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
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