Question: [devteam-bioc] Rsamtools installation error
0
gravatar for Dan Tenenbaum
6.3 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
Hi, On Thu, Feb 14, 2013 at 3:39 PM, Maintainer <maintainer at="" bioconductor.org=""> wrote: > > I am encountering a problem with trying to install Rsamtools from the latest release of Bioconductor. I am using R version 2.14 but the latest release of Bioconductor is for R version 2.15. I am new to R and Bioconductor so I am wondering if these installation errors are due to the wrong version of R. Unfortunately, I tried updating R (in Ubuntu 12.04) but my version of R still remains 2.14. > Follow the instructions at http://cran.r-project.org/bin/linux/ubuntu/ to update your Ubuntu repositories so they point to the latest version of R. > I will continue try to update to R (ver 2.15) but can someone tell me if there is another potential problem based on the errors in my session output. Yes, you need to sudo apt-get insgtall libxml2-dev libcurl-dev Dan Thanks. > > -- output of sessionInfo(): > >> source("http://bioconductor.org/biocLite.R") >> biocLite("Rsamtools") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'Rsamtools' > Installing package(s) into ?/usr/local/lib/R/site-library? > (as ?lib? is unspecified) > also installing the dependencies ?RCurl?, ?XML?, ?rtracklayer? > > trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-3.tar.gz' > Content type 'application/x-gzip' length 868491 bytes (848 Kb) > opened URL > ================================================== > downloaded 848 Kb > > trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.95-0.1.tar.gz' > Content type 'application/x-gzip' length 1724282 bytes (1.6 Mb) > opened URL > ================================================== > downloaded 1.6 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 > > * 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 ?/usr/local/lib/R/site-library/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 > No ability to remove finalizers on externalptr objects in this verison of R > 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 ?/usr/local/lib/R/site-library/XML? > ERROR: dependencies ?RCurl?, ?XML? are not available for package ?rtracklayer? > * removing ?/usr/local/lib/R/site-library/rtracklayer? > ERROR: dependency ?rtracklayer? is not available for package ?Rsamtools? > * removing ?/usr/local/lib/R/site-library/Rsamtools? > > The downloaded packages are in > ?/tmp/RtmpGSb3No/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 >> > > > -- > Sent via the guest posting facility at bioconductor.org. > > > ____________________________________________________________________ ____ > devteam-bioc mailing list > To unsubscribe from this mailing list send a blank email to > devteam-bioc-leave at lists.fhcrc.org > You can also unsubscribe or change your personal options at > https://lists.fhcrc.org/mailman/listinfo/devteam-bioc >
rsamtools biocinstaller • 769 views
ADD COMMENTlink modified 6.3 years ago by tkhodges20 • written 6.3 years ago by Dan Tenenbaum8.2k
Answer: [devteam-bioc] Rsamtools installation error
0
gravatar for tkhodges
6.3 years ago by
tkhodges20
tkhodges20 wrote:
HI Dan, I finally got a chance to try your instructions. Just wanted to let you know everything installed properly and I am now working with Rsamtools and other Bioconductor packages. Thank you very much. Cheers, Theresa On Thu, Feb 14, 2013 at 5:45 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Hi, > > > On Thu, Feb 14, 2013 at 3:39 PM, Maintainer <maintainer@bioconductor.org> > wrote: > > > > I am encountering a problem with trying to install Rsamtools from the > latest release of Bioconductor. I am using R version 2.14 but the latest > release of Bioconductor is for R version 2.15. I am new to R and > Bioconductor so I am wondering if these installation errors are due to the > wrong version of R. Unfortunately, I tried updating R (in Ubuntu 12.04) > but my version of R still remains 2.14. > > > > Follow the instructions at http://cran.r-project.org/bin/linux/ubuntu/ > to update your Ubuntu repositories so they point to the latest version > of R. > > > I will continue try to update to R (ver 2.15) but can someone tell me if > there is another potential problem based on the errors in my session output. > > Yes, you need to > sudo apt-get insgtall libxml2-dev libcurl-dev > > Dan > > > > Thanks. > > > > -- output of sessionInfo(): > > > >> source("http://bioconductor.org/biocLite.R") > >> biocLite("Rsamtools") > > BioC_mirror: 'http://www.bioconductor.org' > > Using R version 2.14, BiocInstaller version 1.2.1. > > Installing package(s) 'Rsamtools' > > Installing package(s) into ‘/usr/local/lib/R/site-library’ > > (as ‘lib’ is unspecified) > > also installing the dependencies ‘RCurl’, ‘XML’, ‘rtracklayer’ > > > > trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-3.tar.gz' > > Content type 'application/x-gzip' length 868491 bytes (848 Kb) > > opened URL > > ================================================== > > downloaded 848 Kb > > > > trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.95-0.1.tar.gz' > > Content type 'application/x-gzip' length 1724282 bytes (1.6 Mb) > > opened URL > > ================================================== > > downloaded 1.6 Mb > > > > trying URL ' > http://www.bioconductor.org/packages/2.9/bioc/src/contrib/rtracklaye r_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 > > > > * 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 ‘/usr/local/lib/R/site-library/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 > > No ability to remove finalizers on externalptr objects in this verison > of R > > 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 ‘/usr/local/lib/R/site-library/XML’ > > ERROR: dependencies ‘RCurl’, ‘XML’ are not available for package > ‘rtracklayer’ > > * removing ‘/usr/local/lib/R/site-library/rtracklayer’ > > ERROR: dependency ‘rtracklayer’ is not available for package ‘Rsamtools’ > > * removing ‘/usr/local/lib/R/site-library/Rsamtools’ > > > > The downloaded packages are in > > ‘/tmp/RtmpGSb3No/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 > >> > > > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > > > __________________________________________________________________ ______ > > devteam-bioc mailing list > > To unsubscribe from this mailing list send a blank email to > > devteam-bioc-leave@lists.fhcrc.org > > You can also unsubscribe or change your personal options at > > https://lists.fhcrc.org/mailman/listinfo/devteam-bioc > > > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.3 years ago by tkhodges20
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