From hpages at fhcrc.org  Sat Sep 25 09:32:17 2010
From: hpages at fhcrc.org (=?ISO-8859-1?Q?Herv=E9_Pag=E8s?=)
Date: Sat, 25 Sep 2010 00:32:17 -0700
Subject: [Rd] running 'make' failed during vignette creation ('R CMD
 build') on Windows
In-Reply-To: <4C91BA56.6040209@fhcrc.org>
References: <4C915CF1.9020304@fhcrc.org> <4C91BA56.6040209@fhcrc.org>
Message-ID: <4C9DA581.6090602@fhcrc.org>

This fixed in current R-alpha (r52991) too. Thanks!

H.


On 09/15/2010 11:33 PM, Herv? Pag?s 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, Herv? Pag?s 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.
>>
>>
>
>


-- 
Herv? Pag?s

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: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] running 'make' failed during vignette creation ('R CMD build') on Windows
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