Compilation or syntax error in IRanges sort_util.c package
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@michael-dondrup-3376
Last seen 7.9 years ago
Dear list, I'm trying to install Bioconductor on Solaris using the SunWPro-12 compilers. cc: Sun C 5.9 SunOS_i386 Patch 124868-08 2008/11/25 > biocLite('IRanges') Running biocinstall version 2.3.10 with R version 2.8.1 Your version of R requires version 2.3 of Bioconductor. trying URL 'http://bioconductor.org/packages/2.3/bioc/src/contrib/IRan ges_1.0.14.tar.gz' Content type 'application/x-gzip' length 175687 bytes (171 Kb) [snip] cc -xc99 -I/homes/mdondrup/bin/R-2.8.1//lib/R/include -I/opt/SUNWspro/include/ -I/vol/tcl-8.4.13/include -I/vol/local/include -I/vol/graphics/include -I/vol/gnu/include -KPIC -g -c solve_user_SEW.c -o solve_user_SEW.o cc -xc99 -I/homes/mdondrup/bin/R-2.8.1//lib/R/include -I/opt/SUNWspro/include/ -I/vol/tcl-8.4.13/include -I/vol/local/include -I/vol/graphics/include -I/vol/gnu/include -KPIC -g -c sort_utils.c -o sort_utils.o "sort_utils.c", line 18: void function cannot return value cc: acomp failed for sort_utils.c make: *** [sort_utils.o] Error 2 ERROR: compilation failed for package 'IRanges' ** Removing '/homes/mdondrup/bin/R-2.8.1/lib/R/library/IRanges' The downloaded packages are in /tmp/1101064.1.interactive.q/RtmpML0kk8/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'IRanges' had non-zero exit status Looking into sort_utils.c line 18 shows that this is the error: A void funtion trying to return something. void _sort_int_array(int *x, int x_nelt) { return qsort(x, x_nelt, sizeof(int), cmpintp); } I do not know why this works with gcc by the way but for me just removing the "return" void _sort_int_array(int *x, int x_nelt) { qsort(x, x_nelt, sizeof(int), cmpintp); } makes the package compilable. I hope that no return value is ever needed somewhere .... Could you devise a patch to make bioconductor installation possible from the repository? Thanks Michael > version _ platform i386-pc-solaris2.10 arch i386 os solaris2.10 system i386, solaris2.10 status Patched major 2 minor 8.1 year 2009 month 03 day 18 svn rev 48212 language R version.string R version 2.8.1 Patched (2009-03-18 r48212) >
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@michael-lawrence-2759
Last seen 7.9 years ago
On Tue, Mar 31, 2009 at 2:21 AM, Michael Dondrup < mdondrup@cebitec.uni-bielefeld.de> wrote: > Dear list, > > I'm trying to install Bioconductor on Solaris using the SunWPro-12 > compilers. > cc: Sun C 5.9 SunOS_i386 Patch 124868-08 2008/11/25 > > > > biocLite('IRanges') > Running biocinstall version 2.3.10 with R version 2.8.1 > Your version of R requires version 2.3 of Bioconductor. > trying URL ' > http://bioconductor.org/packages/2.3/bioc/src/contrib/IRanges_1.0.14 .tar.gz > ' > Content type 'application/x-gzip' length 175687 bytes (171 Kb) > [snip] > cc -xc99 -I/homes/mdondrup/bin/R-2.8.1//lib/R/include > -I/opt/SUNWspro/include/ -I/vol/tcl-8.4.13/include -I/vol/local/include > -I/vol/graphics/include -I/vol/gnu/include -KPIC -g -c solve_user_SEW.c > -o solve_user_SEW.o > cc -xc99 -I/homes/mdondrup/bin/R-2.8.1//lib/R/include > -I/opt/SUNWspro/include/ -I/vol/tcl-8.4.13/include -I/vol/local/include > -I/vol/graphics/include -I/vol/gnu/include -KPIC -g -c sort_utils.c -o > sort_utils.o > "sort_utils.c", line 18: void function cannot return value > cc: acomp failed for sort_utils.c > make: *** [sort_utils.o] Error 2 > ERROR: compilation failed for package 'IRanges' > ** Removing '/homes/mdondrup/bin/R-2.8.1/lib/R/library/IRanges' > > The downloaded packages are in > /tmp/1101064.1.interactive.q/RtmpML0kk8/downloaded_packages > Updating HTML index of packages in '.Library' > Warning message: > In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'IRanges' had non-zero exit status > > Looking into sort_utils.c line 18 shows that this is the error: > A void funtion trying to return something. > > void _sort_int_array(int *x, int x_nelt) > { > return qsort(x, x_nelt, sizeof(int), cmpintp); > } > > I do not know why this works with gcc Probably because qsort returns void, so it's compatible. Obviously, return is pointless in the case of 'void' though. > by the way but for me just removing the "return" > > void _sort_int_array(int *x, int x_nelt) > { > qsort(x, x_nelt, sizeof(int), cmpintp); > } > > makes the package compilable. I hope that no return value is ever needed > somewhere .... > > Could you devise a patch to make bioconductor installation possible from > the repository? > Fixed in svn. Thanks for the report, Michael > > > Thanks > Michael > > > version _ > platform i386-pc-solaris2.10 > arch i386 > os solaris2.10 > system i386, solaris2.10 > status Patched > major 2 > minor 8.1 > year 2009 > month 03 > day 18 > svn rev 48212 > language R > version.string R version 2.8.1 Patched (2009-03-18 r48212) > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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