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Hi,
I am trying to install the SomaticSignatures using R version 3.1.0.
There seems to be a problem with the dependency on NMF:
> biocLite("SomaticSignatures")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version
3.1.0.
Installing package(s) 'SomaticSignatures'
Warning: dependency 'NMF' is not available
trying URL 'http://bioconductor.org/packages/2.14/bioc/bin/macosx/mave
ricks/contrib/3.1/SomaticSignatures_1.0.0.tgz'
Content type 'application/x-gzip' length 1712756 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb
The downloaded binary packages are in
/var/folders/kw/sbc71xm12cz18s24f1mvrzd00000gq/T//RtmpuB97PY/d
ownloaded_packages
Warning message:
installed directory not writable, cannot update packages 'MASS'
library(SomaticSignatures)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
versionCheck = vI[[j]]) :
there is no package called 'NMF'
Error: package or namespace load failed for 'SomaticSignatures'
-- output of sessionInfo():
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.1.0
--
Sent via the guest posting facility at bioconductor.org.
I also run into problem with installation. It's having trouble finding ‘latticeGrob’ in gridExtra' even though I have downloaded maverick package and installed separately.
EDIT: Turns out gridExtra v2.0.0 doesn't export latticeGrob anymore. it's only available in v.0.9.1. I rollback to gridExtra 0.9.1 and i can install now.
> library(SomaticSignatures)
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find,
get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist,
unsplit
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Rsamtools
Loading required package: XVector
Loading required package: Biostrings
Attaching package: ‘VariantAnnotation’
The following object is masked from ‘package:base’:
tabulate
Error : object ‘latticeGrob’ is not exported by 'namespace:gridExtra'
Error: package or namespace load failed for ‘SomaticSignatures’
> library(gridExtra)
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] gridExtra_2.0.0 VariantAnnotation_1.14.6 Rsamtools_1.20.4 Biostrings_2.36.1
[5] XVector_0.8.0 GenomicRanges_1.20.5 GenomeInfoDb_1.4.1 IRanges_2.2.5
[9] S4Vectors_0.6.1 BiocGenerics_0.14.0 SomaticCancerAlterations_1.4.0 BiocInstaller_1.18.3
loaded via a namespace (and not attached):
[1] Rcpp_0.11.6 futile.logger_1.4.1 plyr_1.8.3 GenomicFeatures_1.20.1 bitops_1.0-6
[6] futile.options_1.0.0 tools_3.2.1 zlibbioc_1.14.0 biomaRt_2.24.0 digest_0.6.8
[11] RSQLite_1.0.0 gtable_0.1.2 BSgenome_1.36.2 GGally_0.5.0 DBI_0.3.1
[16] proto_0.3-10 rtracklayer_1.28.6 stringr_1.0.0 grid_3.2.1 reshape_0.8.5
[21] Biobase_2.28.0 exomeCopy_1.14.0 AnnotationDbi_1.30.1 XML_3.98-1.3 BiocParallel_1.2.9
[26] ggplot2_1.0.1 reshape2_1.4.1 lambda.r_1.1.7 magrittr_1.5 MASS_7.3-42
[31] scales_0.2.5 GenomicAlignments_1.4.1 colorspace_1.2-6 stringi_0.5-5 munsell_0.4.2
[36] RCurl_1.95-4.7
As you have already mentioned, the major update of the 'gridExtra' package breaks the import of 'ggbio', and hence loading 'SomaticSignatures' since it depends on 'ggbio'. Rolling back to an older version of 'gridExtra' avoids this until there is a fix for 'ggbio'.
ggbio has been fixed in release and devel; the fixed version will be available via biocLite() tomorrow and immediately via svn.