compilation error for rtracklayer

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rcaloger ▴ 500

@rcaloger-1888

Last seen 9.7 years ago

European Union

Dear all, I am trying to install rtracklayer on my server running linux suse enterprise 10 any suggestion how to solve the problem? cheers raffaele source("http://bioconductor.org/biocLite.R") biocLite("rtracklayer") gcc -std=gnu99 -I/home/calogero/bin/R-2.14.0/lib64/R/include -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/mnt/raidDisk/calogero/Documents/bin/R-2.14.0/lib64/R/library/IRang es/include" -g -Dinline="" -fpic -g -O2 -c ucsc/udc.c -o ucsc/udc.o ucsc/udc.c: In function ?udcInfoViaHttp?: ucsc/udc.c:405: warning: implicit declaration of function ?strptime? ucsc/udc.c:405: warning: comparison between pointer and integer ...... /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.4.1/include- fixed/bits/string2.h:1235: multiple definition of `__strsep_1c' IRanges_stubs.o:/usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.4.1 /include-fixed/bits/string2.h:1235: first defined here collect2: ld returned 1 exit status make: *** [rtracklayer.so] Error 1 ERROR: compilation failed for package ?rtracklayer? * removing ?/mnt/raidDisk/calogero/Documents/bin/R-2.14.0/lib64/R/library/rtrackl ayer? The downloaded packages are in ?/tmp/RtmpbcA6gw/downloaded_packages? Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ?rtracklayer? had non-zero exit status The IRanges > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] tools_2.14.0 > -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit MBC Centro di Biotecnologie Molecolari Via Nizza 52, Torino 10126 tel. ++39 0116706457 Fax ++39 0112366457 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it

rtracklayer rtracklayer • 2.1k views

ADD COMMENT • link updated 13.0 years ago by Michael Lawrence ★ 11k • written 13.0 years ago by rcaloger ▴ 500

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.9 years ago

United States

Well, no real idea here. My guess is that IRanges is bringing in one copy, and the UCSC stuff another. Michael On Sun, Nov 13, 2011 at 10:50 AM, rcaloger <raffaele.calogero@gmail.com>wrote: > Dear all, > I am trying to install rtracklayer on my server running linux suse > enterprise 10 > any suggestion how to solve the problem? > cheers > raffaele > > source("http://bioconductor.**org/biocLite.R<http: bioconductor.org="" bioclite.r=""> > ") > biocLite("rtracklayer") > > gcc -std=gnu99 -I/home/calogero/bin/R-2.14.0/**lib64/R/include > -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/mnt/raidDisk/calogero/** > Documents/bin/R-2.14.0/lib64/**R/library/IRanges/include" -g -Dinline="" > -fpic -g -O2 -c ucsc/udc.c -o ucsc/udc.o > ucsc/udc.c: In function udcInfoViaHttp: > ucsc/udc.c:405: warning: implicit declaration of function strptime > ucsc/udc.c:405: warning: comparison between pointer and integer > ...... > /usr/local/lib/gcc/x86_64-**unknown-linux-gnu/4.4.1/** > include-fixed/bits/string2.h:**1235: multiple definition of `__strsep_1c' > IRanges_stubs.o:/usr/local/**lib/gcc/x86_64-unknown-linux-** > gnu/4.4.1/include-fixed/bits/**string2.h:1235: first defined here > collect2: ld returned 1 exit status > make: *** [rtracklayer.so] Error 1 > ERROR: compilation failed for package rtracklayer > * removing /mnt/raidDisk/calogero/**Documents/bin/R-2.14.0/lib64/** > R/library/rtracklayer > > The downloaded packages are in > /tmp/RtmpbcA6gw/downloaded_**packages > Warning message: > In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package rtracklayer had non-zero exit status > > > The IRanges > > > > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > [1] tools_2.14.0 > > > > -- > > ------------------------------**---------- > Prof. Raffaele A. Calogero > Bioinformatics and Genomics Unit > MBC Centro di Biotecnologie Molecolari > Via Nizza 52, Torino 10126 > tel. ++39 0116706457 > Fax ++39 0112366457 > Mobile ++39 3333827080 > email: raffaele.calogero@unito.it > raffaele[dot]calogero[at]**gmail[dot]com > www: http://www.bioinformatica.**unito.it<http: www.bioinformatic="" a.unito.it=""> > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> [[alternative HTML version deleted]]

