[Bioc-devel] biovizBase Installation rbind Problem
Dan Tenenbaum
dtenenba at fredhutch.org
Fri Dec 12 02:35:40 CET 2014
----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> To: "Dario Strbenac" <dstr7320 at uni.sydney.edu.au>
> Cc: bioc-devel at r-project.org
> Sent: Thursday, December 11, 2014 5:10:34 PM
> Subject: Re: [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.
This turns out to be the same issue as above. Installing the earlier version of RColorBrewer enables spliceR to be installed.
Dan
> Dan
>
>
> >
> > --------------------------------------
> > Dario Strbenac
> > PhD Student
> > University of Sydney
> > Camperdown NSW 2050
> > Australia
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
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