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 <hpa...@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@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@cmp2986 MINGW64 ~/projects/max-generalized-auc (master) > > $ > > > > > > > > On Wed, May 29, 2019 at 8:15 PM Jan Gorecki <j.gore...@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 <tdho...@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@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@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@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@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= > > > > -- > 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