Problem installing cummeRbund in Ubuntu

Question

[mfahim]

Hi There,

I am facing the following error while installing cummeRbund in Ubuntu 15 vivid..

Please help me out.. Thanks :)

installing to /home/fahimish/R/x86_64-pc-linux-gnu-library/3.2/GenomicAlignments/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicAlignments)
ERROR: dependencies 'XML', 'RCurl' are not available for package 'rtracklayer'
* removing '/home/fahimish/R/x86_64-pc-linux-gnu-library/3.2/rtracklayer'
ERROR: dependencies 'rtracklayer', 'biomaRt', 'RCurl' are not available for package 'GenomicFeatures'
* removing '/home/fahimish/R/x86_64-pc-linux-gnu-library/3.2/GenomicFeatures'
ERROR: dependency 'rtracklayer' is not available for package 'BSgenome'
* removing '/home/fahimish/R/x86_64-pc-linux-gnu-library/3.2/BSgenome'
ERROR: dependencies 'BSgenome', 'rtracklayer', 'GenomicFeatures' are not available for package 'VariantAnnotation'
* removing '/home/fahimish/R/x86_64-pc-linux-gnu-library/3.2/VariantAnnotation'
ERROR: dependencies 'GenomicFeatures', 'VariantAnnotation' are not available for package 'biovizBase'
* removing '/home/fahimish/R/x86_64-pc-linux-gnu-library/3.2/biovizBase'
ERROR: dependencies 'rtracklayer', 'biomaRt', 'GenomicFeatures', 'BSgenome', 'biovizBase' are not available for package 'Gviz'
* removing '/home/fahimish/R/x86_64-pc-linux-gnu-library/3.2/Gviz'
ERROR: dependencies 'rtracklayer', 'Gviz' are not available for package 'cummeRbund'
* removing '/home/fahimish/R/x86_64-pc-linux-gnu-library/3.2/cummeRbund'

while there is some issue with library and using personal library is giving the following error.

Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'XML' had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'RCurl' had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'biomaRt' had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'rtracklayer' had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'GenomicFeatures' had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'BSgenome' had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'VariantAnnotation' had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'biovizBase' had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'Gviz' had non-zero exit status
10: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'cummeRbund' had non-zero exit status

Answer 1

[A. Domingues]

AFAIK there are some libraries missing - I think I had the same problem with Ubuntu 14.04. According to this thread, installing these libraries should solve the problem (assuming you have admin rights):

sudo apt-get install libxml2 libcurl libxml2-dev

[mfahim]

Thanks.. Will have a look at the thread.. the command

sudo apt-get install libxml2 libcurl libxml2-dev

did not help.. :(

Cheers

[mfahim]

Hi FMS

Gviz is not loaded.. that's the latest error I am getting.

Loading required package: Gviz
Loading required package: grid
Error : objects 'metadata', 'isTRUEorFALSE', 'isSingleString' are not exported by 'namespace:IRanges'
Error: package 'Gviz' could not be loaded

here is my session info.. I am still unable to make it work.. In windows it is easy but here I am facing problem.. and I have removed windows..

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.04

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

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] rtracklayer_1.28.6   GenomicRanges_1.20.5 GenomeInfoDb_1.4.1  
 [4] IRanges_2.2.5        S4Vectors_0.6.1      fastcluster_1.1.16  
 [7] reshape2_1.4.1       ggplot2_1.0.1        RSQLite_1.0.0       
[10] DBI_0.3.1            BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.6             XVector_0.8.0           magrittr_1.5           
 [4] GenomicAlignments_1.4.1 zlibbioc_1.14.0         MASS_7.3-42            
 [7] BiocParallel_1.2.9      munsell_0.4.2           colorspace_1.2-6       
[10] stringr_1.0.0           plyr_1.8.3              tools_3.2.1            
[13] Biobase_2.24.0          gtable_0.1.2            lambda.r_1.1.7         
[16] futile.logger_1.4.1     digest_0.6.8            futile.options_1.0.0   
[19] bitops_1.0-6            RCurl_1.95-4.7          stringi_0.5-5          
[22] Rsamtools_1.20.4        Biostrings_2.36.1       scales_0.2.5           
[25] XML_3.98-1.3            proto_0.3-10           

[A. Domingues]

But did the compiling worked ok? Another thread suggests one more linux library sudo apt-get install libcurl4-openssl-dev. Further than this, I can't help you sorry. Try to post on the bioconductor mailing-list.