error in DESeq installationm
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Jitendra ▴ 10
@nabiyogesh-11718
Last seen 14 hours ago
United Kingdom

Dear all When I run try to install DESeq it shows this error: > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help > biocLite("DESeq") BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.1 (2016-06-21). Installing package(s) ‘DESeq’ also installing the dependencies ‘XML’, ‘RCurl’, ‘annotate’, ‘genefilter’, ‘geneplotter’ trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.4.tar.gz' Content type 'unknown' length 1599214 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://cran.rstudio.com/src/contrib/RCurl_1.95-4.8.tar.gz' Content type 'unknown' length 916934 bytes (895 KB) ================================================== downloaded 895 KB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/annotate_1.52.0.tar.gz' Content type 'unknown' length 1861023 bytes (1.8 MB) ================================================== downloaded 1.8 MB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/genefilter_1.56.0.tar.gz' Content type 'unknown' length 1407436 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/geneplotter_1.52.0.tar.gz' Content type 'unknown' length 1426298 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/DESeq_1.26.0.tar.gz' Content type 'unknown' length 1698987 bytes (1.6 MB) ================================================== downloaded 1.6 MB * 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... /usr/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/lib64/R/library/XML’ * 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/lib64/R/library/RCurl’ ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘annotate’ * removing ‘/usr/lib64/R/library/annotate’ ERROR: dependency ‘annotate’ is not available for package ‘genefilter’ * removing ‘/usr/lib64/R/library/genefilter’ ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’ * removing ‘/usr/lib64/R/library/geneplotter’ ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq’ * removing ‘/usr/lib64/R/library/DESeq’ The downloaded source packages are in ‘/tmp/RtmpsMJs05/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘XML’ had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘RCurl’ had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘annotate’ had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘genefilter’ had non-zero exit status 5: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘geneplotter’ had non-zero exit status 6: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘DESeq’ had non-zero exit status Thanks

software error • 1.0k views
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@wouterdecoster-10838
Last seen 20 months ago
Antwerp, Belgium

As you can see the error is not in DESeq, the first problem is in the installation of xml, because it cannot find xml2-config which you should install on your system. Depending on your operating system you will need to run something like sudo apt-get install libxml2-dev or sudo yum install libxml2-devel

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