Question: ERROR: compilation failed for package XVector
0
gravatar for Pengcheng Yang
6.2 years ago by
China
Pengcheng Yang50 wrote:
Hi all, *Here is the sessionInfo.* ======================================================== > sessionInfo() R version 3.0.0 (2013-04-03) 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] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Biobase_2.20.0 IRanges_1.18.0 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] stats4_3.0.0 ========================================================= *And here is the error messages when installing XVector_0.1.0* ===================================================== > install.packages(repos=NULL,pkgs="R_package_archive/XVector_0.1.0.tar. gz") * installing *source* package âEUR~XVectorâEUR^(TM) ... ** libs gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include -DNDEBUG -I/usr/local/include -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/incl ude" -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include -DNDEBUG -I/usr/local/include -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/incl ude" -fpic -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o In file included from XVector.h:1, from Ocopy_byteblocks.c:1: ../inst/include/XVector_defines.h:24: error: redefinition of âEUR~struct cached_charseqâEUR^(TM) ../inst/include/XVector_defines.h:27: error: redefinition of typedef âEUR~cachedCharSeqâEUR^(TM) /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/include /IRanges_defines.h:115: error: previous declaration of âEUR~cachedCharSeqâEUR^(TM) was here ../inst/include/XVector_defines.h:29: error: redefinition of âEUR~struct cached_intseqâEUR^(TM) ../inst/include/XVector_defines.h:32: error: redefinition of typedef âEUR~cachedIntSeqâEUR^(TM) /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/include /IRanges_defines.h:120: error: previous declaration of âEUR~cachedIntSeqâEUR^(TM) was here ../inst/include/XVector_defines.h:34: error: redefinition of âEUR~struct cached_doubleseqâEUR^(TM) ../inst/include/XVector_defines.h:37: error: redefinition of typedef âEUR~cachedDoubleSeqâEUR^(TM) /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/include /IRanges_defines.h:125: error: previous declaration of âEUR~cachedDoubleSeqâEUR^(TM) was here ../inst/include/XVector_defines.h:39: error: redefinition of âEUR~struct cached_xvectorlistâEUR^(TM) ../inst/include/XVector_defines.h:47: error: redefinition of typedef âEUR~cachedXVectorListâEUR^(TM) /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/include /IRanges_defines.h:135: error: previous declaration of âEUR~cachedXVectorListâEUR^(TM) was here make: *** [Ocopy_byteblocks.o] Error 1 ERROR: compilation failed for package âEUR~XVectorâEUR^(TM) * removing âEUR~/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/XVectorâEU R^(TM) Warning message: In install.packages(repos = NULL, pkgs = "R_package_archive/XVector_0.1.0.tar.gz") : installation of package âEUR~R_package_archive/XVector_0.1.0.tar.gzâEUR^(TM) had non-zero exit status ======================================================= Thank you in advance. Best, Pengcheng Yang [[alternative HTML version deleted]]
xvector • 2.4k views
ADD COMMENTlink modified 6.2 years ago by Hervé Pagès ♦♦ 14k • written 6.2 years ago by Pengcheng Yang50
Answer: ERROR: compilation failed for package XVector
1
gravatar for Hervé Pagès
6.2 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:
Hi Yang, XVector only exists in Bioc-devel (BioC 2.13) and you're trying to install it with Bioc-release (Bioc 2.12). Mixing packages from release and devel is generally a bad thing and can easily be avoided by installing packages with biocLite(), as explained on our website. Cheers, H. On 07/22/2013 06:30 PM, Pengcheng Yang wrote: > Hi all, > > *Here is the sessionInfo.