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Question: Rsamtools installation error
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5.8 years ago by
Guest User12k
Guest User12k 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. 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. 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/ 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 * 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.
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