[R] R crashes when loading library/package; Windows, Cygwin
Dear list members, This is a question is about building an R package under windows and cygwin. Please bear with me. I have a package in R that compiles well on my stationary computer (WINDOWS NT, R 1.8.1 and prior), and the resulting (package_version).zip file works well there. It contains an R script file and a C file. After installing tools to build the package on my laptop, the package builds successfully in the sense that both (a)rcmd build -binary -docs=normal cultosaurus and (b) R CMD BUILD -binary -docs=normal cultosaurus will successfully create a zipfile. (R version and compiler version below). When I install the package from the local zip file, R seems happy and says package 'cultosaurus' successfully unpacked and MD5 sums checked updating HTML package descriptions Trying to load the library, however, causes R to freeze for 10 seconds or so, without giving any message and then exit (Exit 5). A subset of this package with the C source file removed will successfully build, and successfully load. Then of course there will be an error saying C entry point ... not in load table Therefore the DLL seems to be causing this problem. Any hints or advice would be highly appreciated. Thanks in advance, Sixten version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor2.1 year 2005 month12 day 20 svn rev 36812 language R $ gcc -v Reading specs from /usr/lib/gcc/i686-pc-cygwin/3.4.4/specs Configured with: /gcc/gcc-3.4.4/gcc-3.4.4-1/configure --verbose --prefix=/usr -- exec-prefix=/usr --sysconfdir=/etc --libdir=/usr/lib --libexecdir=/usr/lib --man dir=/usr/share/man --infodir=/usr/share/info --enable-languages=c,ada,c++,d,f77, java,objc --enable-nls --without-included-gettext --enable-version-specific-runt ime-libs --without-x --enable-libgcj --disable-java-awt --with-system-zlib --ena ble-interpreter --disable-libgcj-debug --enable-threads=posix --enable-java-gc=b oehm --disable-win32-registry --enable-sjlj-exceptions --enable-hash-synchroniza tion --enable-libstdcxx-debug : (reconfigured) Thread model: posix gcc version 3.4.4 (cygming special) (gdc 0.12, using dmd 0.125) $ perl -v This is perl, v5.8.8 built for MSWin32-x86-multi-thread (with 21 registered patches, see perl -V for more detail) Copyright 1987-2006, Larry Wall Binary build 816 [255195] provided by ActiveState http://www.ActiveState.com Built Mar 1 2006 18:00:52 Output from building the package.__ $ make rcmd build -binary -docs=normal cultosaurus * checking for file 'cultosaurus/DESCRIPTION' ... OK * preparing 'cultosaurus': * checking DESCRIPTION meta-information ... OK * cleaning src * checking whether 'INDEX' is up-to-date ... OK * removing junk files * checking for LF line-endings in source files * checking for empty directories WARNING: directory cultosaurus/data is empty * building binary distribution WARNING * some HTML links may not be found installing R.css in c:/DOCUME~1/Sixten/LOKALA~1/Temp/Rinst.432 Using auto-selected zip options '' /bin/sh: latex: command not found /bin/sh: latex: command not found /bin/sh: latex: command not found -- Making package cultosaurus /bin/sh: latex: command not found adding build stamp to DESCRIPTION /bin/sh: latex: command not found /bin/sh: latex: command not found making DLL ... /bin/sh: latex: command not found /bin/sh: latex: command not found /bin/sh: latex: command not found making erectus.d from erectus.c gcc -Ic:/program/R/R-2.2.1/include -Wall -O2 -c erectus.c -o erectus.o ar cr cultosaurus.a erectus.o ranlib cultosaurus.a windres --include-dir c:/program/R/R-2.2.1/include -i cultosaurus_res.rc -o cul tosaurus_res.o gcc --shared -s -o cultosaurus.dll cultosaurus.def cultosaurus.a cultosaurus_r es.o -Lc:/program/R/R-2.2.1/src/gnuwin32 -lg2c -lR ... DLL made installing DLL /bin/sh: latex: command not found installing R files /bin/sh: latex: command not found /bin/sh: latex: command not found installing man source files installing indices installing help Building/Updating help pages for package 'cultosaurus' Formats: text html latex example sygehus texthtmllatex example missing link(s): ~~fun~~ /bin/sh: latex: command not found adding MD5 sums packaged installation of package 'cultosaurus' as cultosaurus_0.1.zip * DONE (cultosaurus) $ Sixten Borg IHE Box 2127 S-220 02 Lund Sweden tel: +46 46 32 91 07 fax:+46 46 12 16 04 Kommer man inte upp före klockan fyra på morgonen, så vaknar man inte på hela dan. www.ihe.se *** Note: The information contained in this message and attachments may be privileged and confidential and protected from
