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 >