windows?
On 06/06/2019 4:19 p.m., Toby Hocking wrote: If anybody else has this issue, please add a comment on https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17478 so we are more likely to get R-core to address this. Please don't encourage spam there. Add a comment if you have information to add, but "me too" messages just waste everybody's time. Duncan Murdoch Thanks Toby On Tue, Jun 4, 2019 at 2:58 PM Pages, Herve wrote: On 5/31/19 08:41, Toby Hocking wrote:... In my opinion install.packages should stop with an error (instead of a warning) if this happens. Totally agree with that. Best, H. -- Hervé Pagès 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: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R pkg install should fail for unsuccessful DLL copy on windows?
If anybody else has this issue, please add a comment on https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17478 so we are more likely to get R-core to address this. Thanks Toby On Tue, Jun 4, 2019 at 2:58 PM Pages, Herve wrote: > On 5/31/19 08:41, Toby Hocking wrote:... > > In my opinion install.packages should stop with an error (instead of a > > warning) if this happens. > > Totally agree with that. > > Best, > H. > > -- > Hervé Pagès > > 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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax:(206) 667-1319 > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R pkg install should fail for unsuccessful DLL copy on windows?
On 5/31/19 08:41, Toby Hocking wrote:... > In my opinion install.packages should stop with an error (instead of a > warning) if this happens. Totally agree with that. Best, H. -- Hervé Pagès 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: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R pkg install should fail for unsuccessful DLL copy on windows?
thanks for your input Hervé. 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 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@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;
> >
Re: [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@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 hel
Re: [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@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
GeomTallRecthtml
IntervalRegressionCVhtml
IntervalRegressionCVmargin html
IntervalRegressionInternal html
IntervalRegressionRegularized html
IntervalRegressionUnregularized html
ROChangehtml
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.IntervalRegressionhtml
squared.hinge html
targetIntervalROC ht
Re: [Rd] R pkg install should fail for unsuccessful DLL copy on windows?
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 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@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
> GeomTallRecthtml
> IntervalRegressionCVhtml
> IntervalRegressionCVmargin html
> IntervalRegressionInternal html
> IntervalRegressionRegularized html
> IntervalRegressionUnregularized html
> ROChangehtml
> change.colors html
> change.labels html
> changeLabel html
> check_features_tar
[Rd] R pkg install should fail for unsuccessful DLL copy on windows?
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@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
GeomTallRecthtml
IntervalRegressionCVhtml
IntervalRegressionCVmargin html
IntervalRegressionInternal html
IntervalRegressionRegularized html
IntervalRegressionUnregularized html
ROChangehtml
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
