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lwh863
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@lwh863-19269
Last seen 5.8 years ago
Hi,
I am trying to install the R package Biseq from this site http://bioconductor.org/packages/release/bioc/html/BiSeq.html
I have R version 3.5.1 and I have it installed on a linux server. Here is what I get out when trying to install the package.
> BiocManager::install("BiSeq", version = "3.8") Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02) Installing package(s) 'BiSeq' also installing the dependencies ‘XML’, ‘annotate’, ‘rtracklayer’, ‘globaltest’ trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.16.tar.gz' Content type 'application/x-gzip' length 1599292 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/annotate_1.60.0.tar.gz' Content type 'application/x-gzip' length 1868635 bytes (1.8 MB) ================================================== downloaded 1.8 MB trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/rtracklayer_1.42.1.tar.gz' Content type 'application/x-gzip' length 1381513 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/globaltest_5.36.0.tar.gz' Content type 'application/x-gzip' length 551900 bytes (538 KB) ================================================== downloaded 538 KB trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/BiSeq_1.22.0.tar.gz' Content type 'application/x-gzip' length 898662 bytes (877 KB) ================================================== downloaded 877 KB * 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 ‘/localhome/bric/lwh863/R/x86_64-pc-linux-gnu-library/3.5/XML’ ERROR: dependency ‘XML’ is not available for package ‘annotate’ * removing ‘/localhome/bric/lwh863/R/x86_64-pc-linux-gnu-library/3.5/annotate’ ERROR: dependency ‘XML’ is not available for package ‘rtracklayer’ * removing ‘/localhome/bric/lwh863/R/x86_64-pc-linux-gnu-library/3.5/rtracklayer’ ERROR: dependency ‘annotate’ is not available for package ‘globaltest’ * removing ‘/localhome/bric/lwh863/R/x86_64-pc-linux-gnu-library/3.5/globaltest’ ERROR: dependencies ‘rtracklayer’, ‘globaltest’ are not available for package ‘BiSeq’ * removing ‘/localhome/bric/lwh863/R/x86_64-pc-linux-gnu-library/3.5/BiSeq’ The downloaded source packages are in ‘/tmp/Rtmp3D8nrL/downloaded_packages’ installation path not writeable, unable to update packages: class, codetools, foreign, lattice, MASS, Matrix, mgcv, survival Warning messages: 1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘XML’ had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘annotate’ had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘rtracklayer’ had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘globaltest’ had non-zero exit status 5: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘BiSeq’ had non-zero exit status
Any help would be much appreciated. Thanks