[Bioc-devel] biovizBase Installation rbind Problem

Fri Dec 12 02:10:34 CET 2014

----- 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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