installation packages
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fran vino ▴ 40
@fran-vino-6151
Last seen 9.6 years ago
Dear Bioconductor list, I installed R on UBUNTU, but now how can I install the packages in R. For example if I use: > source("http://bioconductor.org/biocLite.R") > biocLite("DEseq") It results: Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘XML’ had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘annotate’ had non-zero exit status 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘genefilter’ had non-zero exit status 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘geneplotter’ had non-zero exit status 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘DESeq’ had non-zero exit status 6: installed directory not writable, cannot update packages 'foreign', 'Matrix', 'mgcv', 'rpart', 'spatial' but if I try to install XML, it results: > package ‘XML’ is not available (for R version 3.0.1) How can I solve it? Thanks [[alternative HTML version deleted]]
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 3.2 years ago
United States
----- Original Message ----- > From: "fran vino" <biocesca at="" gmail.com=""> > To: bioconductor at r-project.org > Sent: Friday, September 13, 2013 7:21:31 AM > Subject: [BioC] installation packages > > Dear Bioconductor list, > > I installed R on UBUNTU, but now how can I install the packages in R. > For > example if I use: > > > source("http://bioconductor.org/biocLite.R") > > biocLite("DEseq") > > It results: > > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?XML? had non-zero exit status > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?annotate? had non-zero exit status > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?genefilter? had non-zero exit status > 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?geneplotter? had non-zero exit status > 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?DESeq? had non-zero exit status > 6: installed directory not writable, cannot update packages > 'foreign', > 'Matrix', > 'mgcv', 'rpart', 'spatial' > > but if I try to install XML, it results: > > > package ?XML? is not available (for R version 3.0.1) > > > How can I solve it? > The XML problem is probably because you are missing system dependencies: Try this at the unix command line: sudo apt-get install -y libcurl-dev libxml2-dev Then try installing XML again. The other package failures you saw were probably because XML was not installed. The "6: installed directory not writable, cannot update packages" is just a warning and you can ignore it. It's talking about core R packages which are typically installed in a directory that ordinary users can't write to. If you want, you can run biocLite() as root to update those packages. Dan > Thanks > > [[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
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@ivan-gregoretti-3975
Last seen 9.6 years ago
Canada
Please try again but this time do it as root instead of a regular user. Its a common mistake. Ivan Ivan Gregoretti, PhD Bioinformatics On Fri, Sep 13, 2013 at 10:21 AM, fran vino <biocesca@gmail.com> wrote: > Dear Bioconductor list, > > I installed R on UBUNTU, but now how can I install the packages in R. For > example if I use: > > > source("http://bioconductor.org/biocLite.R") > > biocLite("DEseq") > > It results: > > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ‘XML’ had non-zero exit status > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ‘annotate’ had non-zero exit status > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ‘genefilter’ had non-zero exit status > 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ‘geneplotter’ had non-zero exit status > 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ‘DESeq’ had non-zero exit status > 6: installed directory not writable, cannot update packages 'foreign', > 'Matrix', > 'mgcv', 'rpart', 'spatial' > > but if I try to install XML, it results: > > > package ‘XML’ is not available (for R version 3.0.1) > > > How can I solve it? > > Thanks > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > 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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fran vino ▴ 40
@fran-vino-6151
Last seen 9.6 years ago
Hi thanks for your suggestions. I performed the command as root instead of a regular user, how you said me.. When I performed: > biocLite(“XML”), it resulted: Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘XML’ had non-zero exit status Moreover, when I performed: >biocLite(“biomaRt”), it resulted: Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘XML’ had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘biomaRt’ had non-zero exit status So I performed: >install.packages("biomaRt", +repos="http://bioconductor.org/packages/2.12/bioc") and: >install.packages("biomaRt", +repos="http://bioconductor.org/packages/2.12/biomaRt"), to install packages biomaRt, but it resulted: Warning message: In install.packages("biomaRt", repos = " http://bioconductor.org/packages/2.12/bioc") : installation of package ‘biomaRt’ had non-zero exit status Why? How can I solve my problems?? Thanks a lot [[alternative HTML version deleted]]