Re: [R] R crashes when loading library/package; Windows, Cygwin
On 3/24/2006 8:54 AM, Sixten Borg wrote: Dear list members, This is a question is about building an R package under windows and cygwin. Please bear with me. I have a package in R that compiles well on my stationary computer (WINDOWS NT, R 1.8.1 and prior), and the resulting (package_version).zip file works well there. It contains an R script file and a C file. After installing tools to build the package on my laptop, the package builds successfully in the sense that both (a)rcmd build -binary -docs=normal cultosaurus and (b) R CMD BUILD -binary -docs=normal cultosaurus will successfully create a zipfile. (R version and compiler version below). I think you're using a Cygwin compiler instead of the MinGW compiler, and that would likely cause the problem. You should see something like this $ gcc -v Reading specs from f:/minGW/bin/../lib/gcc/mingw32/3.4.4/specs Configured with: ../gcc/configure --with-gcc --with-gnu-ld --with-gnu-as --host= mingw32 --target=mingw32 --prefix=/mingw --enable-threads --disable-nls --enable -languages=c,c++,f77,ada,objc,java --disable-win32-registry --disable-shared --e nable-sjlj-exceptions --enable-libgcj --disable-java-awt --without-x --enable-ja va-gc=boehm --disable-libgcj-debug --enable-interpreter --enable-hash-synchroniz ation --enable-libstdcxx-debug Thread model: win32 gcc version 3.4.4 (mingw special) instead of the gcc version report that you were getting. You can get this compiler from mingw.org; it should come earlier in your path than the Cygwin compiler. Duncan Murdoch When I install the package from the local zip file, R seems happy and says package 'cultosaurus' successfully unpacked and MD5 sums checked updating HTML package descriptions Trying to load the library, however, causes R to freeze for 10 seconds or so, without giving any message and then exit (Exit 5). A subset of this package with the C source file removed will successfully build, and successfully load. Then of course there will be an error saying C entry point ... not in load table Therefore the DLL seems to be causing this problem. Any hints or advice would be highly appreciated. Thanks in advance, Sixten version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor2.1 year 2005 month12 day 20 svn rev 36812 language R $ gcc -v Reading specs from /usr/lib/gcc/i686-pc-cygwin/3.4.4/specs Configured with: /gcc/gcc-3.4.4/gcc-3.4.4-1/configure --verbose --prefix=/usr -- exec-prefix=/usr --sysconfdir=/etc --libdir=/usr/lib --libexecdir=/usr/lib --man dir=/usr/share/man --infodir=/usr/share/info --enable-languages=c,ada,c++,d,f77, java,objc --enable-nls --without-included-gettext --enable-version-specific-runt ime-libs --without-x --enable-libgcj --disable-java-awt --with-system-zlib --ena ble-interpreter --disable-libgcj-debug --enable-threads=posix --enable-java-gc=b oehm --disable-win32-registry --enable-sjlj-exceptions --enable-hash-synchroniza tion --enable-libstdcxx-debug : (reconfigured) Thread model: posix gcc version 3.4.4 (cygming special) (gdc 0.12, using dmd 0.125) $ perl -v This is perl, v5.8.8 built for MSWin32-x86-multi-thread (with 21 registered patches, see perl -V for more detail) Copyright 1987-2006, Larry Wall Binary build 816 [255195] provided by ActiveState http://www.ActiveState.com Built Mar 1 2006 18:00:52 Output from building the package.__ $ make rcmd build -binary -docs=normal cultosaurus * checking for file 'cultosaurus/DESCRIPTION' ... OK * preparing 'cultosaurus': * checking DESCRIPTION meta-information ... OK * cleaning src * checking whether 'INDEX' is up-to-date ... OK * removing junk files * checking for LF line-endings in source files * checking for empty directories WARNING: directory cultosaurus/data is empty * building binary distribution WARNING * some HTML links may not be found installing R.css in c:/DOCUME~1/Sixten/LOKALA~1/Temp/Rinst.432 Using auto-selected zip options '' /bin/sh: latex: command not found /bin/sh: latex: command not found /bin/sh: latex: command not found -- Making package cultosaurus /bin/sh: latex: command not found adding build stamp to DESCRIPTION /bin/sh: latex: command not found /bin/sh: latex: command not found making DLL ... /bin/sh: latex: command not found /bin/sh: latex: command not found /bin/sh: latex: command not found making erectus.d from erectus.c gcc -Ic:/program/R/R-2.2.1/include -Wall -O2 -c erectus.c -o erectus.o ar cr cultosaurus.a erectus.o ranlib cultosaurus.a windres --include-dir c:/program/R/R-2.2.1/include -i cultosaurus_res.rc -o cul tosaurus_res.o gcc
