[R-pkg-devel] Warning in system2(..., stdout = FALSE, stderr = FALSE) :, '"pdflatex"' not found
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
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Re: [R-pkg-devel] unable to run 'make clean' in 'src'
Hi, Georgi et al.:
Thanks to Georgi, I changed my path. That led me to a different
error. A search for the new error led me to:
https://thecoatlessprofessor.com/programming/cpp/installing-rtools-for-compiled-code-via-rcpp/
That recommended:
install.packages("installr")
library("installr")
install.Rtools()
I uninstalled Rtools, then installed them using this, and that
problem disappeared. Now I'm dealing with '"pdflatex" not found". I'll
discuss that in a new thread.
Thanks,
Spencer Graves
On 2019-09-18 06:30, Georgi Boshnakov wrote:
I don't know about Windows 10 but I think that the pointers to Rtools need to
be to the bin subdirectory. Also, it is prudent to have these at the beginning
of the search path, e.g.
PATH=c:\Rtools\bin;c:\Rtools\mingw_64\bin;c:\ProgramF\R\R-3.6.0patched\bin;
I am not sure if the entry for ming_w64 above is (still) needed.
Georgi Boshnakov
-Original Message-
From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf
Of Spencer Graves
Sent: 18 September 2019 07:47
To: R Package Development
Subject: [R-pkg-devel] unable to run 'make clean' in 'src'
Hello:
"R CMD build bssm" complains:
unable to run 'make clean' in 'src'
This is on a Windows 10 computer with R 3.6.1 installed with, I
think, Rtools35.exe. "sessionInfo()" says, "Platform:
x86_64-w64-mingw32/x64 (64-bit)".
This is trying to build a local clone of
"https://github.com/sbgraves237/bssm";, which is only slightly different
from "helske/bssm".
What do you suggest?
Thanks,
Spencer Graves
p.s.
"https://stackoverflow.com/questions/28723882/problems-installing-development-package-from-either-github-or-local#28724622";
documents a discussion of this message from 2015. It asks if "Rtools is
in your PATH?" The "path" includes "C:\RBuildTools\3.5" and "C:\Program
Files\R\R3.6.1\bin" plus other non-R stuff. That discussion also said,
"The .o files in the src directory were messing things up." bssm/src
does not contain any *.o files.
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Re: [R-pkg-devel] script translation - good practice?
Yes. Check out https://www.gnu.org/licenses/license-list.en.html#GPLCompatibleLicenses and also note that CC-BY is not recommended as a software license (by CC themselves). As there is one-way compatibility, it should be possible to clarify the situation by putting your derivative work under the GPL. Although not legally required, it would probably be good manners to inform the original authors. -pd > On 18 Sep 2019, at 14:20 , Raphael Bonnet > wrote: > > Thank you Peter for your response, > > It looks ok for the license. The journal's content appears to be under this > license: > https://creativecommons.org/licenses/by/3.0/ > > Raphael > > Le 18/09/2019 à 14:11, peter dalgaard a écrit : >> Not a lawyer, but... >> >> I would expect that it depends on what license it was published under >> originally. If it doesn't explicitly allow the creation of derivative works, >> then I would be wary. >> >> -pd >> >>> On 18 Sep 2019, at 13:59 , Raphael Bonnet >>> wrote: >>> >>> Hi everyone, >>> >>> I just rewrote a bit of Matlab code into R and that I would like to make it >>> available for the community. >>> Unfortunately this bit of code has been published by authors that I've >>> never contacted. >>> >>> I was wondering if I could submit a package to CRAN by keeping the same >>> license as the journal in which the code was published and citing the paper >>> and the authors. >>> Can I associate myself as [cre, trl] in the description file? >>> >>> Thanks, >>> Raphael >>> >>> __ >>> R-package-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel > -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] script translation - good practice?
Thank you Peter for your response, It looks ok for the license. The journal's content appears to be under this license: https://creativecommons.org/licenses/by/3.0/ Raphael Le 18/09/2019 à 14:11, peter dalgaard a écrit : Not a lawyer, but... I would expect that it depends on what license it was published under originally. If it doesn't explicitly allow the creation of derivative works, then I would be wary. -pd On 18 Sep 2019, at 13:59 , Raphael Bonnet wrote: Hi everyone, I just rewrote a bit of Matlab code into R and that I would like to make it available for the community. Unfortunately this bit of code has been published by authors that I've never contacted. I was wondering if I could submit a package to CRAN by keeping the same license as the journal in which the code was published and citing the paper and the authors. Can I associate myself as [cre, trl] in the description file? Thanks, Raphael __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] script translation - good practice?
Not a lawyer, but... I would expect that it depends on what license it was published under originally. If it doesn't explicitly allow the creation of derivative works, then I would be wary. -pd > On 18 Sep 2019, at 13:59 , Raphael Bonnet > wrote: > > Hi everyone, > > I just rewrote a bit of Matlab code into R and that I would like to make it > available for the community. > Unfortunately this bit of code has been published by authors that I've never > contacted. > > I was wondering if I could submit a package to CRAN by keeping the same > license as the journal in which the code was published and citing the paper > and the authors. > Can I associate myself as [cre, trl] in the description file? > > Thanks, > Raphael > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] script translation - good practice?
Hi everyone, I just rewrote a bit of Matlab code into R and that I would like to make it available for the community. Unfortunately this bit of code has been published by authors that I've never contacted. I was wondering if I could submit a package to CRAN by keeping the same license as the journal in which the code was published and citing the paper and the authors. Can I associate myself as [cre, trl] in the description file? Thanks, Raphael __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] unable to run 'make clean' in 'src'
I don't know about Windows 10 but I think that the pointers to Rtools need to be to the bin subdirectory. Also, it is prudent to have these at the beginning of the search path, e.g. PATH=c:\Rtools\bin;c:\Rtools\mingw_64\bin;c:\ProgramF\R\R-3.6.0patched\bin; I am not sure if the entry for ming_w64 above is (still) needed. Georgi Boshnakov -Original Message- From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf Of Spencer Graves Sent: 18 September 2019 07:47 To: R Package Development Subject: [R-pkg-devel] unable to run 'make clean' in 'src' Hello: "R CMD build bssm" complains: unable to run 'make clean' in 'src' This is on a Windows 10 computer with R 3.6.1 installed with, I think, Rtools35.exe. "sessionInfo()" says, "Platform: x86_64-w64-mingw32/x64 (64-bit)". This is trying to build a local clone of "https://github.com/sbgraves237/bssm";, which is only slightly different from "helske/bssm". What do you suggest? Thanks, Spencer Graves p.s. "https://stackoverflow.com/questions/28723882/problems-installing-development-package-from-either-github-or-local#28724622"; documents a discussion of this message from 2015. It asks if "Rtools is in your PATH?" The "path" includes "C:\RBuildTools\3.5" and "C:\Program Files\R\R3.6.1\bin" plus other non-R stuff. That discussion also said, "The .o files in the src directory were messing things up." bssm/src does not contain any *.o files. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Help
Hello, I' have just tried to submit a package to CRAN which has a Bioconductor dependency. I import "GeneticsPed" in my package but when installing it, have this error: ERROR: dependency 'GeneticsPed' is not available for package 'LRQMM' * removing 'C:/Users/.../LRQMM'. or this check: https://cran.um.ac.ir/web/checks/check_results_LRQMM.html I tried "biocViews " in description file with empty form, but not been succeed. How can i solving this problem? Thanks. Sayyed Reza Alavian [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