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Hi, On Thu, Sep 19, 2013 at 4:09 AM, fran vino <biocesca at="" gmail.com=""> wrote: > Hi thanks for your suggestions. > > I performed the command as root instead of a regular user, how you said > me.. When I performed: > > > > biocLite(?XML?), it resulted: > > > Warning message: > > In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > installation of package ?XML? had non-zero exit status You should go back to the email that Dan wrote to you. The installation of the XML package is likely failing because you are missing an essential library on your system -- it's not related to R. This is what was said: """The XML problem is probably because you are missing system dependencies: Try this at the unix command line: sudo apt-get install -y libcurl-dev libxml2-dev Then try installing XML again.""" Assuming you are running a debian-like version of linux, you will need to install those *-dev packages *on your system*! Run those `sudo apt-get` command from your terminal (not in R) so that the proper libraries (headers) for libcurl ad libxml2 are on your system, then reinstall RCurl via biocLite using R. HTH, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
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@steve-lianoglou-2771
Last seen 14 months ago
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Hi Fran, Please keep all emails on list (hit "reply-all") so that your emails go back to the main bioconductor list as well. In this way you'll have more people able to help you, and others can benefit from our conversations in the future by searching the email archives. Now: > I performed this command and I solved the problem only for installation of XML packages, because if I try to perform biocLite for the other packages it results: > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?rtracklayer? had non-zero exit status > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?GenomicFeatures? had non-zero exit status > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?VariantAnnotation? had non-zero exit status > 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?gmapR? had non-zero exit status > > This is the same warning message that I had with XML packages. How I can solve it? You will need to provide more output than that to get help. You say that after installing libcurl-dev and libxml2-dev on your system, the XML library install worked in R? So when you do `library(XML)` inside R, does it load properly? Can you please provide the entire output when you do: R> library(BiocInstaller) R> biocLite(c("RCurl", "rtracklayer")) Please also include the entire output of sessionInfo() after the above commands fail. Thanks, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
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Hi, when I do library(XML) inside R, it loads properly, but if I do: R> biocLite(c("RCurl", "rtracklayer")), it results: Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘rtracklayer’ had non-zero exit status or: R> biocLite(“Genomic Features”) Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘rtracklayer’ had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘GenomicFeatures’ had non-zero exit status > sessionInfo() R version 3.0.1 (2013-05-16) 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=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8 [7] LC_PAPER=C 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 other attached packages: [1] RCurl_1.95-4.1 bitops_1.0-6 XML_3.98-1.1 [4] BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] tools_3.0. 2013/9/24 Steve Lianoglou <lianoglou.steve@gene.com> > Hi Fran, > > Please keep all emails on list (hit "reply-all") so that your emails go > back to the main bioconductor list as well. > > In this way you'll have more people able to help you, and others can > benefit from our conversations in the future by searching the email > archives. > > Now: > > > I performed this command and I solved the problem only for installation > of XML packages, because if I try to perform biocLite for the other > packages it results: > > Warning messages: > > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > installation of package ‘rtracklayer’ had non-zero exit status > > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > installation of package ‘GenomicFeatures’ had non-zero exit status > > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > installation of package ‘VariantAnnotation’ had non-zero exit status > > 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > installation of package ‘gmapR’ had non-zero exit status > > > > This is the same warning message that I had with XML packages. How I can > solve it? > > You will need to provide more output than that to get help. > > You say that after installing libcurl-dev and libxml2-dev on your system, > the XML library install worked in R? > > So when you do `library(XML)` inside R, does it load properly? > > Can you please provide the entire output when you do: > > R> library(BiocInstaller) > R> biocLite(c("RCurl", "rtracklayer")) > > Please also include the entire output of sessionInfo() after the above > commands fail. > > Thanks, > -steve > > -- > Steve Lianoglou > Computational Biologist > Bioinformatics and Computational Biology > Genentech > > > > [[alternative HTML version deleted]]