* > ======================================================== > > sessionInfo() > R version 3.0.0 (2013-04-03) > 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] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Biobase_2.20.0 IRanges_1.18.0 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] stats4_3.0.0 > > ========================================================= > > *And here is the error messages when installing XVector_0.1.0* > ===================================================== > > > install.packages(repos=NULL,pkgs="R_package_archive/XVector_0.1.0.ta r.gz") > * installing *source* package ?EUR~XVector?EUR^(TM) ... > ** libs > gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include > -DNDEBUG -I/usr/local/include > -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/in clude" > -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o > gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include > -DNDEBUG -I/usr/local/include > -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/in clude" > -fpic -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o > In file included from XVector.h:1, > from Ocopy_byteblocks.c:1: > ../inst/include/XVector_defines.h:24: error: redefinition of ?EUR~struct > cached_charseq?EUR^(TM) > ../inst/include/XVector_defines.h:27: error: redefinition of typedef > ?EUR~cachedCharSeq?EUR^(TM) > /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/inclu de/IRanges_defines.h:115: > error: previous declaration of ?EUR~cachedCharSeq?EUR^(TM) was here > ../inst/include/XVector_defines.h:29: error: redefinition of ?EUR~struct > cached_intseq?EUR^(TM) > ../inst/include/XVector_defines.h:32: error: redefinition of typedef > ?EUR~cachedIntSeq?EUR^(TM) > /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/inclu de/IRanges_defines.h:120: > error: previous declaration of ?EUR~cachedIntSeq?EUR^(TM) was here > ../inst/include/XVector_defines.h:34: error: redefinition of ?EUR~struct > cached_doubleseq?EUR^(TM) > ../inst/include/XVector_defines.h:37: error: redefinition of typedef > ?EUR~cachedDoubleSeq?EUR^(TM) > /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/inclu de/IRanges_defines.h:125: > error: previous declaration of ?EUR~cachedDoubleSeq?EUR^(TM) was here > ../inst/include/XVector_defines.h:39: error: redefinition of ?EUR~struct > cached_xvectorlist?EUR^(TM) > ../inst/include/XVector_defines.h:47: error: redefinition of typedef > ?EUR~cachedXVectorList?EUR^(TM) > /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/inclu de/IRanges_defines.h:135: > error: previous declaration of ?EUR~cachedXVectorList?EUR^(TM) was here > make: *** [Ocopy_byteblocks.o] Error 1 > ERROR: compilation failed for package ?EUR~XVector?EUR^(TM) > * removing > ?EUR~/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/XVector? EUR^(TM) > Warning message: > In install.packages(repos = NULL, pkgs = > "R_package_archive/XVector_0.1.0.tar.gz") : > installation of package > ?EUR~R_package_archive/XVector_0.1.0.tar.gz?EUR^(TM) had non-zero exit > status > ======================================================= > > Thank you in advance. > > Best, > Pengcheng Yang > > [[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 > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD COMMENTlink written 6.2 years ago by Hervé Pagès ♦♦ 14k
Hi Herve, I did have tested using biocLite() method to install XVector. Here is the message: ====================================== > biocLite("XVector") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version 3.0.0. Installing package(s) 'XVector' Warning message: package ???XVector??? is not available (for R version 3.0.0) ====================================== Best, Pengcheng On 2013/7/23 10:48, Hervé Pagès wrote: > Hi Yang, > > XVector only exists in Bioc-devel (BioC 2.13) and you're trying > to install it with Bioc-release (Bioc 2.12). Mixing packages from > release and devel is generally a bad thing and can easily be avoided > by installing packages with biocLite(), as explained on our website. > > Cheers, > H. > > > On 07/22/2013 06:30 PM, Pengcheng Yang wrote: >> Hi all, >> >> *Here is the sessionInfo.