Dear List I'm trying to update Biostrings package but every time with the same error message. * installing *source* package ‘Biostrings’ ... ** libs gcc -I/usr/share/R/include -I"/home/guido/R/x86_64-pc-linux-gnu-library/2.13/IRanges/include" -fpic -std=gnu99 -O3 -pipe -g -c BAB_class.c -o BAB_class.o gcc: error trying to exec 'as': execvp: File name too long make: *** [BAB_class.o] Error 2 ERROR: compilation failed for package ‘Biostrings’ * removing ‘/home/guido/R/x86_64-pc-linux-gnu-library/2.13/Biostrings’ * restoring previous ‘/home/guido/R/x86_64-pc-linux-gnu-library/2.13/Biostrings’ This is my sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=it_IT.UTF-8 [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tcltk_2.13.0 tools_2.13.0 Any idea? Thank you very much Guido -- Guido Leoni National Research Institute on Food and Nutrition (I.N.R.A.N.) via Ardeatina 546 00178 Rome Italy tel + 39 06 51 49 41 (operator) + 39 06 51 49 4498 (direct) [[alternative HTML version deleted]]

On 08/29/2011 08:35 AM, Guido Leoni wrote: > Dear List I'm trying to update Biostrings package but every time with the > same error message. > > * installing *source* package ?Biostrings? ... > ** libs > gcc -I/usr/share/R/include > -I"/home/guido/R/x86_64-pc-linux-gnu-library/2.13/IRanges/include" -fpic > -std=gnu99 -O3 -pipe -g -c BAB_class.c -o BAB_class.o > gcc: error trying to exec 'as': execvp: File name too long > make: *** [BAB_class.o] Error 2 > ERROR: compilation failed for package ?Biostrings? Weird. Do other packages requiring source build work, e.g., Biobase? If not, it sounds like a system configuration issue. If so, try updating IRanges, then Biostrings? I'm not sure what else to suggest, perhaps downloading the Biostrings source (as tar.gz) and running from the command line CFLAGS="-v" R CMD INSTALL --libs-only Biostrings_2.20.3.tar.gz and looking for a suspicious path name that might actually trigger the 'File name too long' message. Martin > * removing ?/home/guido/R/x86_64-pc-linux-gnu- library/2.13/Biostrings? > * restoring previous > ?/home/guido/R/x86_64-pc-linux-gnu-library/2.13/Biostrings? > This is my sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C > [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=it_IT.UTF-8 > [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tcltk_2.13.0 tools_2.13.0 > > > Any idea? > Thank you very much > Guido > > > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

On 08/29/2011 08:35 AM, Guido Leoni wrote: > Dear List I'm trying to update Biostrings package but every time with the > same error message. > > * installing *source* package ?Biostrings? ... > ** libs > gcc -I/usr/share/R/include > -I"/home/guido/R/x86_64-pc-linux-gnu-library/2.13/IRanges/include" -fpic > -std=gnu99 -O3 -pipe -g -c BAB_class.c -o BAB_class.o > gcc: error trying to exec 'as': execvp: File name too long > make: *** [BAB_class.o] Error 2 > ERROR: compilation failed for package ?Biostrings? Weird. Do other packages requiring source build work, e.g., Biobase? If not, it sounds like a system configuration issue. If so, try updating IRanges, then Biostrings? I'm not sure what else to suggest, perhaps downloading the Biostrings source (as tar.gz) and running from the command line CFLAGS="-v" R CMD INSTALL --libs-only Biostrings_2.20.3.tar.gz and looking for a suspicious path name that might actually trigger the 'File name too long' message. Martin > * removing ?/home/guido/R/x86_64-pc-linux-gnu- library/2.13/Biostrings? > * restoring previous > ?/home/guido/R/x86_64-pc-linux-gnu-library/2.13/Biostrings? > This is my sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C > [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=it_IT.UTF-8 > [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tcltk_2.13.0 tools_2.13.0 > > > Any idea? > Thank you very much > Guido > > > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