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Hi Fran, On Wed, Sep 25, 2013 at 2:25 AM, fran vino <biocesca at="" gmail.com=""> wrote: > Hi, > > when I do library(XML) inside R, it loads properly, but if I do: > > R> biocLite(c("RCurl", "rtracklayer")), it results: > > Warning message: > > In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > installation of package ?rtracklayer? had non-zero exit status Surely there must have been more errors than these ... please paste in the entire output you get that includes the errors. The information you are providing is not sufficient to offer any help. We need to see the actual errors that are reported during the installation of rtracklayer, not the notice afterwards that says it wasn't able to be installed. At least from the sessionInfo you provided below, we can tell that RCurl now installs successfully, though. > R> biocLite(?Genomic Features?) This command did not produce the errors below, as there is no package with that name (notice the space)! Please, load BiocInstaller, then type `biocLite("rtracklayer")` and then copy and paste *everything* that happens after that. -steve > Warning messages: > > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > installation of package ?rtracklayer? had non-zero exit status > > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > installation of package ?GenomicFeatures? had non-zero exit status > > > > sessionInfo() > > R version 3.0.1 (2013-05-16) > > 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=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8 > > [7] LC_PAPER=C 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 > > other attached packages: > > [1] RCurl_1.95-4.1 bitops_1.0-6 XML_3.98-1.1 > > [4] BiocInstaller_1.10.3 > > loaded via a namespace (and not attached): > > [1] tools_3.0. > > > 2013/9/24 Steve Lianoglou <lianoglou.steve at="" gene.com=""> > >> Hi Fran, >> >> Please keep all emails on list (hit "reply-all") so that your emails go >> back to the main bioconductor list as well. >> >> In this way you'll have more people able to help you, and others can >> benefit from our conversations in the future by searching the email >> archives. >> >> Now: >> >> > I performed this command and I solved the problem only for installation >> of XML packages, because if I try to perform biocLite for the other >> packages it results: >> > Warning messages: >> > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >> > installation of package ?rtracklayer? had non-zero exit status >> > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >> > installation of package ?GenomicFeatures? had non-zero exit status >> > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >> > installation of package ?VariantAnnotation? had non-zero exit status >> > 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >> > installation of package ?gmapR? had non-zero exit status >> > >> > This is the same warning message that I had with XML packages. How I can >> solve it? >> >> You will need to provide more output than that to get help. >> >> You say that after installing libcurl-dev and libxml2-dev on your system, >> the XML library install worked in R? >> >> So when you do `library(XML)` inside R, does it load properly? >> >> Can you please provide the entire output when you do: >> >> R> library(BiocInstaller) >> R> biocLite(c("RCurl", "rtracklayer")) >> >> Please also include the entire output of sessionInfo() after the above >> commands fail. >> >> Thanks, >> -steve >> >> -- >> Steve Lianoglou >> Computational Biologist >> Bioinformatics and Computational Biology >> Genentech >> >> >> >> > > [[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 -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
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biocLite("rtracklayer") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. Installing package(s) 'rtracklayer' provo con l'URL ' http://bioconductor.org/packages/2.12/bioc/src/contrib/rtracklayer_1.2 0.4.tar.gz ' Content type 'application/x-gzip' length 1323236 bytes (1.3 Mb) URL aperto ================================================== downloaded 1.3 Mb * installing *source* package ‘rtracklayer’ ... ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c R_init_rtracklayer.c -o R_init_rtracklayer.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c bigWig.c -o bigWig.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c chain_io.c -o chain_io.o chain_io.c: In function ‘read_chain_file’: chain_io.c:119: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c twoBit.c -o twoBit.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c handlers.c -o handlers.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c utils.c -o utils.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/bbiRead.c -o ucsc/bbiRead.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/cirTree.c -o ucsc/cirTree.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/common.c -o ucsc/common.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/dnaseq.c -o ucsc/dnaseq.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/dnautil.c -o ucsc/dnautil.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/errabort.c -o ucsc/errabort.