* >> ======================================================== >> > sessionInfo() >> R version 3.0.0 (2013-04-03) >> 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] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] Biobase_2.20.0 IRanges_1.18.0 BiocGenerics_0.6.0 >> >> loaded via a namespace (and not attached): >> [1] stats4_3.0.0 >> >> ========================================================= >> >> *And here is the error messages when installing XVector_0.1.0* >> ===================================================== >> > >> install.packages(repos=NULL,pkgs="R_package_archive/XVector_0.1.0.t ar.gz") >> >> * installing *source* package ?EUR~XVector?EUR^(TM) ... >> ** libs >> gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include >> -DNDEBUG -I/usr/local/include >> -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/i nclude" >> >> -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o >> gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include >> -DNDEBUG -I/usr/local/include >> -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/i nclude" >> >> -fpic -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o >> In file included from XVector.h:1, >> from Ocopy_byteblocks.c:1: >> ../inst/include/XVector_defines.h:24: error: redefinition of ?EUR~struct >> cached_charseq?EUR^(TM) >> ../inst/include/XVector_defines.h:27: error: redefinition of typedef >> ?EUR~cachedCharSeq?EUR^(TM) >> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/incl ude/IRanges_defines.h:115: >> >> error: previous declaration of ?EUR~cachedCharSeq?EUR^(TM) was here >> ../inst/include/XVector_defines.h:29: error: redefinition of ?EUR~struct >> cached_intseq?EUR^(TM) >> ../inst/include/XVector_defines.h:32: error: redefinition of typedef >> ?EUR~cachedIntSeq?EUR^(TM) >> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/incl ude/IRanges_defines.h:120: >> >> error: previous declaration of ?EUR~cachedIntSeq?EUR^(TM) was here >> ../inst/include/XVector_defines.h:34: error: redefinition of ?EUR~struct >> cached_doubleseq?EUR^(TM) >> ../inst/include/XVector_defines.h:37: error: redefinition of typedef >> ?EUR~cachedDoubleSeq?EUR^(TM) >> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/incl ude/IRanges_defines.h:125: >> >> error: previous declaration of ?EUR~cachedDoubleSeq?EUR^(TM) was here >> ../inst/include/XVector_defines.h:39: error: redefinition of ?EUR~struct >> cached_xvectorlist?EUR^(TM) >> ../inst/include/XVector_defines.h:47: error: redefinition of typedef >> ?EUR~cachedXVectorList?EUR^(TM) >> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/incl ude/IRanges_defines.h:135: >> >> error: previous declaration of ?EUR~cachedXVectorList?EUR^(TM) was here >> make: *** [Ocopy_byteblocks.o] Error 1 >> ERROR: compilation failed for package ?EUR~XVector?EUR^(TM) >> * removing >> ?EUR~/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/XVector ?EUR^(TM) >> >> Warning message: >> In install.packages(repos = NULL, pkgs = >> "R_package_archive/XVector_0.1.0.tar.gz") : >> installation of package >> ?EUR~R_package_archive/XVector_0.1.0.tar.gz?EUR^(TM) had non-zero exit >> status >> ======================================================= >> >> Thank you in advance. >> >> Best, >> Pengcheng Yang >> >> [[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 >> >
ADD REPLYlink written 6.2 years ago by Pengcheng Yang50
On Tue, Jul 23, 2013 at 6:44 PM, Pengcheng Yang <pengchy at="" gmail.com=""> wrote: > Hi Herve, > > I did have tested using biocLite() method to install XVector. Here is the > message: > > > ====================================== >> biocLite("XVector") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version 3.0.0. > Installing package(s) 'XVector' > Warning message: > package ???XVector??? is not available (for R version 3.0.0) > ====================================== > Note that it says you are running Bioconductor 2.12. As Herv? mentioned, you need to be running Bioconductor 2.13. You can upgrade either by giving the useDevel() command, or setting up a separate installation of R and then running useDevel() in that version of R. Or you can follow the detailed instructions here: http://bioconductor.org/developers/how-to/useDevel/ Dan > Best, > Pengcheng > > > On 2013/7/23 10:48, Hervé Pagès wrote: >> >> Hi Yang, >> >> XVector only exists in Bioc-devel (BioC 2.13) and you're trying >> to install it with Bioc-release (Bioc 2.12). Mixing packages from >> release and devel is generally a bad thing and can easily be avoided >> by installing packages with biocLite(), as explained on our website. >> >> Cheers, >> H. >> >> >> On 07/22/2013 06:30 PM, Pengcheng Yang wrote: >>> >>> Hi all, >>> >>> *Here is the sessionInfo.