search for: buildvignett

I am currently writing a (private) package in which I produce pdf files from within R using LaTeX. To do so I mainly copied some lines from the buildVignettes() function in the tools package. This uses the texi2dvi which is included in R's bin directory: system(paste(file.path(R.home(), "bin", "texi2dvi"), "--quiet --pdf", bft)) This runs fine on Linux and I assumed that as it is included in buildV...

Dear All, I have been checking the metafor package against R-devel. R CMD check --as-cran metafor yields one note: FOSS licence with BuildVignettes: false Yes, I have 'BuildVignettes: FALSE' in my DESCRIPTION file. I see at http://developer.r-project.org/blosxom.cgi/R-devel/NEWS: Tue, 25 Jun 2013 CHANGES IN R-devel UTILITIES 'R CMD check --as-cran' warns about a false value of the 'DESCRIPTION' field 'Build...

I have packages where I know CRAN and other test platforms do not have all the resources to build the vignettes, for example, access to databases. Previously I think putting BuildVignettes: false in the DESCRIPTION file resolved this, by preventing CRAN checks from attempting to run the vignette code. (If it was not this, then there was some other magic I don't understand.) Now, when I specify --as-cran, the checks fail when attempting to check R code from vignettes, even...

...Sys.getenv("TEXINPUTS") | R\bin\R.exe --slave TEXINPUTS ".;;E:/biocbld/bbs-2.7-bioc/R/share/texmf/tex/latex;" So on Linux if I cd to the inst/doc folder of a package source tree that has a Makefile and run echo "tools:::buildVignettes('pkgname', '.')" | R --slave it fails with error: ! LaTeX Error: File `Sweave.sty' not found. while doing the same thing on Windows works. Is there any reason for not setting the environments variables that are defined in ${R_HOME}/bin/Rcmd (the shell script wrappe...

Dear all, When running function 'testQAReport()', which uses function 'buildVignettes()' to create a pdf-file I get the following error: > source("testQAReport.R") > testQAReport() Error in .get_package_metadata(pkgdir) : Files 'DESCRIPTION' and 'DESCRIPTION.in' are missing. Since I did not get this error in earlier versions of R, could y...

...ions" document step by step, but went I run "Rcmd build", an error occurs. It goes like this: " * creating vignettes ... ERROR . . . . :7: Emergency stop L7L ==> Fatal error occurred, no output PDF file produced!texify: pdflatex failed for some reason <see log file>. buildVignettes<dir ='. '> Error in texi2dvi<fil =bft,pdf =TRUE, clean =FALSE, quiet = quiest > : running 'texi2dvi' on "test.tex' failed Calls : buildVignettes -> texi2dvi Execution halted " Thank you for your help! Francois Aucoin [[alternative HTML version del...

...UN = f, ..., SIMPLIFY = FALSE) : invalid primitive operation given for dispatch Execution halted I have not been able to reproduce this on other systems, but the basic approach to a simpler reproducible example is to install the DirichletMultinomial Bioconductor package and then > tools::buildVignettes(dir="DirichletMultinomial") where the 'dir' argument points to the uncompressed tarball. There is C code in the package, but not reached by this code chunk. Attempts to simplify the code generally results in the error disappearing. R -d valgrind -e "tools::buildVignette...

In a package 'vig' R CMD build vig (or tools::buildVignettes(dir="vig") with $ cat vig/vignettes/vig1.Rnw \documentclass{article} \begin{document} <<>>= x <- 1 @ \end{document} $ cat vig/vignettes/vig2.Rnw \documentclass{article} \begin{document} <<>>= x @ \end{document} produces vig2.pdf where x is defined with valu...

...mkdir -pv /usr/lib/R/library/$PK/html # copy description (which contains version number) and CONTENTS (for index) cp $PK/DESCRIPTION /usr/lib/R/library/$PK # build and move vignettes if present if [ -d $PK/inst/doc ]; then mkdir -pv /usr/lib/R/library/$PK/doc R CMD buildVignettes\($PK,$PK\) cp $PK/inst/doc/* /usr/lib/R/library/$PK/doc fi # make html files R CMD perl /usr/share/R/perl/build-help.pl --html /home/baron/$PK /usr/lib/R/library rm -rf $PK done # rebuild indices (doesn't work) R CMD make.packages.html

...> * cleaning src > * installing the package to process help pages > * saving partial Rd database > * creating vignettes ...sh: line 1: 16259 Segmentation fault (core dumped) '/u/maechler/R/D/r-devel/inst/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpV1grVw/xshell3e793c7d5258' 2>&1 > ERROR > > *** caught segfault *** > address 0x1, cause 'memory not mapped' > > Traceback: > 1: .Call(C_stri_locate_all_regex, str, pattern, omit...