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/hash.c -o ucsc/hash.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/linefile.c -o ucsc/linefile.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/localmem.c -o ucsc/localmem.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/sqlNum.c -o ucsc/sqlNum.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/zlibFace.c -o ucsc/zlibFace.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/dystring.c -o ucsc/dystring.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/hmmstats.c -o ucsc/hmmstats.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/obscure.c -o ucsc/obscure.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/pipeline.c -o ucsc/pipeline.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/rangeTree.c -o ucsc/rangeTree.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/rbTree.c -o ucsc/rbTree.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/memalloc.c -o ucsc/memalloc.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/dlist.c -o ucsc/dlist.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -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 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/net.c -o ucsc/net.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/bits.c -o ucsc/bits.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/twoBit.c -o ucsc/twoBit.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/internet.c -o ucsc/internet.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/https.c -o ucsc/https.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/base64.c -o ucsc/base64.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/verbose.c -o ucsc/verbose.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/os.c -o ucsc/os.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/wildcmp.c -o ucsc/wildcmp.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g -fpic -O3 -pipe -g -c ucsc/_portimpl.c -o ucsc/_portimpl.o gcc -std=gnu99 -shared -o rtracklayer.so IRanges_stubs.o R_init_rtracklayer.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errabort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -L/usr/lib64/R/lib -lR installing to /home/marco/R/x86_64-pc-linux-gnu- library/3.0/rtracklayer/libs ** R ** data ** demo ** inst ** preparing package for lazy loading Warning in .simpleDuplicateClass(def, prev) : the specification for class “GroupedIRanges” in package ‘XVector’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : the specification for class “SharedRaw_Pool” in package ‘XVector’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : the specification for class “SharedVector” in package ‘XVector’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : the specification for class “SharedVector_Pool” in package ‘XVector’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : the specification for class “XDoubleViews” in package ‘XVector’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : the specification for class “XIntegerViews” in package ‘XVector’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : the specification for class “XRawList” in package ‘XVector’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : the specification for class “XVector” in package ‘XVector’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : the specification for class “XVectorList” in package ‘XVector’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class Warning: no function found corresponding to methods exports from ‘XVector’ for: ‘showAsCell’ Warning: multiple methods tables found for ‘subseq’ Warning: multiple methods tables found for ‘subseq<-’ Warning: multiple methods tables found for ‘xvcopy’ Warning: multiple methods tables found for ‘compact’ Warning: multiple methods tables found for ‘as.vector’ Warning: replacing previous import ‘.__C__GroupedIRanges’ when loading ‘XVector’ Warning: replacing previous import ‘.__C__SharedDouble’ when loading ‘XVector’ Warning: replacing previous import ‘.__C__SharedInteger’ when loading ‘XVector’ Warning: replacing previous import ‘.__C__SharedRaw’ when loading ‘XVector’ Warning: replacing previous import ‘.__C__SharedRaw_Pool’ when loading ‘XVector’ Warning: replacing previous import ‘.__C__SharedVector’ when loading ‘XVector’ Warning: replacing previous import ‘.__C__SharedVector_Pool’ when loading ‘XVector’ Warning: replacing previous import ‘.__C__XDouble’ when loading ‘XVector’ Warning: replacing previous import ‘.__C__XInteger’ when loading ‘XVector’ Warning: replacing previous import ‘.__C__XIntegerViews’ when loading ‘XVector’ Warning: replacing previous import ‘.__C__XRaw’ when loading ‘XVector’ Warning: replacing previous import ‘.__C__XRawList’ when loading ‘XVector’ Warning: replacing previous import ‘.__C__XVector’ when loading ‘XVector’ Warning: replacing previous import ‘.