ADD COMMENT • link 13.0 years ago Michael Lawrence ★ 11k

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I'd try to remove that -Dinline flag, or to set the optimization level to -O0. For the latter, download and unpack rtracklayer tar xzf rtracklayer_x.y.z.tar.gz then create or edit a plain text file ~/.R/Makevars with CFLAGS=-O0 (that's 'Oh-zero') then R CMD INSTALL --preclean rtracklayer Alternatively, to avoid -Dinline="' I think you need to edit rtracklayer/src/Makevars.common. Martin On 11/13/2011 11:38 AM, Michael Lawrence wrote: > Well, no real idea here. My guess is that IRanges is bringing in one copy, > and the UCSC stuff another. > > Michael > > On Sun, Nov 13, 2011 at 10:50 AM, rcaloger<raffaele.calogero at="" gmail.com="">wrote: > >> Dear all, >> I am trying to install rtracklayer on my server running linux suse >> enterprise 10 >> any suggestion how to solve the problem? >> cheers >> raffaele >> >> source("http://bioconductor.**org/biocLite.R<http: bioconductor.or="" g="" bioclite.r=""> >> ") >> biocLite("rtracklayer") >> >> gcc -std=gnu99 -I/home/calogero/bin/R-2.14.0/**lib64/R/include >> -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/mnt/raidDisk/calogero/** >> Documents/bin/R-2.14.0/lib64/**R/library/IRanges/include" -g -Dinline="" >> -fpic -g -O2 -c ucsc/udc.c -o ucsc/udc.o >> ucsc/udc.c: In function ?udcInfoViaHttp?: >> ucsc/udc.c:405: warning: implicit declaration of function ?strptime? >> ucsc/udc.c:405: warning: comparison between pointer and integer >> ...... >> /usr/local/lib/gcc/x86_64-**unknown-linux-gnu/4.4.1/** >> include-fixed/bits/string2.h:**1235: multiple definition of `__strsep_1c' >> IRanges_stubs.o:/usr/local/**lib/gcc/x86_64-unknown-linux-** >> gnu/4.4.1/include-fixed/bits/**string2.h:1235: first defined here >> collect2: ld returned 1 exit status >> make: *** [rtracklayer.so] Error 1 >> ERROR: compilation failed for package ?rtracklayer? >> * removing ?/mnt/raidDisk/calogero/**Documents/bin/R-2.14.0/lib64/** >> R/library/rtracklayer? >> >> The downloaded packages are in >> ?/tmp/RtmpbcA6gw/downloaded_**packages? >> Warning message: >> In install.packages(pkgs = pkgs, repos = repos, ...) : >> installation of package ?rtracklayer? had non-zero exit status >> >> >> The IRanges >> >> >>> sessionInfo() >> R version 2.14.0 (2011-10-31) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.2.1 >> >> loaded via a namespace (and not attached): >> [1] tools_2.14.0 >>> >> >> -- >> >> ------------------------------**---------- >> Prof. Raffaele A. Calogero >> Bioinformatics and Genomics Unit >> MBC Centro di Biotecnologie Molecolari >> Via Nizza 52, Torino 10126 >> tel. ++39 0116706457 >> Fax ++39 0112366457 >> Mobile ++39 3333827080 >> email: raffaele.calogero at unito.it >> raffaele[dot]calogero[at]**gmail[dot]com >> www: http://www.bioinformatica.**unito.it<http: www.bioinformati="" ca.unito.it=""> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > 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

