Biseq installation error
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Entering edit mode
lwh863 • 0
@lwh863-19269
Last seen 2.6 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 

biseq package installation r • 266 views
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@martin-morgan-1513
Last seen 17 days ago
United States

Simplify the problem by trying to install first only the XML package, with the hints at A: noe able to install geoquery package

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