* >>> ======================================================== >>> > sessionInfo() >>> R version 3.0.0 (2013-04-03) >>> 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] parallel stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] Biobase_2.20.0 IRanges_1.18.0 BiocGenerics_0.6.0 >>> >>> loaded via a namespace (and not attached): >>> [1] stats4_3.0.0 >>> >>> ========================================================= >>> >>> *And here is the error messages when installing XVector_0.1.0* >>> ===================================================== >>> > >>> >>> install.packages(repos=NULL,pkgs="R_package_archive/XVector_0.1.0. tar.gz") >>> * installing *source* package ?EUR~XVector?EUR^(TM) ... >>> ** libs >>> gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include >>> -DNDEBUG -I/usr/local/include >>> >>> -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/ include" >>> -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o >>> gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include >>> -DNDEBUG -I/usr/local/include >>> >>> -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/ include" >>> -fpic -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o >>> In file included from XVector.h:1, >>> from Ocopy_byteblocks.c:1: >>> ../inst/include/XVector_defines.h:24: error: redefinition of ?EUR~struct >>> cached_charseq?EUR^(TM) >>> ../inst/include/XVector_defines.h:27: error: redefinition of typedef >>> ?EUR~cachedCharSeq?EUR^(TM) >>> >>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/inc lude/IRanges_defines.h:115: >>> error: previous declaration of ?EUR~cachedCharSeq?EUR^(TM) was here >>> ../inst/include/XVector_defines.h:29: error: redefinition of ?EUR~struct >>> cached_intseq?EUR^(TM) >>> ../inst/include/XVector_defines.h:32: error: redefinition of typedef >>> ?EUR~cachedIntSeq?EUR^(TM) >>> >>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/inc lude/IRanges_defines.h:120: >>> error: previous declaration of ?EUR~cachedIntSeq?EUR^(TM) was here >>> ../inst/include/XVector_defines.h:34: error: redefinition of ?EUR~struct >>> cached_doubleseq?EUR^(TM) >>> ../inst/include/XVector_defines.h:37: error: redefinition of typedef >>> ?EUR~cachedDoubleSeq?EUR^(TM) >>> >>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/inc lude/IRanges_defines.h:125: >>> error: previous declaration of ?EUR~cachedDoubleSeq?EUR^(TM) was here >>> ../inst/include/XVector_defines.h:39: error: redefinition of ?EUR~struct >>> cached_xvectorlist?EUR^(TM) >>> ../inst/include/XVector_defines.h:47: error: redefinition of typedef >>> ?EUR~cachedXVectorList?EUR^(TM) >>> >>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/inc lude/IRanges_defines.h:135: >>> error: previous declaration of ?EUR~cachedXVectorList?EUR^(TM) was here >>> make: *** [Ocopy_byteblocks.o] Error 1 >>> ERROR: compilation failed for package ?EUR~XVector?EUR^(TM) >>> * removing >>> >>> ?EUR~/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/XVecto r?EUR^(TM) >>> Warning message: >>> In install.packages(repos = NULL, pkgs = >>> "R_package_archive/XVector_0.1.0.tar.gz") : >>> installation of package >>> ?EUR~R_package_archive/XVector_0.1.0.tar.gz?EUR^(TM) had non-zero exit >>> status >>> ======================================================= >>> >>> Thank you in advance. >>> >>> Best, >>> Pengcheng Yang >>> >>> [[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 >>> >> > > _______________________________________________ > 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
ADD REPLYlink written 6.2 years ago by Dan Tenenbaum8.2k
