[R-pkg-devel] Reproducing CRAN pre-tests
Hi, I am trying to submit an updated version of my package PGRdup to CRAN. The package has compiled code in C. I do development in a windows environment. The update was to fix issues in https://cran.r-project.org/web/checks/check_results_PGRdup.html. I have successfully fixed PCRE2 compatability issues and the issue with " ‘strncpy’ specified bound depends on the length of the source argument". For all instances of of strncpy I had changed the dependency on the length of the source argument to that of destination argument. On submission, now one issue remains with debian pre-test. /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] https://win-builder.r-project.org/incoming_pretest/PGRdup_0.2.3.4_20190919_090630/Debian/00check.log How to reproduce this error. I have tried rhub platforms windows-x86_64-devel, ubuntu-gcc-release, fedora-clang-devel, linux-x86_64-rocker-gcc-san, linux-x86_64-rocker-gcc-san and ubuntu-rchk without any success. How to reproduce the pre-test results in a windows environment? and how to fix this specific error? Regards, -- J.Aravind Scientist, Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi - 110 012 Email: j.arav...@icar.gov.in [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Reproducing CRAN pre-tests
On 19/09/2019 6:51 a.m., Aravind J. wrote: Hi, I am trying to submit an updated version of my package PGRdup to CRAN. The package has compiled code in C. I do development in a windows environment. The update was to fix issues in https://cran.r-project.org/web/checks/check_results_PGRdup.html. I have successfully fixed PCRE2 compatability issues and the issue with " ‘strncpy’ specified bound depends on the length of the source argument". For all instances of of strncpy I had changed the dependency on the length of the source argument to that of destination argument. On submission, now one issue remains with debian pre-test. /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] https://win-builder.r-project.org/incoming_pretest/PGRdup_0.2.3.4_20190919_090630/Debian/00check.log How to reproduce this error. I have tried rhub platforms windows-x86_64-devel, ubuntu-gcc-release, fedora-clang-devel, linux-x86_64-rocker-gcc-san, linux-x86_64-rocker-gcc-san and ubuntu-rchk without any success. How to reproduce the pre-test results in a windows environment? and how to fix this specific error? The install.out file points to the error here: fdouble_metaphone.c: In function ‘DoubleMetaphone’: fdouble_metaphone.c:271:33: note: length computed here 271 | strncpy(original->str, str, strlen(str) + 1); Presumably you need to limit the copy to the destination length. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Warning in system2(..., stdout = FALSE, stderr = FALSE) :, '"pdflatex"' not found
Update: A web search for 'installing pdflatex for "R CMD" on Windows
10?' suggested I install MiKTeX. I did that from miktex.org, and it got
me past that error. Spencer
On 2019-09-19 01:50, Spencer Graves wrote:
Hello, All:
What's the recommended way to get pdflatex installed on Windows
10 to run "R CMD"?
I ask, because "R CMD build bssm" under Windows 10 produced
'Warning in system2(..., stdout = FALSE, stderr = FALSE) : '"pdflatex"'
not found'.
This was after installing Rtools using the following (recommended
by
"https://thecoatlessprofessor.com/programming/cpp/installing-rtools-for-compiled-code-via-rcpp/";):
install.packages("installr")
library("installr")
install.Rtools()
Below please find the output in a commands window including
"sessionInfo()".
Thanks,
Spencer Graves
>R CMD build bssm
* checking for file 'bssm/DESCRIPTION' ... OK
* preparing 'bssm':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'bssm.Rmd' using rmarkdown
[WARNING] Note with key '1' defined at line 318 column 1 but not used.
Warning in system2(..., stdout = FALSE, stderr = FALSE) :
'"pdflatex"' not found
Error: processing vignette 'bssm.Rmd' failed with diagnostics:
Failed to compile bssm.tex. See https://yihui.name/tinytex/r/#debugging
for debugging tips.
--- failed re-building 'bssm.Rmd'
--- re-building 'growth_model.Rmd' using rmarkdown
Warning in system2(..., stdout = FALSE, stderr = FALSE) :
'"pdflatex"' not found
Error: processing vignette 'growth_model.Rmd' failed with diagnostics:
Failed to compile growth_model.tex. See
https://yihui.name/tinytex/r/#debugging for debugging tips.
--- failed re-building 'growth_model.Rmd'
SUMMARY: processing the following files failed:
'bssm.Rmd' 'growth_model.Rmd'
Error: Vignette re-building failed.
Execution halted
C:\Users\spenc\Documents\R\bssm\bssm>
C:\Users\spenc\Documents\R\bssm\bssm>pdflatex
'pdflatex' is not recognized as an internal or external command,
operable program or batch file.
C:\Users\spenc\Documents\R\bssm\bssm>r
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
Natural language support but running in an English locale
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.
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.1
[[alternative HTML version deleted]]
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Re: [R-pkg-devel] Warning in system2(..., stdout = FALSE, stderr = FALSE) :, '"pdflatex"' not found
On 9/19/19 6:29 AM, Spencer Graves wrote:
Update: A web search for 'installing pdflatex for "R CMD" on Windows
10?' suggested I install MiKTeX. I did that from miktex.org, and it
got me past that error. Spencer
Please note these things are documented in R Installation and
Administration Manual (see Appendix D)
Best
Tomas
On 2019-09-19 01:50, Spencer Graves wrote:
Hello, All:
What's the recommended way to get pdflatex installed on Windows
10 to run "R CMD"?
