[Rd] iconv.dll in Windows
I recently built R-devel on Windows XP (sessionInfo below), and when loading libraries that require the iconv.dll was getting an error stating that 'This application has failed to start because iconv.dll was not found. Re-installing the application may fix this problem.'. An R-2.8.1 that I installed using the Windows installer has this dll in R-2.8.1/bin, whereas in R-devel it is still in R-devel/src/gnuwin32/unicode. Moving the dll to R-devel/bin alleviates the problem. I built using the recent recommendations of P. Dalgaard (make Rpwd.exe, make link-recommended, make all recommended). I don't see anything in the NEWS for this version, but maybe I missed something? Best, Jim sessionInfo() R version 2.9.0 Under development (unstable) (2009-03-11 r48117) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] XML_1.99-0 -- James W. MacDonald, M.S. Biostatistician Douglas Lab 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] NAMESPACE/DESCRIPTION and imports
Hi, Could someone point me to the relevant documentation that covers what should be in the DESCRIPTION file for packages that have functions imported via the NAMESPACE file? I have read the R Extensions manual, but I cannot find where it covers the DESCRIPTION file vis a vis importing from a namespace. An example: I have a package foo that uses two functions x and y from package bar. Both packages have namespaces, and I just want to import the functions from bar rather than attaching the package. I put Imports: bar in my DESCRIPTION file and importFrom(bar, x, y) in my NAMESPACE file. I have a vignette that uses both x and y from bar, and when I run R CMD build foo, at the vignette building step it errors out because it cannot find function x. If I add Depends: bar to my DESCRIPTION file it all works, but bar is attached and it seems I have not accomplished what I wanted. I am obviously misunderstanding something but I don't know what. Best, Jim James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662 ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Is rcompgen still recommended?
I just built R-devel from source on OS X (Tiger), using the subversion sources. Running ./tools/rsync-recommended didn't download rcompgen. I checked http://cran.r-project/src/contrib/2.7.0/Recommended and indeed, this package is not there. If I try to install using install.packages I get install.packages(rcompgen, type=source) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://cran.fhcrc.org/src/contrib/rcompgen_0.1-17.tar.gz' Content type 'application/x-gzip' length 29240 bytes (28 Kb) opened URL == downloaded 28 Kb * Installing *source* package 'rcompgen' ... Error: Invalid DESCRIPTION file Invalid Priority field. Packages with priorities 'base' or 'recommended' or 'defunct-base' must already be known to R. See the information on DESCRIPTION files in section 'Creating R packages' of the 'Writing R Extensions' manual. Execution halted ERROR: installing package DESCRIPTION failed ** Removing '/Users/jmacdon/R-devel/library/rcompgen' The downloaded packages are in /private/tmp/Rtmpb0Refs/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(rcompgen, type = source) : installation of package 'rcompgen' had non-zero exit status I assume I am missing something obvious, but don't know what it is. Any pointers? Best, Jim sessionInfo() R version 2.7.0 Under development (unstable) (2008-02-18 r44516) i386-apple-darwin8.11.1 locale: C attached base packages: [1] stats graphics grDevices datasets utils methods base loaded via a namespace (and not attached): [1] tcltk_2.7.0 tools_2.7.0 -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Best practices - R CMD check and vignettes
Hi, I have a package that contains two vignettes that both use saved objects in the examples directory of the package. With previous versions of R I could have a code chunk in the vignette like this: echo=false= load(../examples/somedata.Rdata) @ followed by a code chunk like eval=false= foo - bar(data) @ that simulated the actual reading in of the data (I use a saved object to limit package size). This passed check with previous versions of R, but under R-2.6.0alpha, the vignettes are dumped into an inst directory in the package.Rcheck directory, where Sweave() and texi2dvi() are run. Unfortunately, the above code chunks no longer work. I can certainly hard code the first chunk to find the .Rdata file, but I have to imagine there is a much more elegant way to do this. Any suggestions? Best, Jim -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R from SVN fails to build on win32
I get the following error when building R from the subversion server as well as the latest tarball. I am on Windows XP, and I recently updated my MinGW installation. It's quite possible I am doing something wrong, but I am not sure what that might be. making console.d from console.c making dataentry.d from dataentry.c making dynload.d from dynload.c making edit.d from edit.c making editor.d from editor.c making embeddedR.d from embeddedR.c making extra.d from extra.c making opt.d from opt.c making pager.d from pager.c making preferences.d from preferences.c making psignal.d from psignal.c making rhome.d from rhome.c making rui.d from rui.c making run.d from run.c making shext.d from shext.c making sys-win32.d from sys-win32.c making system.d from system.c making dos_glob.d from dos_glob.c gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c console.c -o console.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c dataentry.c -o dataentry.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c dynload.c -o dynload.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c edit.c -o edit.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c editor.c -o editor.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c embeddedR.c -o embeddedR.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -DLEA_MALLOC -c extra.c -o extra.