This fixed in current R-alpha (r52991) too. Thanks! H.
On 09/15/2010 11:33 PM, Hervé Pagès wrote:
I think I found the problem. During the recent transition from Perl-based to R-based 'R CMD check/build', the rcmdfn() function in src/gnuwin32/front-ends/rcmdfn.c has been hacked quite a bit. This function gets called right after the R front-end is started and its main purpose is to process the user arguments passed to the front-end and to fire the appropriate subprocess. This function also calls process_Renviron() for putting the variables defined in ${R_HOME}/etc/rcmd_environ into the environment of the front-end process. Problem: before revision 52153 this code ... } else if (strcmp(p, "build") == 0) { snprintf(cmd, CMD_LEN, "perl %s/bin/build.pl", RHome); } ... was *after* this line process_Renviron(env_path); But starting with rev 52153, it was moved *before* the call to process_Renviron() (and also modified to handle Rcmd build internally). The new code looks more complicated: ... } else if (cmdarg > 0 && argc > cmdarg && strcmp(argv[cmdarg], "build") == 0) { /* handle Rcmd build internally */ snprintf(cmd, CMD_LEN, "%s/%s/Rterm.exe -e tools:::.build_packages() R_DEFAULT_PACKAGES= LC_COLLATE=C --no-restore --slave --args ", getRHOME(3), BINDIR); for (i = cmdarg + 1; i < argc; i++) { strcat(cmd, "nextArg"); if (strlen(cmd) + strlen(argv[i]) > 9900) { fprintf(stderr, "command line too long\n"); return(27); } strcat(cmd, argv[i]); } status = system(cmd); return(status); } else { ... but basically, it still fires a subprocess and then the function returns. process_Renviron() was not called so the subprocess doesn't see those environment variables anymore. Then the same happened to 'R CMD build' (rev 52245), and to many other 'R CMD things': their corresponding code chunks in rcmdfn() went moved up one by one to end up before the call to process_Renviron(). So none of the 'R CMD' subcommands sees the environment variables that they used to see anymore. Only a normal 'R' command still gets them. Cheers, H. On 09/15/2010 04:55 PM, Hervé Pagès wrote:Hi, This is a follow-up to the problem reported here: https://stat.ethz.ch/pipermail/r-devel/2010-September/058460.html After I updated R-2.12 to 2010-09-13 r52905 on the Bioc build system, some of the packages that have a Makefile in <pkg>/inst/doc still don't build on Windows. For example, 'R\bin\R.exe CMD build adSplit' gives: * checking for file 'adSplit/DESCRIPTION' ... OK * preparing 'adSplit': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes * creating vignettes ... ERROR Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: DBI Loading required package: hu6800.db Loading required package: AnnotationDbi Loading required package: org.Hs.eg.db determining 1000 random DLD-scores with 20 probe sets each (wait for 10 dots) .......... epstopdf splitSet.eps pdflatex tr_2005_02 This is pdfTeX, Version 3.1415926-1.40.9 (MiKTeX 2.7) entering extended mode (tr_2005_02.tex LaTeX2e <2009/09/24> Babel <v3.8l> and hyphenation patterns for english, dumylang, nohyphenation, ge rman, ngerman, french, loaded. ("C:\Program Files\MiKTeX 2.7\tex\latex\base\report.cls" Document Class: report 2007/10/19 v1.4h Standard LaTeX document class ("C:\Program Files\MiKTeX 2.7\tex\latex\base\size11.clo")) (compdiag.sty ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\ifpdf.sty") ("C:\Program Files\MiKTeX 2.7\tex\latex\graphics\graphicx.sty" ("C:\Program Files\MiKTeX 2.7\tex\latex\graphics\keyval.sty") ("C:\Program Files\MiKTeX 2.7\tex\latex\graphics\graphics.sty" ("C:\Program Files\MiKTeX 2.7\tex\latex\graphics\trig.sty") ("C:\Program Files\MiKTeX 2.7\tex\latex\00miktex\graphics.cfg") ("C:\Program Files\MiKTeX 2.7\tex\latex\pdftex-def\pdftex.def"))) ("C:\Program Files\MiKTeX 2.7\tex\latex\graphics\color.sty" ("C:\Program Files\MiKTeX 2.7\tex\latex\00miktex\color.cfg")) ("C:\Program Files\MiKTeX 2.7\tex\latex\hyperref\hyperref.sty" ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\ltxcmds.sty") ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\kvsetkeys.sty" ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\infwarerr.sty") ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\etexcmds.sty")) ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\pdfescape.sty" ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\pdftexcmds.sty" ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\ifluatex.sty"))) ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\ifvtex.sty") ("C:\Program Files\MiKTeX 2.7\tex\latex\ifxetex\ifxetex.sty") ("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\hycolor.sty" ("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\xcolor-patch.sty")) ("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\letltxmacro.sty") ("C:\Program Files\MiKTeX 2.7\tex\latex\hyperref\pd1enc.def") ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\intcalc.sty") ("C:\Program Files\MiKTeX 2.7\tex\latex\00miktex\hyperref.cfg") ("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\kvoptions.sty") Implicit mode ON; LaTeX internals redefined ("C:\Program Files\MiKTeX 2.7\tex\latex\ltxmisc\url.sty") ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\bitset.sty" ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\bigintcalc.sty")) ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\atbegshi.sty")) * hyperref using driver hpdftex * ("C:\Program Files\MiKTeX 2.7\tex\latex\hyperref\hpdftex.def" ("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\atveryend.sty") ("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\rerunfilecheck.sty" ("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\uniquecounter.sty"))) ("C:\Program Files\MiKTeX 2.7\tex\latex\ntgclass\a4.sty") ("C:\Program Files\MiKTeX 2.7\tex\latex\geometry\geometry.sty" ("C:\Program Files\MiKTeX 2.7\tex\latex\geometry\geometry.cfg")) ("C:\Program Files\MiKTeX 2.7\tex\latex\tools\theorem.sty" ("C:\Program Files\MiKTeX 2.7\tex\latex\tools\thp.sty")) ("C:\Program Files\MiKTeX 2.7\tex\latex\tools\thb.sty")) ("C:\Program Files\MiKTeX 2.7\tex\latex\ams\math\amsmath.sty" For additional information on amsmath, use the `?' option. ("C:\Program Files\MiKTeX 2.7\tex\latex\ams\math\amstext.sty" ("C:\Program Files\MiKTeX 2.7\tex\latex\ams\math\amsgen.sty")) ("C:\Program Files\MiKTeX 2.7\tex\latex\ams\math\amsbsy.sty") ("C:\Program Files\MiKTeX 2.7\tex\latex\ams\math\amsopn.sty")) ! LaTeX Error: File `Sweave.sty' not found. Type X to quit or <RETURN> to proceed, or enter new name. (Default extension: sty) Enter file name: ! Emergency stop. <read *> l.39 \begin {document} ! ==> Fatal error occurred, no output PDF file produced! Transcript written on tr_2005_02.log. make: *** [pdf] Error 1 Error in tools::buildVignettes(dir = ".") : running 'make' failed Execution halted What's different though with this updated R, it that now I get an error instead of a timeout. Maybe the code that fires the R subprocess in charge of running tools::buildVignettes() now does better error checking/handling, I don't know (it seems to have changed between the 2 versions of R). A new mystery is why the tilingArray package now does build on Windows (it was timing out with the previous version of R). I already sent the content of adSplit/inst/doc/Makefile in the previous thread and tilingArray does nothing different: all: findsegments costMatrix assessNorm segmentation plotAlongChrom clean findsegments: findsegments.tex pdflatex findsegments pdflatex findsegments costMatrix: costMatrix.tex pdflatex costMatrix pdflatex costMatrix assessNorm: assessNorm.tex cp -p ../scripts/assessNorm.pdf . segmentation: segmentation.tex cp -p ../scripts/segmentation.pdf . plotAlongChrom: plotAlongChrom.tex pdflatex plotAlongChrom pdflatex plotAlongChrom clean: rm -f *.out *.bbl *.log *.aux *.blg *.brf *.toc *.tex rm -f *.dvi *.ps findsegments-* costMatrix-* plotAlongChrom-* Rplots.pdf Another thing that is really puzzling is that if I cd to adSplit/inst/doc and run 'R CMD make' then it works. Any help/comment on this will be highly appreciated. Thanks, H.
-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
