Problem installing BSgenome.Hsapiens.UCSC.hg19
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mhwaldron104 ▴ 10
@mhwaldron104-8774
Last seen 8.6 years ago
United States

Trying to install this package in R-3.2.2, and get the following error:

> source("http://www.bioconductor.org/biocLite.R")

> biocLite("BSgenome.Hsapiens.UCSC.hg19")

BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
Installing package(s) ‘BSgenome.Hsapiens.UCSC.hg19’
trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz'
Content type 'application/x-gzip' length 688190187 bytes (656.3 MB)
==================================================
downloaded 656.3 MB

* installing *source* package ‘BSgenome.Hsapiens.UCSC.hg19’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Error : .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:
  call: parseURI("")
  error: cannot parse URI
Error: loading failed
Execution halted
ERROR: loading failed

 

 

software error • 3.6k views
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@james-w-macdonald-5106
Last seen 14 hours ago
United States

You need to show the output from sessionInfo() whenever you post about a problem. See the posting guide.

You probably have an outdated package somewhere. Try

library(BiocInstaller)

biocValid()

To figure out what the problem is, or simply

biocLite()

to fix it.

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Thanks, I followed the suggestions above but I still get the same error. Note that I was able to install this on the same system (RHEL5) under R-3.1.1, so not sure why it's not working in R-3.2.2. Here's the sessionInfo() output:

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.18.4

loaded via a namespace (and not attached):
[1] tools_3.2.2

 

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Hi - I had a similar problem when tray to load BSgenome packages. The problem was some entry in the LD_LIBRARY_PATH environment variable (Linux). I reset my LD_LIBRARY_PATH to the bare minimum and this solved the problem. Seems some package (probably) loaded the wrong version of a share library.

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Hi, I had the same problem when installing the BSgenome. Could you please show us how you solve this in detail? I am not that familiar with Linux. Thanks in advance!

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Arne Muller ▴ 20
@arne-muller-8308
Last seen 7.8 years ago
United States

Hi. The BSgenome package has a dependency on the XML package (via rtracklayer). The XML package itself depends on the system library libxml2 which must be installed in your system with version 2.6.3 or higher. On my old Linux redhat system the library were too old. I can give hints how to solve this on linux, only.

On linux do:

echo $LD_LIBRARY_PATH 

and check each of the library entries (separated by : ) for the existence of lib.xml2* . You can do this to check for libxml2* in all of these paths:

for p in `echo $LD_LIBRARY_PATH | tr ':' '\n'` ; do find $p -name 'libxml2*' ; done

Id the full version number of the library is not printed you can get the version number for the libraries in a directory with like this:

 ldconfig -nv DIRECTORY

in my case: 

$ ldconfig -nv /usr/prog/pcsi/RH5/lib

/usr/prog/pcsi/RH5/lib:

    libxml2.so.2 -> libxml2.so.2.9.2

You need to arrange your LD_LIBRARY_PATH  so that the path with the libxml2 version >= 2.6.3 comes first, e.g. in my case I did edited my ~/.bashrc and set the following line:

export LD_LIBRARY_PATH=/usr/prog/pcsi/RH5/lib:$LD_LIBRARY_PATH

You may have to install this library if it is not found (you can install the libxml2 and libxml2-devel RPMs).

    hope this helps

 

 

   

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Had the same problem installing BSgenome.Hsapiens.UCSC.hg19 on R-3.2.0, running CentOS 5.11 (libxml was at 2.6.26)

on a hunch from the previous post, I upgraded the libxml2 packages to 2.7.6 (gotten from rpm.bone.net) & ran the INSTALL again, it worked!

--

ftp://ftp.pbone.net/mirror/ftp5.gwdg.de/pub/opensuse/repositories/home:/L2G/CentOS_5/x86_64/libxml2-2.7.6-1.3.x86_64.rpm
ftp://ftp.pbone.net/mirror/ftp5.gwdg.de/pub/opensuse/repositories/home:/L2G/CentOS_5/x86_64/libxml2-devel-2.7.6-1.3.x86_64.rpm
ftp://ftp.pbone.net/mirror/ftp5.gwdg.de/pub/opensuse/repositories/home:/L2G/CentOS_5/x86_64/libxml2-python-2.7.6-1.3.x86_64.rpm
ftp://ftp.pbone.net/mirror/ftp5.gwdg.de/pub/opensuse/repositories/home:/L2G/RHEL_5/i386/libxml2-devel-2.7.6-1.3.i386.rpm
ftp://ftp.pbone.net/mirror/ftp5.gwdg.de/pub/opensuse/repositories/home:/L2G/RHEL_5/i386/libxml2-2.7.6-1.3.i386.rpm

--

# R CMD INSTALL BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz

BTW, downloaded the tarball first, since it's huge.  It would save a lot of time if installs happens to fail due to dependency issues.

Also I encounter a problem with getting the latest rev of RcppArmdillo, which needed gcc version higher than the stock CentOS5 (gcc 4.1.2), grab the devtoolset-2 (gcc 4.8.2) & run the following before upgrading RcppArmdillo.  Perhaps other packages need higher rev of gcc

# scl enable devtoolset-2 bash

this sets up the environment, so gcc 4.8.2 is used instead of the stock gcc 4.1.2

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OH MY GOD!! This exactly solved my problem. Thanks a lot ! 

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