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c opt.c -o opt.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c pager.c -o pager.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c preferences.c -o preferences.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c psignal.c -o psignal.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c rhome.c -o rhome.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c rui.c -o rui.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c run.c -o run.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c shext.c -o shext.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c sys-win32.c -o sys-win32.o sys-win32.c: In function `do_system': sys-win32.c:183: warning: `hERR' might be used uninitialized in this function gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c system.c -o system.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c dos_glob.c -o dos_glob.o gcc -c -o e_pow.o e_pow.S gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c malloc.c -o malloc.o windres -I ../include -i dllversion.rc -o dllversion.o c:\MinGW\bin\windres.exe: unknown format type `../include' c:\MinGW\bin\windres.exe: supported formats: rc res coff make[3]: *** [dllversion.o] Error 1 make[2]: *** [../../bin/R.dll] Error 2 make[1]: *** [rbuild] Error 2 make: *** [all] Error 2 Best, Jim James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Build error/zlib question
Hi, I am unable to build a package I maintain using a relatively current build of R-2.4.0 alpha, whereas the package builds just fine on R-2.3.1. Both versions of R were built from source. I'm hoping a guRu might be able to give some help. Some snippets from the build process: R-2.3.1 making DLL ... gcc -Ic:/R-2.3.1/src/extra/zlib -DHAVE_ZLIB -Ic:/R-2.3.1/include -Wall -O2 -c read_cdffile.c -o read_cdffile.o read_cdffile.c: In function `readQC': read_cdffile.c:565: warning: unused variable `param_unit' windres --include-dir c:/R-2.3.1/include -i makecdfenv_res.rc -o makecdfenv_res.o gcc -shared -s -o makecdfenv.dll makecdfenv.def read_cdffile.o makecdfenv_res.o -Lc:/R-2.3.1/bin -lR ... DLL made R-2.4.0 beta making DLL ... gcc -Ic:/rw2040dev/src/extra/zlib -DHAVE_ZLIB -Ic:/rw2040dev/include -Wall -O2 -std=gnu99 -c read_cdffile.c -o read_cdffile.o read_cdffile.c: In function `readQC': read_cdffile.c:565: warning: unused variable `param_unit' windres --include-dir c:/rw2040dev/include -i makecdfenv_res.rc -o makecdfenv_res.o gcc -shared -s -o makecdfenv.dll makecdfenv.def read_cdffile.o makecdfenv_res.o -Lc:/rw2040dev/bin -lR read_cdffile.o:read_cdffile.c:(.text+0x42): undefined reference to `gzgets' read_cdffile.o:read_cdffile.c:(.text+0xf3): undefined reference to `gzopen' read_cdffile.o:read_cdffile.c:(.text+0x10f): undefined reference to `gzgets' read_cdffile.o:read_cdffile.c:(.text+0x140): undefined reference to `gzrewind' read_cdffile.o:read_cdffile.c:(.text+0x177): undefined reference to `gzclose' collect2: ld returned 1 exit status make[3]: *** [makecdfenv.dll] Error 1 make[2]: *** [srcDynlib] Error 2 make[1]: *** [all] Error 2 make: *** [pkg-makecdfenv] Error 2 version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status alpha major 2 minor 4.0 year 2006 month 09 day10 svn rev39242 language R version.string R version 2.4.0 alpha (2006-09-10 r39242) TIA, Jim James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Segfault with too many menu items on Rgui
Hi all, In the CHANGES file for R-2.3.0alpha, there is the following statement: winMenuAdd() now has no limits on the number of menus or items, and names are now limited to 500 (not 50) bytes. However, I can reproducibly get a segfault using this (admittedly silly) example: for( i in 1:5) winMenuAdd(paste(Test, letters[i], sep=)) for(i in 1:5) for(j in 1:24) winMenuAddItem(paste(Test, letters[i], sep=), as.character(j), paste(rep(letters[j], 4), collapse=)) This is probably almost never a problem, but many Bioconductor packages have vignettes that are added to a 'Vignettes' menu item. If you load enough of these packages you will get a segfault. version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status alpha major 2 minor 3.0 year 2006 month 03 day29 svn rev37607 language R version.string Version 2.3.0 alpha (2006-03-29 r37607) Best, Jim James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Using .onUnload() to unload compiled code
If one wants to unload compiled code for a package containing a namespace, my understanding is that .onUnload() should be used, with a call to library.dynam.unload(). This is used in e.g., the stats and methods packages, but it appears to me that the compiled code is not being unloaded when the package is detached(). Am I misunderstanding something? Best, Jim search() [1] .GlobalEnvpackage:methods package:stats package:graphics [5] package:grDevices package:utils package:datasets Autoloads [9] package:base stats:::.onUnload function (libpath) library.dynam.unload(stats, libpath) environment: namespace:stats getLoadedDLLs() Filename Dynamic.Lookup base base FALSE iconvC:/rw2030dev/modules/iconv.dll TRUE grDevices C:/rw2030dev/library/grDevices/libs/grDevices.dll FALSE stats C:/rw2030dev/library/stats/libs/stats.dll FALSE methods C:/rw2030dev/library/methods/libs/methods.dll FALSE detach(3) search() [1] .GlobalEnvpackage:methods package:graphics package:grDevices [5] package:utils package:datasets Autoloads package:base getLoadedDLLs() Filename Dynamic.Lookup base base FALSE iconvC:/rw2030dev/modules/iconv.dll TRUE grDevices C:/rw2030dev/library/grDevices/libs/grDevices.dll FALSE stats C:/rw2030dev/library/stats/libs/stats.dll FALSE methods C:/rw2030dev/library/methods/libs/methods.dll FALSE R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status Under development (unstable) major 2 minor 3.0 year 2006 month 01 day01 svn rev36947 language R version.string Version 2.3.0 Under development (unstable) (2006-01-01 r36947) James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
