[Bioc-devel] biovizBase Installation rbind Problem
----- Original Message -----
From: "Dario Strbenac" <dstr7320 at uni.sydney.edu.au> To: bioc-devel at r-project.org Sent: Thursday, December 11, 2014 5:00:11 PM Subject: [Bioc-devel] biovizBase Installation rbind Problem 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'
See https://support.bioconductor.org/p/63510/#63529
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'
I'm not sure about this one, let me get back to you. Dan
-------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia
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