[Bioc-devel] biovizBase Installation rbind Problem

[Dario Strbenac]

Hello,

I can't install biovizBase, although I have the correct versions of all packages in Depends and Imports fields.

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
> 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 -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O2 -pipe -g  -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O2 -pipe -g  -c bin_offsets.c -o bin_offsets.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/usr/lib/R/lib -lR
installing to /dskh/nobackup/biostat/Bioconductor/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 '/dskh/nobackup/biostat/Bioconductor/biovizBase'
* restoring previous '/dskh/nobackup/biostat/Bioconductor/biovizBase'

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
 [1] BiocInstaller_1.16.1     dichromat_2.0-0          RColorBrewer_1.1-2      
 [4] VariantAnnotation_1.12.6 Rsamtools_1.18.2         AnnotationDbi_1.28.1    
 [7] Biobase_2.26.0           scales_0.2.4             Hmisc_3.14-6            
[10] Formula_1.1-2            survival_2.37-7          lattice_0.20-29         
[13] Biostrings_2.34.0        XVector_0.6.0            GenomicRanges_1.18.3    
[16] GenomeInfoDb_1.2.3       IRanges_2.0.0            S4Vectors_0.4.0         
[19] BiocGenerics_0.12.1     

loaded via a namespace (and not attached):
 [1] BBmisc_1.8              BSgenome_1.34.0         BatchJobs_1.5          
 [4] BiocParallel_1.0.0      DBI_0.3.1               GenomicAlignments_1.2.1
 [7] GenomicFeatures_1.18.2  RCurl_1.95-4.5          RSQLite_1.0.0          
[10] Rcpp_0.11.3             XML_3.98-1.1            acepack_1.3-3.3        
[13] base64enc_0.1-2         biomaRt_2.22.0          bitops_1.0-6           
[16] brew_1.0-6              checkmate_1.5.0         cluster_1.15.3         
[19] codetools_0.2-9         colorspace_1.2-4        digest_0.6.6           
[22] fail_1.2                foreach_1.4.2           foreign_0.8-61         
[25] iterators_1.0.7         latticeExtra_0.6-26     munsell_0.4.2          
[28] nnet_7.3-8              plyr_1.8.1              rpart_4.1-8            
[31] rtracklayer_1.26.2      sendmailR_1.2-1         stringr_0.6.2          
[34] tools_3.1.2             zlibbioc_1.12.0

Are there important and undeclared dependencies for biovizBase ?

I also get different errors for a few other packages I'm trying to update

                 Installed Built   ReposVer
AllelicImbalance "1.0.0"   "3.0.3" "1.4.0" 
GGtools          "4.10.0"  "3.0.3" "5.2.0" 
Gviz             "1.6.0"   "3.0.3" "1.10.3"
ReportingTools   "2.2.0"   "3.0.3" "2.6.0" 
biomvRCNS        "1.2.0"   "3.0.3" "1.6.0" 
biovizBase       "1.10.8"  "3.0.3" "1.14.0"
casper           "1.4.0"   "3.0.3" "2.0.0" 
cummeRbund       "2.4.1"   "3.0.3" "2.8.2" 
ggbio            "1.10.16" "3.0.3" "1.14.0"
intansv          "1.2.0"   "3.0.3" "1.6.0" 
methyAnalysis    "1.4.2"   "3.0.3" "1.8.0" 
qrqc             "1.16.0"  "3.0.3" "1.20.0"
spliceR          "1.3.1"   "3.0.3" "1.8.0" 

> biocLite("spliceR")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.2.
Installing package(s) 'spliceR'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/spliceR_1.8.0.tar.gz'
Content type 'application/x-gzip' length 356213 bytes (347 Kb)
opened URL
==================================================
downloaded 347 Kb

* installing *source* package 'spliceR' ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O2 -pipe -g  -c utils.c -o utils.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o spliceR.so utils.o -L/usr/lib/R/lib -lR
installing to /dskh/nobackup/biostat/Bioconductor/spliceR/libs
** R
** inst
** preparing package for lazy loading
Error : object 'renameSeqlevels' is not exported by 'namespace:GenomicRanges'
Error : package 'Gviz' could not be loaded
ERROR: lazy loading failed for package 'spliceR'
* removing '/dskh/nobackup/biostat/Bioconductor/spliceR'
* restoring previous '/dskh/nobackup/biostat/Bioconductor/spliceR'

--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia