[BioC] installation packages
Dan Du
tooyoung at gmail.com
Fri Sep 27 11:07:49 CEST 2013
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]]
>
> _______________________________________________
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