__C__XVectorList’ when loading ‘XVector’ Warning: replacing previous import ‘SharedRaw’ when loading ‘XVector’ Warning: replacing previous import ‘SharedRaw.read’ when loading ‘XVector’ Warning: replacing previous import ‘SharedRaw.readComplexes’ when loading ‘XVector’ Warning: replacing previous import ‘SharedRaw.readInts’ when loading ‘XVector’ Warning: replacing previous import ‘SharedRaw.write’ when loading ‘XVector’ Warning: replacing previous import ‘SharedRaw.writeInts’ when loading ‘XVector’ Warning: replacing previous import ‘SharedVector.compare’ when loading ‘XVector’ Warning: replacing previous import ‘SharedVector.copy’ when loading ‘XVector’ Warning: replacing previous import ‘XDouble’ when loading ‘XVector’ Warning: replacing previous import ‘XInteger’ when loading ‘XVector’ Warning: replacing previous import ‘XNumeric’ when loading ‘XVector’ Warning: replacing previous import ‘XRaw’ when loading ‘XVector’ Warning: replacing previous import ‘XVectorList’ when loading ‘XVector’ Warning: replacing previous import ‘compact’ when loading ‘XVector’ Warning: replacing previous import ‘duplicated.XRawList’ when loading ‘XVector’ Warning: replacing previous import ‘subseq’ when loading ‘XVector’ Warning: replacing previous import ‘subseq<-’ when loading ‘XVector’ Warning: replacing previous import ‘unlist_list_of_XVectorList’ when loading ‘XVector’ Warning: replacing previous import ‘unsplit_list_of_XVectorList’ when loading ‘XVector’ Warning: replacing previous import ‘window.GroupedIRanges’ when loading ‘XVector’ Warning: replacing previous import ‘window.XVector’ when loading ‘XVector’ Warning: replacing previous import ‘window.XVectorList’ when loading ‘XVector’ Warning: replacing previous import ‘xvcopy’ when loading ‘XVector’ Warning: multiple methods tables found for ‘append’ Warning: multiple methods tables found for ‘subseq’ Warning: multiple methods tables found for ‘subseq<-’ Warning: replacing previous import ‘subseq’ when loading ‘Biostrings’ Warning: replacing previous import ‘subseq<-’ when loading ‘Biostrings’ Error : objects ‘GAlignments’, ‘GAlignmentPairs’ are not exported by 'namespace:GenomicRanges' ERROR: lazy loading failed for package ‘rtracklayer’ * removing ‘/home/marco/R/x86_64-pc-linux-gnu-library/3.0/rtracklayer’ The downloaded source packages are in ‘/tmp/Rtmpr8T9FR/downloaded_packages’ Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘rtracklayer’ had non-zero exit status 2013/9/26 Steve Lianoglou <lianoglou.steve@gene.com> > Hi Fran, > > On Wed, Sep 25, 2013 at 2:25 AM, fran vino <biocesca@gmail.com> wrote: > > Hi, > > > > when I do library(XML) inside R, it loads properly, but if I do: > > > > R> biocLite(c("RCurl", "rtracklayer")), it results: > > > > Warning message: > > > > In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > > > installation of package ‘rtracklayer’ had non-zero exit status > > Surely there must have been more errors than these ... please paste in > the entire output you get that includes the errors. > > The information you are providing is not sufficient to offer any help. > We need to see the actual errors that are reported during the > installation of rtracklayer, not the notice afterwards that says it > wasn't able to be installed. > > At least from the sessionInfo you provided below, we can tell that > RCurl now installs successfully, though. > > > R> biocLite(“Genomic Features”) > > This command did not produce the errors below, as there is no package > with that name (notice the space)! > > Please, load BiocInstaller, then type `biocLite("rtracklayer")` and > then copy and paste *everything* that happens after that. > > -steve > > > Warning messages: > > > > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > > > installation of package ‘rtracklayer’ had non-zero exit status > > > > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > > > installation of package ‘GenomicFeatures’ had non-zero exit status > > > > > > > sessionInfo() > > > > R version 3.0.1 (2013-05-16) > > > > 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=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8 > > > > [7] LC_PAPER=C 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 > > > > other attached packages: > > > > [1] RCurl_1.95-4.1 bitops_1.0-6 XML_3.98-1.1 > > > > [4] BiocInstaller_1.10.3 > > > > loaded via a namespace (and not attached): > > > > [1] tools_3.0. > > > > > > 2013/9/24 Steve Lianoglou <lianoglou.steve@gene.com> > > > >> Hi Fran, > >> > >> Please keep all emails on list (hit "reply-all") so that your emails go > >> back to the main bioconductor list as well. > >> > >> In this way you'll have more people able to help you, and others can > >> benefit from our conversations in the future by searching the email > >> archives. > >> > >> Now: > >> > >> > I performed this command and I solved the problem only for > installation > >> of XML packages, because if I try to perform biocLite for the other > >> packages it results: > >> > Warning messages: > >> > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > >> > installation of package ‘rtracklayer’ had non-zero exit status > >> > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > >> > installation of package ‘GenomicFeatures’ had non-zero exit status > >> > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > >> > installation of package ‘VariantAnnotation’ had non-zero exit status > >> > 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > >> > installation of package ‘gmapR’ had non-zero exit status > >> > > >> > This is the same warning message that I had with XML packages. How I > can > >> solve it? > >> > >> You will need to provide more output than