biovizBase package installation fails
3
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Entering edit mode
@villeqrantanen-7147
Last seen 8.0 years ago
Finland

I get an error when installing biovizBase, that seems to come from the package R code itself:

> biocLite("biovizBase")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.2.
Installing package(s) 'biovizBase'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/biovizBase_1.14.0.tar.gz'
Content type 'application/x-gzip' length 2429664 bytes (2.3 Mb)
opened URL
==================================================
downloaded 2.3 Mb

* installing *source* package ‘biovizBase’ ...
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function ‘scan_bam_bin_offsets’:
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
/usr/include/string.h:399: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
/usr/include/string.h:399: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness
bin_offsets.c:57: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
/usr/include/string.h:399: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness
bin_offsets.c:57: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness
bin_offsets.c:57: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness
bin_offsets.c:57: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness
/usr/include/string.h:146: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/biovizBase/libs
** R
** data
** inst
** preparing package for lazy loading
Error in rbind(deparse.level, ...) : 
  numbers of columns of arguments do not match
Error : unable to load R code in package ‘biovizBase’
ERROR: lazy loading failed for package ‘biovizBase’
* removing ‘/usr/lib64/R/library/biovizBase’

The downloaded source packages are in
    ‘/tmp/Rtmp9Ubt7U/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘biovizBase’ had non-zero exit status

 

I dont seem to get around this problem, since it's not dependent on missing libraries etc..  

 

Here's my system info:

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-redhat-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=fi_FI.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fi_FI.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_1.16.1

loaded via a namespace (and not attached):
[1] tools_3.1.2
biovizbase installation • 3.0k views
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Entering edit mode

FYI I've been getting the same error. The programmer in our group is a bit stumped with this, so no idea what the problem is.

 

Error in rbind(deparse.level, ...) : 
  numbers of columns of arguments do not match
Error : unable to load R code in package ‘biovizBase’
ERROR: lazy loading failed for package ‘biovizBase’
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4
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 22 months ago
United States

The problem has to do with a recent change to the RColorBrewer package. It works with an older version which you can get here:

http://cran.r-project.org/src/contrib/Archive/RColorBrewer/RColorBrewer_1.0-5.tar.gz

I will contact the RColorBrewer and biovizBase maintainers and let them know about this issue.

Dan

 

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Entering edit mode

biovizBase has been updated in Bioconductor version 3.0 (to biovizBase version 1.14.1) and devel; the updated version should be available tomorrow after noon Seattle time.

Unfortunately, users of Bioconductor versions before 3.0 (i.e., biovizBase before 1.14.0) will need to ensure that the old version of the RColorBrewer package mentioned by Dan is installed.

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@martin-morgan-1513
Last seen 17 days ago
United States

That's a bit of a mystery. It seems like the error occurs when R is trying to update installed packages. I notice that the installation directory is /usr/lib64/R/library/, which is not specific to a particular version of R; maybe you are installing over an old (ancient?) R? This also implies that you are installing packages as super-user, whereas it is better practice to install packages as a regular user, perhaps to a directory where other users have read access.

As a test, you might try using .libPaths() to point to a non-system directory, something like .libPaths('/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1') before running biocLite().

If this seems like it's in the right direction, see the help page ?.libPaths for approaches to making this kind of separation of R installation and user package installation more permanent; for my own use the default R library path is 'read only', and when R tries to install it's first new package it prompts me to create the appropriate 'personal' directory.

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@amitadlakha2000-7150
Last seen 8.0 years ago
United Kingdom

Hi Martin, thanks for suggestion for ville.q.rantanenI tried it myself (I'm using R-3.1.2.) - .libPaths to a non-system directory, and sadly I still get the same error at the ** preparing package for lazy loading** stage

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Entering edit mode

Thanks for the test; I think that suggestion was a red herring; more news later...

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