I ask, because "R CMD build bssm" under Windows 10 produced
'Warning in system2(..., stdout = FALSE, stderr = FALSE) : '"pdflatex"'
not found'.
This was after installing Rtools using the following (recommended
by
"https://thecoatlessprofessor.com/programming/cpp/installing-rtools-for-compiled-code-via-rcpp/";):
install.packages("installr")
library("installr")
install.Rtools()
Below please find the output in a commands window including
"sessionInfo()".
Thanks,
Spencer Graves
>R CMD build bssm
* checking for file 'bssm/DESCRIPTION' ... OK
* preparing 'bssm':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'bssm.Rmd' using rmarkdown
[WARNING] Note with key '1' defined at line 318 column 1 but not used.
Warning in system2(..., stdout = FALSE, stderr = FALSE) :
'"pdflatex"' not found
Error: processing vignette 'bssm.Rmd' failed with diagnostics:
Failed to compile bssm.tex. See https://yihui.name/tinytex/r/#debugging
for debugging tips.
--- failed re-building 'bssm.Rmd'
--- re-building 'growth_model.Rmd' using rmarkdown
Warning in system2(..., stdout = FALSE, stderr = FALSE) :
'"pdflatex"' not found
Error: processing vignette 'growth_model.Rmd' failed with diagnostics:
Failed to compile growth_model.tex. See
https://yihui.name/tinytex/r/#debugging for debugging tips.
--- failed re-building 'growth_model.Rmd'
SUMMARY: processing the following files failed:
'bssm.Rmd' 'growth_model.Rmd'
Error: Vignette re-building failed.
Execution halted
C:\Users\spenc\Documents\R\bssm\bssm>
C:\Users\spenc\Documents\R\bssm\bssm>pdflatex
'pdflatex' is not recognized as an internal or external command,
operable program or batch file.
C:\Users\spenc\Documents\R\bssm\bssm>r
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
Natural language support but running in an English locale
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.
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.1
[[alternative HTML version deleted]]
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Re: [R-pkg-devel] Warning in system2(..., stdout = FALSE, stderr = FALSE) :, '"pdflatex"' not found
On 2019-09-19 12:19, Tomas Kalibera wrote:
On 9/19/19 6:29 AM, Spencer Graves wrote:
Update: A web search for 'installing pdflatex for "R CMD" on Windows
10?' suggested I install MiKTeX. I did that from miktex.org, and it
got me past that error. Spencer
Please note these things are documented in R Installation and
Administration Manual (see Appendix D)
Thanks for documenting this. It's important to have that as part
of this thread.
I perhaps should have thought to look there, but I didn't. And
the web searches I tried didn't lead me there. Spencer
Best
Tomas
On 2019-09-19 01:50, Spencer Graves wrote:
Hello, All:
What's the recommended way to get pdflatex installed on Windows
10 to run "R CMD"?
I ask, because "R CMD build bssm" under Windows 10 produced
'Warning in system2(..., stdout = FALSE, stderr = FALSE) : '"pdflatex"'
not found'.
This was after installing Rtools using the following (recommended
by
"https://thecoatlessprofessor.com/programming/cpp/installing-rtools-for-compiled-code-via-rcpp/";):
install.packages("installr")
library("installr")
install.Rtools()
Below please find the output in a commands window including
"sessionInfo()".
Thanks,
Spencer Graves
>R CMD build bssm
* checking for file 'bssm/DESCRIPTION' ... OK
* preparing 'bssm':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'bssm.Rmd' using rmarkdown
[WARNING] Note with key '1' defined at line 318 column 1 but not used.
Warning in system2(..., stdout = FALSE, stderr = FALSE) :
'"pdflatex"' not found
Error: processing vignette 'bssm.Rmd' failed with diagnostics:
Failed to compile bssm.tex. See https://yihui.name/tinytex/r/#debugging
for debugging tips.
--- failed re-building 'bssm.Rmd'
--- re-building 'growth_model.Rmd' using rmarkdown
Warning in system2(..., stdout = FALSE, stderr = FALSE) :
'"pdflatex"' not found
Error: processing vignette 'growth_model.Rmd' failed with diagnostics:
Failed to compile growth_model.tex. See
https://yihui.name/tinytex/r/#debugging for debugging tips.
--- failed re-building 'growth_model.Rmd'
SUMMARY: processing the following files failed:
'bssm.Rmd' 'growth_model.Rmd'
Error: Vignette re-building failed.
Execution halted
C:\Users\spenc\Documents\R\bssm\bssm>
C:\Users\spenc\Documents\R\bssm\bssm>pdflatex
'pdflatex' is not recognized as an internal or external command,
operable program or batch file.
C:\Users\spenc\Documents\R\bssm\bssm>r
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
Natural language support but running in an English locale
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.
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.1
[[alternative HTML version deleted]]
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