Thank you very much for your tips. It was sufficient to recompile all the installed bioconductor packages to solve the problem. source("http://bioconductor.org/biocLite.R") pkgs <- rownames(installed.packages()) biocLite(pkgs) Probably some updates of my ubuntu system broke the dependancies of some packages. Thank you again Guido 2011/8/29 Harris A. Jaffee <hj@jhu.edu> > On my system, gcc just runs whatever 'as' comes up first in my PATH. > I wouldn't be surprised that this is typical, but it's possible that > gcc would have its assembler configure in. > > If there an 'as' besides /usr/bin/as, this suggests a user environment > foul-up rather than one by gcc or make. > > Anyway, I suggest working up from the bottom, by hand: > > $ /usr/bin/as </dev> > If that works, try > > $ as </dev> > And just to make sure: > > $ which as > > If all of these work, and the last one gives /usr/bin/as, then we are > back to suspecting gcc itself or make. Then the first thing to do is > to see how gcc performs in a baby case like my command > > > $ strace -f -o debug_output_file gcc -o foo.o foo.c >> > > > Look for lines in the output containing "execve". You will see what > assembler is being exec'd and possibly the ENAMETOOLONG failure (see > 'man 2 exec'). > > > On Aug 29, 2011, at 1:18 PM, Harris A. Jaffee wrote: > > It sounds like it's the pathname to the assembler (as) which gcc wants to >> execute, that is too long. This could be a foul-up on the part of gcc or >> make, and that will be a real nightmare to chase down. Or perhaps he has >> his own utility (maybe by accident) named "as" somewhere. In this case, >> the command >> >> $ which as >> >> will be revealing. >> >> I would suspect that *any* compilation-with-assembly will fail, and this >> just happens to be the first one that is being attempted. >> >> How about testing with a trivial C source file like this? >> >> foo.c: >> >> main() >> { >> printf("hello\n"); >> } >> >> The following command will need an assembler (and give some debugging): >> >> $ strace -f -o debug_output_file gcc -o foo.o foo.c >> >> On Aug 29, 2011, at 12:10 PM, Martin Morgan wrote: >> >> On 08/29/2011 08:35 AM, Guido Leoni wrote: >>> >>>> Dear List I'm trying to update Biostrings package but every time with >>>> the >>>> same error message. >>>> >>>> * installing *source* package ‘Biostrings’ ... >>>> ** libs >>>> gcc -I/usr/share/R/include >>>> -I"/home/guido/R/x86_64-pc-**linux-gnu- library/2.13/**IRanges/include" >>>> -fpic >>>> -std=gnu99 -O3 -pipe -g -c BAB_class.c -o BAB_class.o >>>> gcc: error trying to exec 'as': execvp: File name too long >>>> make: *** [BAB_class.o] Error 2 >>>> ERROR: compilation failed for package ‘Biostrings’ >>>> >>> >>> Weird. Do other packages requiring source build work, e.g., Biobase? If >>> not, it sounds like a system configuration issue. If so, try updating >>> IRanges, then Biostrings? >>> >>> I'm not sure what else to suggest, perhaps downloading the Biostrings >>> source (as tar.gz) and running from the command line >>> >>> CFLAGS="-v" R CMD INSTALL --libs-only Biostrings_2.20.3.tar.gz >>> >>> and looking for a suspicious path name that might actually trigger the >>> 'File name too long' message. >>> >>> Martin >>> >>> * removing ‘/home/guido/R/x86_64-pc-**linux-gnu-library/2.13/** >>>> Biostrings’ >>>> * restoring previous >>>> ‘/home/guido/R/x86_64-pc-**linux-gnu-library/2.13/**Biostrings’ >>>> This is my sessionInfo() >>>> R version 2.13.0 (2011-04-13) >>>> Platform: x86_64-pc-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8 >>>> [5] LC_MONETARY=C LC_MESSAGES=it_IT.UTF-8 >>>> [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> loaded via a namespace (and not attached): >>>> [1] tcltk_2.13.0 tools_2.13.0 >>>> >>>> >>>> Any idea? >>>> Thank you very much >>>> Guido >>>> >>>> >>>> >>>> >>>> >>>> -- Guido Leoni National Research Institute on Food and Nutrition (I.N.R.A.N.) via Ardeatina 546 00178 Rome Italy tel + 39 06 51 49 41 (operator) + 39 06 51 49 4498 (direct) [[alternative HTML version deleted]]