 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@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
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> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>

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