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Question: biovizBase package installation fails
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gravatar for ville.q.rantanen
3.0 years ago by
Finland
ville.q.rantanen0 wrote:

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
ADD COMMENTlink modified 3.0 years ago by Dan Tenenbaum ♦♦ 8.2k • written 3.0 years ago by ville.q.rantanen0

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’
ADD REPLYlink written 3.0 years ago by amitadlakha20000
4
gravatar for Dan Tenenbaum
3.0 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

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

 

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Dan Tenenbaum ♦♦ 8.2k

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.

ADD REPLYlink modified 2.9 years ago by Dan Tenenbaum ♦♦ 8.2k • written 2.9 years ago by Martin Morgan ♦♦ 20k
0
gravatar for Martin Morgan
3.0 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

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.

ADD COMMENTlink written 3.0 years ago by Martin Morgan ♦♦ 20k
0
gravatar for amitadlakha2000
3.0 years ago by
United Kingdom
amitadlakha20000 wrote:

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

ADD COMMENTlink written 3.0 years ago by amitadlakha20000

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

ADD REPLYlink written 3.0 years ago by Martin Morgan ♦♦ 20k
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