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Question: Installation of SomaticSignatures
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3.6 years ago by
Guest User12k
Guest User12k wrote:
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.
ADD COMMENTlink modified 3.5 years ago by Julian Gehring1.3k • written 3.6 years ago by Guest User12k

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         

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by chang02_2320

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'.

ADD REPLYlink written 2.4 years ago by Julian Gehring1.3k

ggbio has been fixed in release and devel; the fixed version will be available via biocLite() tomorrow and immediately via svn.

ADD REPLYlink written 2.4 years ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for Julian Gehring
3.5 years ago by
Julian Gehring1.3k
Julian Gehring1.3k wrote:
Hi Sigve, The problem your are experiencing comes from a problem between R and OS mavericks. With mavericks, some basic build tools were changed. To make a long story short, that means that R package binaries created with earlier versions of mac operating systems are not compatible with mavericks. The 'NMF' package (which comes from CRAN) is still available, but does not have a binary build for mavericks yet (see http://cran.r-project.org/web/packages/NMF/index.html). I would expect that this will become available soon. This is in the hands of the CRAN repository maintainers, and it seem that waiting is the best strategy. On the other hand, CRAN has a separate directory with os mavericks builds. I'm not sure why they are not linked to the repo or the web page. You could give it a try and install http://cran.r-project.org/bin/macosx/contrib/r-release/NMF_0.20.5.tgz manually. Best wishes Julian On 08.05.2014 10:40, Sigve at embl-heidelberg.de wrote: > 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/ma vericks/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. >
ADD COMMENTlink written 3.5 years ago by Julian Gehring1.3k
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