that to get help. > >> > >> You say that after installing libcurl-dev and libxml2-dev on your > system, > >> the XML library install worked in R? > >> > >> So when you do `library(XML)` inside R, does it load properly? > >> > >> Can you please provide the entire output when you do: > >> > >> R> library(BiocInstaller) > >> R> biocLite(c("RCurl", "rtracklayer")) > >> > >> Please also include the entire output of sessionInfo() after the above > >> commands fail. > >> > >> Thanks, > >> -steve > >> > >> -- > >> Steve Lianoglou > >> Computational Biologist > >> Bioinformatics and Computational Biology > >> Genentech > >> > >> > >> > >> > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > Steve Lianoglou > Computational Biologist > Bioinformatics and Computational Biology > Genentech > [[alternative HTML version deleted]]
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Hi Fran, It seems there is a mixture of release and devel packages, at least for GenomicRanges and XVector (which is not supposed to be there for 2.12 release). running the 2 lines below should tell more, removing those packages which are 'too new' and reinstall may help. library(BiocInstaller) biocValid() HTH, Dan On Thu, 2013-09-26 at 16:29 +0200, fran vino wrote: > biocLite("rtracklayer") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. > Installing package(s) 'rtracklayer' > provo con l'URL ' > http://bioconductor.org/packages/2.12/bioc/src/contrib/rtracklayer_1 .20.4.tar.gz > ' > Content type 'application/x-gzip' length 1323236 bytes (1.3 Mb) > URL aperto > ================================================== > downloaded 1.3 Mb > > * installing *source* package rtracklayer ... > ** libs > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c IRanges_stubs.c -o IRanges_stubs.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c R_init_rtracklayer.c -o R_init_rtracklayer.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c bigWig.c -o bigWig.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c chain_io.c -o chain_io.o > chain_io.c: In function read_chain_file: > chain_io.c:119: warning: ignoring return value of fgets, declared with > attribute warn_unused_result > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c twoBit.c -o twoBit.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c handlers.c -o handlers.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c utils.c -o utils.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/bbiRead.c -o ucsc/bbiRead.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/cirTree.c -o ucsc/cirTree.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/common.c -o ucsc/common.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/dnaseq.c -o ucsc/dnaseq.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/dnautil.c -o ucsc/dnautil.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/errabort.c -o ucsc/errabort.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/hash.c -o ucsc/hash.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/linefile.c -o ucsc/linefile.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/localmem.c -o ucsc/localmem.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/sqlNum.c -o ucsc/sqlNum.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/zlibFace.c -o ucsc/zlibFace.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/dystring.c -o ucsc/dystring.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/hmmstats.c -o ucsc/hmmstats.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/obscure.c -o ucsc/obscure.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/pipeline.c -o ucsc/pipeline.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/rangeTree.c -o ucsc/rangeTree.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/rbTree.c -o ucsc/rbTree.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/memalloc.c -o ucsc/memalloc.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/dlist.c -o ucsc/dlist.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -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 > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/net.c -o ucsc/net.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/bits.c -o ucsc/bits.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/twoBit.c -o ucsc/twoBit.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/internet.c -o ucsc/internet.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/https.c -o ucsc/https.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/base64.c -o ucsc/base64.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/verbose.c -o ucsc/verbose.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/os.c -o ucsc/os.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/wildcmp.c -o ucsc/wildcmp.