Question: bioc package installation problem
0
gravatar for carol white
6.0 years ago by
carol white680
European Union
carol white680 wrote:
Hi, I can't install ShortRead package. Is it because biocLite doesn't install automatically the dependencies and I have to install them before ShortRead? Best, Carol ---------------------------------------------------------------------- ---- source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.2.1, ?biocLite for help >  biocLite("ShortRead") BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'ShortRead' also installing the dependencies ‘RCurl’, ‘XML’, ‘rtracklayer’, ‘Rsamtools’ trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-4.1.tar.gz' Content type 'application/x-gzip' length 870915 bytes (850 Kb) opened URL ================================================== downloaded 850 Kb trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.96-1.1.tar.gz' Content type 'application/x-gzip' length 1578308 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 Mb trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/ rtracklayer_1.14.4.tar.gz' Content type 'application/x-gzip' length 1606020 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 Mb trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/ Rsamtools_1.6.3.tar.gz' Content type 'application/x-gzip' length 2088820 bytes (2.0 Mb) opened URL ================================================== downloaded 2.0 Mb trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/ ShortRead_1.12.4.tar.gz' Content type 'application/x-gzip' length 2104718 bytes (2.0 Mb) opened URL ================================================== downloaded 2.0 Mb * installing *source* package ‘RCurl’ ... ** package ‘RCurl’ successfully unpacked and MD5 sums checked checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ‘RCurl’ * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/RCurl’ * installing *source* package ‘XML’ ... ** package ‘XML’ successfully unpacked and MD5 sums checked checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package ‘XML’ * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/XML’ ERROR: dependencies ‘RCurl’, ‘XML’ are not available for package ‘rtracklayer’ * removing ‘/home/carol/R/x86_64-pc-linux-gnu- library/2.14/rtracklayer’ ERROR: dependency ‘rtracklayer’ is not available for package ‘Rsamtools’ * removing ‘/home/carol/R/x86_64-pc-linux-gnu- library/2.14/Rsamtools’ ERROR: dependency ‘Rsamtools’ is not available for package ‘ShortRead’ * removing ‘/home/carol/R/x86_64-pc-linux-gnu- library/2.14/ShortRead’ The downloaded packages are in     ‘/tmp/Rtmpn9i2Os/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, ...) :   installation of package ‘RCurl’ had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, ...) :   installation of package ‘XML’ had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, ...) :   installation of package ‘rtracklayer’ had non-zero exit status 4: In install.packages(pkgs = pkgs, repos = repos, ...) :   installation of package ‘Rsamtools’ had non-zero exit status 5: In install.packages(pkgs = pkgs, repos = repos, ...) :   installation of package ‘ShortRead’ had non-zero exit status [[alternative HTML version deleted]]
shortread biocinstaller • 1.0k views
ADD COMMENTlink modified 6.0 years ago by Dan Tenenbaum8.2k • written 6.0 years ago by carol white680
Answer: bioc package installation problem
0
gravatar for Dan Tenenbaum
6.0 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
On Tue, Apr 9, 2013 at 12:03 PM, carol white <wht_crl at="" yahoo.com=""> wrote: > Hi, > I can't install ShortRead package. Is it because biocLite doesn't install automatically the dependencies and I have to install them before ShortRead? > > > Best, > > Carol > > -------------------------------------------------------------------- ------ > > source("http://bioconductor.org/biocLite.R") > BiocInstaller version 1.2.1, ?biocLite for help >> biocLite("ShortRead") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'ShortRead' > also installing the dependencies ?RCurl?, ?XML?, ?rtracklayer?, ?Rsamtools? > > trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-4.1.tar.gz' > Content type 'application/x-gzip' length 870915 bytes (850 Kb) > opened URL > ================================================== > downloaded 850 Kb > > trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.96-1.1.tar.gz' > Content type 'application/x-gzip' length 1578308 bytes (1.5 Mb) > opened URL > ================================================== > downloaded 1.5 Mb > > trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contri b/rtracklayer_1.14.4.tar.gz' > Content type 'application/x-gzip' length 1606020 bytes (1.5 Mb) > opened URL > ================================================== > downloaded 1.5 Mb > > trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contri b/Rsamtools_1.6.3.tar.gz' > Content type 'application/x-gzip' length 2088820 bytes (2.0 Mb) > opened URL > ================================================== > downloaded 2.0 Mb > > trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contri b/ShortRead_1.12.4.tar.gz' > Content type 'application/x-gzip' length 2104718 bytes (2.0 Mb) > opened URL > ================================================== > downloaded 2.0 Mb > > * installing *source* package ?RCurl? ... > ** package ?RCurl? successfully unpacked and MD5 sums checked > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ?RCurl? > * removing ?/home/carol/R/x86_64-pc-linux-gnu-library/2.14/RCurl? > * installing *source* package ?XML? ... > ** package ?XML? successfully unpacked and MD5 sums checked > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -E > checking for sed... /bin/sed > checking for pkg-config... /usr/bin/pkg-config > checking for xml2-config... no > Cannot find xml2-config This means you need libcurl/libxml2 on your system. I'm not sure which linux distribution you are running but on Ubuntu the command to install this is: sudo apt-get insgtall libxml2-dev libcurl-dev Dan > ERROR: configuration failed for package ?XML? > * removing ?/home/carol/R/x86_64-pc-linux-gnu-library/2.14/XML? > ERROR: dependencies ?RCurl?, ?XML? are not available for package ?rtracklayer? > * removing ?/home/carol/R/x86_64-pc-linux-gnu- library/2.14/rtracklayer? > ERROR: dependency ?rtracklayer? is not available for package ?Rsamtools? > * removing ?/home/carol/R/x86_64-pc-linux-gnu- library/2.14/Rsamtools? > ERROR: dependency ?Rsamtools? is not available for package ?ShortRead? > * removing ?/home/carol/R/x86_64-pc-linux-gnu- library/2.14/ShortRead? > > The downloaded packages are in > ?/tmp/Rtmpn9i2Os/downloaded_packages? > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?RCurl? had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?XML? had non-zero exit status > 3: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?rtracklayer? had non-zero exit status > 4: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?Rsamtools? had non-zero exit status > 5: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?ShortRead? had non-zero exit status > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 6.0 years ago by Dan Tenenbaum8.2k
Thanks Dan. I have Ubuntu. which one should I install?  sudo apt-get install libxml2-dev libcurl-dev Reading package lists... Done Building dependency tree Reading state information... Done Package libcurl-dev is a virtual package provided by:   libcurl4-openssl-dev 7.22.0-3ubuntu4   libcurl4-nss-dev 7.22.0-3ubuntu4   libcurl4-gnutls-dev 7.22.0-3ubuntu4 You should explicitly select one to install. E: Package 'libcurl-dev' has no installation candidate ________________________________ From: Dan Tenenbaum <dtenenba@fhcrc.org> Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch> Sent: Tuesday, April 9, 2013 9:07 PM Subject: Re: [BioC] bioc package installation problem > Hi, > I can't install ShortRead package. Is it because biocLite doesn't install automatically the dependencies and I have to install them before ShortRead? > > > Best, > > Carol > > -------------------------------------------------------------------- ------ > > source("http://bioconductor.org/biocLite.R") > BiocInstaller version 1.2.1, ?biocLite for help >>  biocLite("ShortRead") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'ShortRead' > also installing the dependencies ‘RCurl’, ‘XML’, ‘rtracklayer’, ‘Rsamtools’ > > trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-4.1.tar.gz' > Content type 'application/x-gzip' length 870915 bytes (850 Kb) > opened URL > ================================================== > downloaded 850 Kb > > trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.96-1.1.tar.gz' > Content type 'application/x-gzip' length 1578308 bytes (1.5 Mb) > opened URL > ================================================== > downloaded 1.5 Mb > > trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contri b/rtracklayer_1.14.4.tar.gz' > Content type 'application/x-gzip' length 1606020 bytes (1.5 Mb) > opened URL > ================================================== > downloaded 1.5 Mb > > trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contri b/Rsamtools_1.6.3.tar.gz' > Content type 'application/x-gzip' length 2088820 bytes (2.0 Mb) > opened URL > ================================================== > downloaded 2.0 Mb > > trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contri b/ShortRead_1.12.4.tar.gz' > Content type 'application/x-gzip' length 2104718 bytes (2.0 Mb) > opened URL > ================================================== > downloaded 2.0 Mb > > * installing *source* package ‘RCurl’ ... > ** package ‘RCurl’ successfully unpacked and MD5 sums checked > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ‘RCurl’ > * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/RCurl’ > * installing *source* package ‘XML’ ... > ** package ‘XML’ successfully unpacked and MD5 sums checked > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -E > checking for sed... /bin/sed > checking for pkg-config... /usr/bin/pkg-config > checking for xml2-config... no > Cannot find xml2-config This means you need libcurl/libxml2 on your system. I'm not sure which linux distribution you are running but on Ubuntu the command to install this is: sudo apt-get insgtall libxml2-dev libcurl-dev Dan > ERROR: configuration failed for package ‘XML’ > * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/XML’ > ERROR: dependencies ‘RCurl’, ‘XML’ are not available for package ‘rtracklayer’ > * removing ‘/home/carol/R/x86_64-pc-linux-gnu- library/2.14/rtracklayer’ > ERROR: dependency ‘rtracklayer’ is not available for package ‘Rsamtools’ > * removing ‘/home/carol/R/x86_64-pc-linux-gnu- library/2.14/Rsamtools’ > ERROR: dependency ‘Rsamtools’ is not available for package ‘ShortRead’ > * removing ‘/home/carol/R/x86_64-pc-linux-gnu- library/2.14/ShortRead’ > > The downloaded packages are in >    ‘/tmp/Rtmpn9i2Os/downloaded_packages’ > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : >  installation of package ‘RCurl’ had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, ...) : >  installation of package ‘XML’ had non-zero exit status > 3: In install.packages(pkgs = pkgs, repos = repos, ...) : >  installation of package ‘rtracklayer’ had non-zero exit status > 4: In install.packages(pkgs = pkgs, repos = repos, ...) : >  installation of package ‘Rsamtools’ had non-zero exit status > 5: In install.packages(pkgs = pkgs, repos = repos, ...) : >  installation of package ‘ShortRead’ had non-zero exit status >        [[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]]
ADD REPLYlink written 6.0 years ago by carol white680
On Tue, Apr 9, 2013 at 12:34 PM, carol white <wht_crl at="" yahoo.com=""> wrote: > Thanks Dan. > > I have Ubuntu. which one should I install? > > sudo apt-get install libxml2-dev libcurl-dev > Reading package lists... Done > Building dependency tree > Reading state information... Done > Package libcurl-dev is a virtual package provided by: > libcurl4-openssl-dev 7.22.0-3ubuntu4 > libcurl4-nss-dev 7.22.0-3ubuntu4 > libcurl4-gnutls-dev 7.22.0-3ubuntu4 Our Linux build machine has all three installed, so: sudo apt-get install libxml2-dev libcurl4-openssl-dev libcurl4-nss-dev libcurl4-gnutls-dev Dan > You should explicitly select one to install. > > E: Package 'libcurl-dev' has no installation candidate > > ________________________________ > From: Dan Tenenbaum <dtenenba at="" fhcrc.org=""> > To: carol white <wht_crl at="" yahoo.com=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Sent: Tuesday, April 9, 2013 9:07 PM > Subject: Re: [BioC] bioc package installation problem > > On Tue, Apr 9, 2013 at 12:03 PM, carol white <wht_crl at="" yahoo.com=""> wrote: >> Hi, >> I can't install ShortRead package. Is it because biocLite doesn't install >> automatically the dependencies and I have to install them before ShortRead? >> >> >> Best, >> >> Carol >> >> ------------------------------------------------------------------- ------- >> >> source("http://bioconductor.org/biocLite.R") >> BiocInstaller version 1.2.1, ?biocLite for help >>> biocLite("ShortRead") >> BioC_mirror: 'http://www.bioconductor.org' >> Using R version 2.14, BiocInstaller version 1.2.1. >> Installing package(s) 'ShortRead' >> also installing the dependencies ?RCurl?, ?XML?, ?rtracklayer?, >> ?Rsamtools? >> >> trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-4.1.tar.gz' >> Content type 'application/x-gzip' length 870915 bytes (850 Kb) >> opened URL >> ================================================== >> downloaded 850 Kb >> >> trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.96-1.1.tar.gz' >> Content type 'application/x-gzip' length 1578308 bytes (1.5 Mb) >> opened URL >> ================================================== >> downloaded 1.5 Mb >> >> trying URL >> 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/rtrackla yer_1.14.4.tar.gz' >> Content type 'application/x-gzip' length 1606020 bytes (1.5 Mb) >> opened URL >> ================================================== >> downloaded 1.5 Mb >> >> trying URL >> 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/Rsamtool s_1.6.3.tar.gz' >> Content type 'application/x-gzip' length 2088820 bytes (2.0 Mb) >> opened URL >> ================================================== >> downloaded 2.0 Mb >> >> trying URL >> 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/ShortRea d_1.12.4.tar.gz' >> Content type 'application/x-gzip' length 2104718 bytes (2.0 Mb) >> opened URL >> ================================================== >> downloaded 2.0 Mb >> >> * installing *source* package ?RCurl? ... >> ** package ?RCurl? successfully unpacked and MD5 sums checked >> checking for curl-config... no >> Cannot find curl-config >> ERROR: configuration failed for package ?RCurl? >> * removing ?/home/carol/R/x86_64-pc-linux-gnu-library/2.14/RCurl? >> * installing *source* package ?XML? ... >> ** package ?XML? successfully unpacked and MD5 sums checked >> checking for gcc... gcc >> checking for C compiler default output file name... a.out >> checking whether the C compiler works... yes >> checking whether we are cross compiling... no >> checking for suffix of executables... >> checking for suffix of object files... o >> checking whether we are using the GNU C compiler... yes >> checking whether gcc accepts -g... yes >> checking for gcc option to accept ISO C89... none needed >> checking how to run the C preprocessor... gcc -E >> checking for sed... /bin/sed >> checking for pkg-config... /usr/bin/pkg-config >> checking for xml2-config... no >> Cannot find xml2-config > > > This means you need libcurl/libxml2 on your system. I'm not sure which linux > distribution you are running but on Ubuntu the command to install this > is: > > sudo apt-get insgtall libxml2-dev libcurl-dev > > > Dan > > >> ERROR: configuration failed for package ?XML? >> * removing ?/home/carol/R/x86_64-pc-linux-gnu-library/2.14/XML? >> ERROR: dependencies ?RCurl?, ?XML? are not available for package >> ?rtracklayer? >> * removing ?/home/carol/R/x86_64-pc-linux-gnu- library/2.14/rtracklayer? >> ERROR: dependency ?rtracklayer? is not available for package ?Rsamtools? >> * removing ?/home/carol/R/x86_64-pc-linux-gnu- library/2.14/Rsamtools? >> ERROR: dependency ?Rsamtools? is not available for package ?ShortRead? >> * removing ?/home/carol/R/x86_64-pc-linux-gnu- library/2.14/ShortRead? >> >> The downloaded packages are in >> ?/tmp/Rtmpn9i2Os/downloaded_packages? >> Warning messages: >> 1: In install.packages(pkgs = pkgs, repos = repos, ...) : >> installation of package ?RCurl? had non-zero exit status >> 2: In install.packages(pkgs = pkgs, repos = repos, ...) : >> installation of package ?XML? had non-zero exit status >> 3: In install.packages(pkgs = pkgs, repos = repos, ...) : >> installation of package ?rtracklayer? had non-zero exit status >> 4: In install.packages(pkgs = pkgs, repos = repos, ...) : >> installation of package ?Rsamtools? had non-zero exit status >> 5: In install.packages(pkgs = pkgs, repos = repos, ...) : >> installation of package ?ShortRead? had non-zero exit status >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD REPLYlink written 6.0 years ago by Dan Tenenbaum8.2k
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