I am resubmitting this bug report but with additional information. I am running this with windows 10: w64-mingw32 with R Under development (unstable) (2017-12-04 r73829). I build 'httk' from the command prompt using 'R CMD build httk' after installing the required packages. Then when the vignettes are being created, it crashes. Today I installed the latest versions of Rtools,

A new problem has cropped up with compiling vignettes for my package BayesFactor. I'm not sure when it started, but I can tell you it didn't occur on R 2.15.3, and it does on 3.0.0 RC (2013-03-31 r62463) (session info is at the bottom of this message). I have defined methods for which.min and which.max for a class (I've defined both S3 and S4 methods for the class

Hello, I'm trying to rebuild a package (using R version 3.3.2 (2016-10-31)) that has not seen any changes since it was last built without problems in previous R versions. It fails during vignette building with: ---<--------------------cut here---------------start------------------->--- $ R CMD build diveMove * checking for file ?diveMove/DESCRIPTION? ... OK * preparing ?diveMove?: *

...meta-information ... OK * cleaning src * installing the package to process help pages * saving partial Rd database * creating vignettes ...sh: line 1: 16259 Segmentation fault (core dumped) '/u/maechler/R/D/r-devel/inst/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpV1grVw/xshell3e793c7d5258' 2>&1 ERROR *** caught segfault *** address 0x1, cause 'memory not mapped' Traceback: 1: .Call(C_stri_locate_all_regex, str, pattern, omit_no_match, opts_regex) 2: stri_locate...

...t;> * installing the package to process help pages >> * saving partial Rd database >> * creating vignettes ...sh: line 1: 16259 Segmentation fault >> (core dumped) '/u/maechler/R/D/r-devel/inst/bin/Rscript' --vanilla >> --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > >> '/tmp/RtmpV1grVw/xshell3e793c7d5258' 2>&1 >> ERROR >> >> *** caught segfault *** >> address 0x1, cause 'memory not mapped' >> >> Traceback: >> 1: .Call(C_stri_l...

...;R CMD build', but the error can be reproduced with other means, as outlined below. When trying to build the vignette from the git version of your package (as part of R CMD build), I see the same error message. Investigating further, the "tangled" file diveMove.R from 'tools::buildVignette("diveMove.Rnw")' has 68 lines and stops short of the code chunk "zoc" where the error occurs. Running that code obviously works fine. However, 'tools::buildVignette("diveMove.Rnw", weave = FALSE)' outputs a longer (154 lines) diveMove.R (presumably con...

Hi, I have the following error when building a package * creating vignettes ... ERROR Error: chunk 3 Error in pmatch(x, table, duplicates.ok) : argument is not of mode character Error in buildVignettes(dir = ".") : Error: chunk 3 Error in pmatch(x, table, duplicates.ok) : argument is not of mode character Execution halted I use R-2.0.1 under debian linux 2.6.9 Thanks for any idea Philippe -- Philippe Hup? UMR 144 - Service Bioinformatique Institut Curie Laboratoire de...

...s, > Sys.getenv("MAKE") MAKE "" when (at a DOS prompt) X:>set MAKE Environment variable MAKE not defined On linux, > Sys.getenv("MAKE") MAKE "make" even when (in a shell) % echo $MAKE returns nothing. This has consequences, e.g., in buildVignette where system(Sys.getenv("MAKE")) dutifully does nothing on Windows, but evaluates the vignette Makefile on linux. > sessionInfo() R version 2.4.0 Under development (unstable) (2006-06-08 r38315) i386-pc-mingw32 > sessionInfo() R version 2.4.0 Under development (unstable) (2006-...

...#39; does not exist' error. (For any value of 'foo', even the default 'RweaveLatex'.) Looking up the source code for function .Sweave that is called by 'R CMD Sweave', I notice that the argument 'driver', if used, is added to the vector of arguments of ''buildVignette' without being named. It ends up being passed to argument 'dir', hence rhe error. I believe the simple patch below should fix the issue, but I wasn't able to test it. Hope this helps. v. Vincent Goulet Professeur titulaire ?cole d'actuariat, Universit? Laval Index: src/li...

...ook/delia.R [...] ${R} --vanilla --verbose < ${SUITE} the output of trying to build this package includes: * creating vignettes ... ERROR E:\biocbld\BBS-2~1.8-B\R/bin/R --vanilla --verbose < ../cookbook/delia.R E:biocbldBBS-2~1.8-BR/bin/R: not found make: *** [pdf] Error 127 Error in tools::buildVignettes(dir = ".") : running 'make' failed Execution halted It seems R_HOME is not getting resolved to a valid path. That's strange because R CMD echo shows the right thing: E:\sandbox>\biocbld\bbs-2.8-bioc\R\bin\R CMD echo %R_HOME% e:/biocbld/bbs-2.8-bioc/R That's a nice...