ADD REPLY • link 13.0 years ago Martin Morgan 25k

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I this should work now (in version 1.14.4). The -Dinline="" was a kludge. The real problem that was meant to fix has been resolved, I hope. Michael On Sun, Nov 13, 2011 at 12:57 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > I'd try to remove that -Dinline flag, or to set the optimization level to > -O0. For the latter, download and unpack rtracklayer > > tar xzf rtracklayer_x.y.z.tar.gz > > then create or edit a plain text file ~/.R/Makevars with > > CFLAGS=-O0 > > (that's 'Oh-zero') then > > R CMD INSTALL --preclean rtracklayer > > Alternatively, to avoid -Dinline="' I think you need to edit > rtracklayer/src/Makevars.**common. > > Martin > > > On 11/13/2011 11:38 AM, Michael Lawrence wrote: > >> Well, no real idea here. My guess is that IRanges is bringing in one copy, >> and the UCSC stuff another. >> >> Michael >> >> On Sun, Nov 13, 2011 at 10:50 AM, rcaloger<raffaele.calogero@**gmail.com<raffaele.calogero@gmail.com> >> >wrote: >> >> Dear all, >>> I am trying to install rtracklayer on my server running linux suse >>> enterprise 10 >>> any suggestion how to solve the problem? >>> cheers >>> raffaele >>> >>> source("http://bioconductor.****org/biocLite.R<http: **="">>> bioconductor.org/biocLite.R <http: bioconductor.org="" bioclite.r="">> >>> ") >>> biocLite("rtracklayer") >>> >>> gcc -std=gnu99 -I/home/calogero/bin/R-2.14.0/****lib64/R/include >>> -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/mnt/raidDisk/calogero/** >>> Documents/bin/R-2.14.0/lib64/****R/library/IRanges/include" -g >>> -Dinline="" >>> >>> -fpic -g -O2 -c ucsc/udc.c -o ucsc/udc.o >>> ucsc/udc.c: In function udcInfoViaHttp: >>> ucsc/udc.c:405: warning: implicit declaration of function strptime >>> ucsc/udc.c:405: warning: comparison between pointer and integer >>> ...... >>> /usr/local/lib/gcc/x86_64-****unknown-linux-gnu/4.4.1/** >>> include-fixed/bits/string2.h:****1235: multiple definition of >>> `__strsep_1c' >>> IRanges_stubs.o:/usr/local/****lib/gcc/x86_64-unknown-linux-**** >>> gnu/4.4.1/include-fixed/bits/****string2.h:1235: first defined here >>> >>> collect2: ld returned 1 exit status >>> make: *** [rtracklayer.so] Error 1 >>> ERROR: compilation failed for package rtracklayer >>> * removing /mnt/raidDisk/calogero/****Documents/bin/R-2.14.0/lib64/**** >>> >>> R/library/rtracklayer >>> >>> The downloaded packages are in >>> /tmp/RtmpbcA6gw/downloaded_****packages >>> >>> Warning message: >>> In install.packages(pkgs = pkgs, repos = repos, ...) : >>> installation of package rtracklayer had non-zero exit status >>> >>> >>> The IRanges >>> >>> >>> sessionInfo() >>>> >>> R version 2.14.0 (2011-10-31) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=C LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] BiocInstaller_1.2.1 >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.14.0 >>> >>>> >>>> >>> -- >>> >>> ------------------------------****---------- >>> >>> Prof. Raffaele A. Calogero >>> Bioinformatics and Genomics Unit >>> MBC Centro di Biotecnologie Molecolari >>> Via Nizza 52, Torino 10126 >>> tel. ++39 0116706457 >>> Fax ++39 0112366457 >>> Mobile ++39 3333827080 >>> email: raffaele.calogero@unito.it >>> raffaele[dot]calogero[at]****gmail[dot]com >>> www: http://www.bioinformatica.**un**ito.it <http: unito.it="">< >>> http://www.**bioinformatica.unito.it<http: www.bioinformatica.uni="" to.it=""> >>> > >>> >>> ______________________________****_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/****listinfo/bioconductor<https: sta="" t.ethz.ch="" mailman="" **listinfo="" bioconductor=""> >>> <https: **="" stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https:="" st="" at.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> > >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.****conductor<http: news.gmane.**="">>> org/gmane.science.biology.**informatics.conductor<http: news.gman="" e.org="" gmane.science.biology.informatics.conductor=""> >>> > >>> >> >> [[alternative HTML version deleted]] >> >> >> >> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<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 > [[alternative HTML version deleted]]

ADD REPLY • link 13.0 years ago Michael Lawrence ★ 11k

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