Hi Pengcheng, On 07/23/2013 07:21 PM, Dan Tenenbaum wrote: > On Tue, Jul 23, 2013 at 6:44 PM, Pengcheng Yang <pengchy at="" gmail.com=""> wrote: >> Hi Herve, >> >> I did have tested using biocLite() method to install XVector. Here is the >> message: >> >> >> ====================================== >>> biocLite("XVector") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version 3.0.0. >> Installing package(s) 'XVector' >> Warning message: >> package ???XVector??? is not available (for R version 3.0.0) >> ====================================== >> > > > Note that it says you are running Bioconductor 2.12. As Herv? > mentioned, you need to be running Bioconductor 2.13. > > You can upgrade either by giving the > useDevel() > command, or setting up a separate installation of R and then running > useDevel() in that version of R. > > Or you can follow the detailed instructions here: > > http://bioconductor.org/developers/how-to/useDevel/ That's if you really want to install the XVector package but why you'd want to do that? I mean, this is an infrastructure package that is new in Bioc-devel. You don't need it in Bioc-release (and it's incompatible with Bioc-release anyway, as you've learned), and you don't need to install it explicitly in Bioc-devel since it will get automatically installed when you install other (more useful) packages that depend on it. H. > > Dan > > > >> Best, >> Pengcheng >> >> >> On 2013/7/23 10:48, Hervé Pagès wrote: >>> >>> Hi Yang, >>> >>> XVector only exists in Bioc-devel (BioC 2.13) and you're trying >>> to install it with Bioc-release (Bioc 2.12). Mixing packages from >>> release and devel is generally a bad thing and can easily be avoided >>> by installing packages with biocLite(), as explained on our website. >>> >>> Cheers, >>> H. >>> >>> >>> On 07/22/2013 06:30 PM, Pengcheng Yang wrote: >>>> >>>> Hi all, >>>> >>>> *Here is the sessionInfo.* >>>> ======================================================== >>>>> sessionInfo() >>>> R version 3.0.0 (2013-04-03) >>>> 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] parallel stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] Biobase_2.20.0 IRanges_1.18.0 BiocGenerics_0.6.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] stats4_3.0.0 >>>> >>>> ========================================================= >>>> >>>> *And here is the error messages when installing XVector_0.1.0* >>>> ===================================================== >>>>> >>>> >>>> install.packages(repos=NULL,pkgs="R_package_archive/XVector_0.1.0 .tar.gz") >>>> * installing *source* package ?EUR~XVector?EUR^(TM) ... >>>> ** libs >>>> gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include >>>> -DNDEBUG -I/usr/local/include >>>> >>>> -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges /include" >>>> -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o >>>> gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include >>>> -DNDEBUG -I/usr/local/include >>>> >>>> -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges /include" >>>> -fpic -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o >>>> In file included from XVector.h:1, >>>> from Ocopy_byteblocks.c:1: >>>> ../inst/include/XVector_defines.h:24: error: redefinition of ?EUR~struct >>>> cached_charseq?EUR^(TM) >>>> ../inst/include/XVector_defines.h:27: error: redefinition of typedef >>>> ?EUR~cachedCharSeq?EUR^(TM) >>>> >>>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/in clude/IRanges_defines.h:115: >>>> error: previous declaration of ?EUR~cachedCharSeq?EUR^(TM) was here >>>> ../inst/include/XVector_defines.h:29: error: redefinition of ?EUR~struct >>>> cached_intseq?EUR^(TM) >>>> ../inst/include/XVector_defines.h:32: error: redefinition of typedef >>>> ?EUR~cachedIntSeq?EUR^(TM) >>>> >>>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/in clude/IRanges_defines.h:120: >>>> error: previous declaration of ?EUR~cachedIntSeq?EUR^(TM) was here >>>> ../inst/include/XVector_defines.h:34: error: redefinition of ?EUR~struct >>>> cached_doubleseq?EUR^(TM) >>>> ../inst/include/XVector_defines.h:37: error: redefinition of typedef >>>> ?EUR~cachedDoubleSeq?EUR^(TM) >>>> >>>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/in clude/IRanges_defines.h:125: >>>> error: previous declaration of ?EUR~cachedDoubleSeq?EUR^(TM) was here >>>> ../inst/include/XVector_defines.h:39: error: redefinition of ?EUR~struct >>>> cached_xvectorlist?EUR^(TM) >>>> ../inst/include/XVector_defines.h:47: error: redefinition of typedef >>>> ?EUR~cachedXVectorList?EUR^(TM) >>>> >>>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/in clude/IRanges_defines.h:135: >>>> error: previous declaration of ?EUR~cachedXVectorList?EUR^(TM) was here >>>> make: *** [Ocopy_byteblocks.o] Error 1 >>>> ERROR: compilation failed for package ?EUR~XVector?EUR^(TM) >>>> * removing >>>> >>>> ?EUR~/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/XVect or?EUR^(TM) >>>> Warning message: >>>> In install.packages(repos = NULL, pkgs = >>>> "R_package_archive/XVector_0.1.0.tar.gz") : >>>> installation of package >>>> ?EUR~R_package_archive/XVector_0.1.0.tar.gz?EUR^(TM) had non-zero exit >>>> status >>>> ======================================================= >>>> >>>> Thank you in advance. >>>> >>>> Best, >>>> Pengcheng Yang >>>> >>>> [[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 >>>> >>> >> >> _______________________________________________ >> 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD REPLYlink written 6.2 years ago by Hervé Pagès ♦♦ 14k
Hi Herve, Originally, I wanted to install spliceR, which depends on GenomicRanges, then which depends on XVector. I have installed other depended packages successfully by local methods. But not XVector. Thanks Herve, I have installed XVector now, but haven't tested it. Best, Pengcheng On 2013/7/24 13:48, Hervé Pagès wrote: > Hi Pengcheng, > > On 07/23/2013 07:21 PM, Dan Tenenbaum wrote: >> On Tue, Jul 23, 2013 at 6:44 PM, Pengcheng Yang <pengchy at="" gmail.com=""> >> wrote: >>> Hi Herve, >>> >>> I did have tested using biocLite() method to install XVector. Here >>> is the >>> message: >>> >>> >>> ====================================== >>>> biocLite("XVector") >>> BioC_mirror: http://bioconductor.org >>> Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version >>> 3.0.0. >>> Installing package(s) 'XVector' >>> Warning message: >>> package ???XVector??? is not available (for R version 3.0.0) >>> ====================================== >>> >> >> >> Note that it says you are running Bioconductor 2.12. As Herv? >> mentioned, you need to be running Bioconductor 2.13. >> >> You can upgrade either by giving the >> useDevel() >> command, or setting up a separate installation of R and then running >> useDevel() in that version of R. >> >> Or you can follow the detailed instructions here: >> >> http://bioconductor.org/developers/how-to/useDevel/ > > That's if you really want to install the XVector package but why > you'd want to do that? I mean, this is an infrastructure package > that is new in Bioc-devel. You don't need it in Bioc-release (and > it's incompatible with Bioc-release anyway, as you've learned), > and you don't need to install it explicitly in Bioc-devel since > it will get automatically installed when you install other (more > useful) packages that depend on it. > > H. > >> >> Dan >> >> >> >>> Best, >>> Pengcheng >>> >>> >>> On 2013/7/23 10:48, Hervé Pagès wrote: >>>> >>>> Hi Yang, >>>> >>>> XVector only exists in Bioc-devel (BioC 2.13) and you're trying >>>> to install it with Bioc-release (Bioc 2.12). Mixing packages from >>>> release and devel is generally a bad thing and can easily be avoided >>>> by installing packages with biocLite(), as explained on our website. >>>> >>>> Cheers, >>>> H. >>>> >>>> >>>> On 07/22/2013 06:30 PM, Pengcheng Yang wrote: >>>>> >>>>> Hi all, >>>>> >>>>> *Here is the sessionInfo.* >>>>> ======================================================== >>>>>> sessionInfo() >>>>> R version 3.0.0 (2013-04-03) >>>>> 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] parallel stats graphics grDevices utils datasets methods >>>>> [8] base >>>>> >>>>> other attached packages: >>>>> [1] Biobase_2.20.0 IRanges_1.18.0 BiocGenerics_0.6.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] stats4_3.0.0 >>>>> >>>>> ========================================================= >>>>> >>>>> *And here is the error messages when installing XVector_0.1.0* >>>>> ===================================================== >>>>>> >>>>> >>>>> install.packages(repos=NULL,pkgs="R_package_archive/XVector_0.1. 