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 > -I"/home/marco/R/x86_64-pc-linux-gnu-library/3.0/IRanges/include" -g > -fpic -O3 -pipe -g -c ucsc/_portimpl.c -o ucsc/_portimpl.o > gcc -std=gnu99 -shared -o rtracklayer.so IRanges_stubs.o > R_init_rtracklayer.o bigWig.o chain_io.o twoBit.o handlers.o utils.o > ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o > ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o > ucsc/errabort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o > ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o > ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o > ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o > ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o > ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -L/usr/lib64/R/lib -lR > installing to /home/marco/R/x86_64-pc-linux-gnu- library/3.0/rtracklayer/libs > ** R > ** data > ** demo > ** inst > ** preparing package for lazy loading > Warning in .simpleDuplicateClass(def, prev) : > the specification for class GroupedIRanges in package XVector seems > equivalent to one from package IRanges and is not turning on duplicate > class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > the specification for class SharedRaw_Pool in package XVector seems > equivalent to one from package IRanges and is not turning on duplicate > class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > the specification for class SharedVector in package XVector seems > equivalent to one from package IRanges and is not turning on duplicate > class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > the specification for class SharedVector_Pool in package XVector > seems equivalent to one from package IRanges and is not turning on > duplicate class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > the specification for class XDoubleViews in package XVector seems > equivalent to one from package IRanges and is not turning on duplicate > class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > the specification for class XIntegerViews in package XVector seems > equivalent to one from package IRanges and is not turning on duplicate > class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > the specification for class XRawList in package XVector seems > equivalent to one from package IRanges and is not turning on duplicate > class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > the specification for class XVector in package XVector seems > equivalent to one from package IRanges and is not turning on duplicate > class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > the specification for class XVectorList in package XVector seems > equivalent to one from package IRanges and is not turning on duplicate > class definitions for this class > Warning: no function found corresponding to methods exports from XVector > for: showAsCell > Warning: multiple methods tables found for subseq > Warning: multiple methods tables found for subseq<- > Warning: multiple methods tables found for xvcopy > Warning: multiple methods tables found for compact > Warning: multiple methods tables found for as.vector > Warning: replacing previous import .__C__GroupedIRanges when loading > XVector > Warning: replacing previous import .__C__SharedDouble when loading > XVector > Warning: replacing previous import .__C__SharedInteger when loading > XVector > Warning: replacing previous import .__C__SharedRaw when loading XVector > Warning: replacing previous import .__C__SharedRaw_Pool when loading > XVector > Warning: replacing previous import .__C__SharedVector when loading > XVector > Warning: replacing previous import .__C__SharedVector_Pool when loading > XVector > Warning: replacing previous import .__C__XDouble when loading XVector > Warning: replacing previous import .__C__XInteger when loading XVector > Warning: replacing previous import .__C__XIntegerViews when loading > XVector > Warning: replacing previous import .__C__XRaw when loading XVector > Warning: replacing previous import .__C__XRawList when loading XVector > Warning: replacing previous import .__C__XVector when loading XVector > Warning: replacing previous import .__C__XVectorList when loading > XVector > Warning: replacing previous import SharedRaw when loading XVector > Warning: replacing previous import SharedRaw.read when loading XVector > Warning: replacing previous import SharedRaw.readComplexes when loading > XVector > Warning: replacing previous import SharedRaw.readInts when loading > XVector > Warning: replacing previous import SharedRaw.write when loading XVector > Warning: replacing previous import SharedRaw.writeInts when loading > XVector > Warning: replacing previous import SharedVector.compare when loading > XVector > Warning: replacing previous import SharedVector.copy when loading > XVector > Warning: replacing previous import XDouble when loading XVector > Warning: replacing previous import XInteger when loading XVector > Warning: replacing previous import XNumeric when loading XVector > Warning: replacing previous import XRaw when loading XVector > Warning: replacing previous import XVectorList when loading XVector > Warning: replacing previous import compact when loading XVector > Warning: replacing previous import duplicated.XRawList when loading > XVector > Warning: replacing previous import subseq when loading XVector > Warning: replacing previous import subseq<- when loading XVector > Warning: replacing previous import unlist_list_of_XVectorList when > loading XVector > Warning: replacing previous import unsplit_list_of_XVectorList when > loading XVector > Warning: replacing previous import window.GroupedIRanges when loading > XVector > Warning: replacing previous import window.XVector when loading XVector > Warning: replacing previous