0.tar.gz") >>>>> >>>>> * installing *source* package ?EUR~XVector?EUR^(TM) ... >>>>> ** libs >>>>> gcc -std=gnu99 >>>>> -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include >>>>> -DNDEBUG -I/usr/local/include >>>>> >>>>> -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRange s/include" >>>>> >>>>> -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o >>>>> gcc -std=gnu99 >>>>> -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include >>>>> -DNDEBUG -I/usr/local/include >>>>> >>>>> -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRange s/include" >>>>> >>>>> -fpic -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o >>>>> In file included from XVector.h:1, >>>>> from Ocopy_byteblocks.c:1: >>>>> ../inst/include/XVector_defines.h:24: error: redefinition of >>>>> ?EUR~struct >>>>> cached_charseq?EUR^(TM) >>>>> ../inst/include/XVector_defines.h:27: error: redefinition of typedef >>>>> ?EUR~cachedCharSeq?EUR^(TM) >>>>> >>>>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/i nclude/IRanges_defines.h:115: >>>>> >>>>> error: previous declaration of ?EUR~cachedCharSeq?EUR^(TM) was here >>>>> ../inst/include/XVector_defines.h:29: error: redefinition of >>>>> ?EUR~struct >>>>> cached_intseq?EUR^(TM) >>>>> ../inst/include/XVector_defines.h:32: error: redefinition of typedef >>>>> ?EUR~cachedIntSeq?EUR^(TM) >>>>> >>>>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/i nclude/IRanges_defines.h:120: >>>>> >>>>> error: previous declaration of ?EUR~cachedIntSeq?EUR^(TM) was here >>>>> ../inst/include/XVector_defines.h:34: error: redefinition of >>>>> ?EUR~struct >>>>> cached_doubleseq?EUR^(TM) >>>>> ../inst/include/XVector_defines.h:37: error: redefinition of typedef >>>>> ?EUR~cachedDoubleSeq?EUR^(TM) >>>>> >>>>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/i nclude/IRanges_defines.h:125: >>>>> >>>>> error: previous declaration of ?EUR~cachedDoubleSeq?EUR^(TM) was here >>>>> ../inst/include/XVector_defines.h:39: error: redefinition of >>>>> ?EUR~struct >>>>> cached_xvectorlist?EUR^(TM) >>>>> ../inst/include/XVector_defines.h:47: error: redefinition of typedef >>>>> ?EUR~cachedXVectorList?EUR^(TM) >>>>> >>>>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/i nclude/IRanges_defines.h:135: >>>>> >>>>> error: previous declaration of ?EUR~cachedXVectorList?EUR^(TM) was >>>>> here >>>>> make: *** [Ocopy_byteblocks.o] Error 1 >>>>> ERROR: compilation failed for package ?EUR~XVector?EUR^(TM) >>>>> * removing >>>>> >>>>> ?EUR~/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/XVec tor?EUR^(TM) >>>>> >>>>> Warning message: >>>>> In install.packages(repos = NULL, pkgs = >>>>> "R_package_archive/XVector_0.1.0.tar.gz") : >>>>> installation of package >>>>> ?EUR~R_package_archive/XVector_0.1.0.tar.gz?EUR^(TM) had non- zero >>>>> exit >>>>> status >>>>> ======================================================= >>>>> >>>>> Thank you in advance. >>>>> >>>>> Best, >>>>> Pengcheng Yang >>>>> >>>>> [[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 >>>>> >>>> >>> >>> _______________________________________________ >>> 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 >
ADD REPLYlink written 6.2 years ago by Pengcheng Yang50
Thank you Dan, I have installed successfully as you suggested. Best, Pengcheng On 2013/7/24 10:21, Dan Tenenbaum wrote: > On Tue, Jul 23, 2013 at 6:44 PM, Pengcheng Yang <pengchy at="" gmail.com=""> wrote: >> Hi Herve, >> >> I did have tested using biocLite() method to install XVector. Here is the >> message: >> >> >> ====================================== >>> biocLite("XVector") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version 3.0.0. >> Installing package(s) 'XVector' >> Warning message: >> package ???XVector??? is not available (for R version 3.0.0) >> ====================================== >> > > Note that it says you are running Bioconductor 2.12. As Herv? > mentioned, you need to be running Bioconductor 2.13. > > You can upgrade either by giving the > useDevel() > command, or setting up a separate installation of R and then running > useDevel() in that version of R. > > Or you can follow the detailed instructions here: > > http://bioconductor.org/developers/how-to/useDevel/ > > Dan > > > >> Best, >> Pengcheng >> >> >> On 2013/7/23 10:48, Hervé Pagès wrote: >>> Hi Yang, >>> >>> XVector only exists in Bioc-devel (BioC 2.13) and you're trying >>> to install it with Bioc-release (Bioc 2.12). Mixing packages from >>> release and devel is generally a bad thing and can easily be avoided >>> by installing packages with biocLite(), as explained on our website. >>> >>> Cheers, >>> H. >>> >>> >>> On 07/22/2013 06:30 PM, Pengcheng Yang wrote: >>>> Hi all, >>>> >>>> *Here is the sessionInfo.* >>>> ======================================================== >>>>> sessionInfo() >>>> R version 3.0.0 (2013-04-03) >>>> 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] parallel stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] Biobase_2.20.0 IRanges_1.18.0 BiocGenerics_0.6.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] stats4_3.0.0 >>>> >>>> ========================================================= >>>> >>>> *And here is the error messages when installing XVector_0.1.0* >>>> ===================================================== >>>> install.packages(repos=NULL,pkgs="R_package_archive/XVector_0.1.0 .tar.gz") >>>> * installing *source* package ?EUR~XVector?EUR^(TM) ... >>>> ** libs >>>> gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include >>>> -DNDEBUG -I/usr/local/include >>>> >>>> -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges /include" >>>> -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o >>>> gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include >>>> -DNDEBUG -I/usr/local/include >>>> >>>> -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges /include" >>>> -fpic -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o >>>> In file included from XVector.h:1, >>>> from Ocopy_byteblocks.c:1: >>>> ../inst/include/XVector_defines.h:24: error: redefinition of ?EUR~struct >>>> cached_charseq?EUR^(TM) >>>> ../inst/include/XVector_defines.h:27: error: redefinition of typedef >>>> ?EUR~cachedCharSeq?EUR^(TM) >>>> >>>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/in clude/IRanges_defines.h:115: >>>> error: previous declaration of ?EUR~cachedCharSeq?EUR^(TM) was here >>>> ../inst/include/XVector_defines.h:29: error: redefinition of ?EUR~struct >>>> cached_intseq?EUR^(TM) >>>> ../inst/include/XVector_defines.h:32: error: redefinition of typedef >>>> ?EUR~cachedIntSeq?EUR^(TM) >>>> >>>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/in clude/IRanges_defines.h:120: >>>> error: previous declaration of ?EUR~cachedIntSeq?EUR^(TM) was here >>>> ../inst/include/XVector_defines.h:34: error: redefinition of ?EUR~struct >>>> cached_doubleseq?EUR^(TM) >>>> ../inst/include/XVector_defines.h:37: error: redefinition of typedef >>>> ?EUR~cachedDoubleSeq?EUR^(TM) >>>> >>>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/in clude/IRanges_defines.h:125: >>>> error: previous declaration of ?EUR~cachedDoubleSeq?EUR^(TM) was here >>>> ../inst/include/XVector_defines.h:39: error: redefinition of ?EUR~struct >>>> cached_xvectorlist?EUR^(TM) >>>> ../inst/include/XVector_defines.h:47: error: redefinition of typedef >>>> ?EUR~cachedXVectorList?EUR^(TM) >>>> >>>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/in clude/IRanges_defines.h:135: >>>> error: previous declaration of ?EUR~cachedXVectorList?EUR^(TM) was here >>>> make: *** [Ocopy_byteblocks.o] Error 1 >>>> ERROR: compilation failed for package ?EUR~XVector?EUR^(TM) >>>> * removing >>>> >>>> ?EUR~/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/XVect or?EUR^(TM) >>>> Warning message: >>>> In install.packages(repos = NULL, pkgs = >>>> "R_package_archive/XVector_0.1.0.tar.gz") : >>>> installation of package >>>> ?EUR~R_package_archive/XVector_0.1.0.tar.gz?EUR^(TM) had non-zero exit >>>> status >>>> ======================================================= >>>> >>>> Thank you in advance. >>>> >>>> Best, >>>> Pengcheng Yang >>>> >>>> [[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 >>>> >> _______________________________________________ >> 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
ADD REPLYlink written 6.2 years ago by Pengcheng Yang50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 223 users visited in the last hour