import window.XVectorList when loading > XVector > Warning: replacing previous import xvcopy when loading XVector > Warning: multiple methods tables found for append > Warning: multiple methods tables found for subseq > Warning: multiple methods tables found for subseq<- > Warning: replacing previous import subseq when loading Biostrings > Warning: replacing previous import subseq<- when loading Biostrings > Error : objects GAlignments, GAlignmentPairs are not exported by > 'namespace:GenomicRanges' > ERROR: lazy loading failed for package rtracklayer > * removing /home/marco/R/x86_64-pc-linux-gnu-library/3.0/rtracklayer > > The downloaded source packages are in > /tmp/Rtmpr8T9FR/downloaded_packages > Warning message: > In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package rtracklayer had non-zero exit status > > > > 2013/9/26 Steve Lianoglou <lianoglou.steve at="" gene.com=""> > > > Hi Fran, > > > > On Wed, Sep 25, 2013 at 2:25 AM, fran vino <biocesca at="" gmail.com=""> wrote: > > > Hi, > > > > > > when I do library(XML) inside R, it loads properly, but if I do: > > > > > > R> biocLite(c("RCurl", "rtracklayer")), it results: > > > > > > Warning message: > > > > > > In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > > > > > installation of package rtracklayer had non-zero exit status > > > > Surely there must have been more errors than these ... please paste in > > the entire output you get that includes the errors. > > > > The information you are providing is not sufficient to offer any help. > > We need to see the actual errors that are reported during the > > installation of rtracklayer, not the notice afterwards that says it > > wasn't able to be installed. > > > > At least from the sessionInfo you provided below, we can tell that > > RCurl now installs successfully, though. > > > > > R> biocLite(Genomic Features) > > > > This command did not produce the errors below, as there is no package > > with that name (notice the space)! > > > > Please, load BiocInstaller, then type `biocLite("rtracklayer")` and > > then copy and paste *everything* that happens after that. > > > > -steve > > > > > Warning messages: > > > > > > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > > > > > installation of package rtracklayer had non-zero exit status > > > > > > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > > > > > installation of package GenomicFeatures had non-zero exit status > > > > > > > > > > sessionInfo() > > > > > > R version 3.0.1 (2013-05-16) > > > > > > 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=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8 > > > > > > [7] LC_PAPER=C 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 > > > > > > other attached packages: > > > > > > [1] RCurl_1.95-4.1 bitops_1.0-6 XML_3.98-1.1 > > > > > > [4] BiocInstaller_1.10.3 > > > > > > loaded via a namespace (and not attached): > > > > > > [1] tools_3.0. > > > > > > > > > 2013/9/24 Steve Lianoglou <lianoglou.steve at="" gene.com=""> > > > > > >> Hi Fran, > > >> > > >> Please keep all emails on list (hit "reply-all") so that your emails go > > >> back to the main bioconductor list as well. > > >> > > >> In this way you'll have more people able to help you, and others can > > >> benefit from our conversations in the future by searching the email > > >> archives. > > >> > > >> Now: > > >> > > >> > I performed this command and I solved the problem only for > > installation > > >> of XML packages, because if I try to perform biocLite for the other > > >> packages it results: > > >> > Warning messages: > > >> > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > >> > installation of package rtracklayer had non-zero exit status > > >> > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > >> > installation of package GenomicFeatures had non-zero exit status > > >> > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > >> > installation of package VariantAnnotation had non-zero exit status > > >> > 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > >> > installation of package gmapR had non-zero exit status > > >> > > > >> > This is the same warning message that I had with XML packages. How I > > can > > >> solve it? > > >> > > >> You will need to provide more output than that to get help. > > >> > > >> You say that after installing libcurl-dev and libxml2-dev on your > > system, > > >> the XML library install worked in R? > > >> > > >> So when you do `library(XML)` inside R, does it load properly? > > >> > > >> Can you please provide the entire output when you do: > > >> > > >> R> library(BiocInstaller) > > >> R> biocLite(c("RCurl", "rtracklayer")) > > >> > > >> Please also include the entire output of sessionInfo() after the above > > >> commands fail. > > >> > > >> Thanks, > > >> -steve > > >> > > >> -- > > >> Steve Lianoglou > > >> Computational Biologist > > >> Bioinformatics and Computational Biology > > >> Genentech > > >> > > >> > > >> > > >> > > > > > > [[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 > > > > > > > > -- > > Steve Lianoglou > > Computational Biologist > > Bioinformatics and Computational Biology > > Genentech > > > > [[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
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