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CHECK report for SomaticSignatures on tokay2

This page was generated on 2019-04-09 12:16:08 -0400 (Tue, 09 Apr 2019).

Package 1525/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SomaticSignatures 2.19.1
Julian Gehring
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/SomaticSignatures
Branch: master
Last Commit: 5815ff0
Last Changed Date: 2018-12-13 16:20:46 -0400 (Thu, 13 Dec 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: SomaticSignatures
Version: 2.19.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SomaticSignatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SomaticSignatures_2.19.1.tar.gz
StartedAt: 2019-04-09 06:04:27 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:14:14 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 587.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: SomaticSignatures.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SomaticSignatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SomaticSignatures_2.19.1.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SomaticSignatures.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SomaticSignatures/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SomaticSignatures' version '2.19.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SomaticSignatures' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpmQUK4d/R.INSTALL10304e3b4d7b/SomaticSignatures/man/decomposition-functions.Rd:75: file link 'NMF' in package 'NMF' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpmQUK4d/R.INSTALL10304e3b4d7b/SomaticSignatures/man/number-signatures.Rd:98: file link 'evar' in package 'NMF' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SomaticSignatures.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'NMF'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
number-signatures 21.39      0   21.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
number-signatures 24.59      0   24.59
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/SomaticSignatures.Rcheck/00check.log'
for details.



Installation output

SomaticSignatures.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SomaticSignatures_2.19.1.tar.gz && rm -rf SomaticSignatures.buildbin-libdir && mkdir SomaticSignatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SomaticSignatures.buildbin-libdir SomaticSignatures_2.19.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SomaticSignatures_2.19.1.zip && rm SomaticSignatures_2.19.1.tar.gz SomaticSignatures_2.19.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  127k  100  127k    0     0  1957k      0 --:--:-- --:--:-- --:--:-- 2190k

install for i386

* installing *source* package 'SomaticSignatures' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SomaticSignatures'
    finding HTML links ... done
    MutationalSignatures-class              html  
    SomaticSignatures-package               html  
    cluster-spetrum                         html  
    decomposition-functions                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpmQUK4d/R.INSTALL10304e3b4d7b/SomaticSignatures/man/decomposition-functions.Rd:75: file link 'NMF' in package 'NMF' does not exist and so has been treated as a topic
    gc                                      html  
    granges-utils                           html  
    finding level-2 HTML links ... done

    hs-chrs                                 html  
    kmers-data                              html  
    kmers                                   html  
    motif-functions                         html  
    mutation-context                        html  
    mutation-distribution                   html  
    mutational-normalization                html  
    mutational-plots                        html  
    mutational-signatures                   html  
    mutect                                  html  
    number-signatures                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpmQUK4d/R.INSTALL10304e3b4d7b/SomaticSignatures/man/number-signatures.Rd:98: file link 'evar' in package 'NMF' does not exist and so has been treated as a topic
    sca-data                                html  
    signature-plot-functions                html  
    signatures21-data                       html  
    utils                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SomaticSignatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SomaticSignatures' as SomaticSignatures_2.19.1.zip
* DONE (SomaticSignatures)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SomaticSignatures' successfully unpacked and MD5 sums checked

Tests output

SomaticSignatures.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> 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 objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:S4Vectors':

    new2

The following object is masked from 'package:base':

    isFALSE

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 39/40

Attaching package: 'NMF'

The following object is masked from 'package:DelayedArray':

    seed

The following object is masked from 'package:BiocParallel':

    register

The following object is masked from 'package:S4Vectors':

    nrun

The following object is masked from 'package:testthat':

    compare

> 
> test_check("SomaticSignatures")
MutationalSignatures:
  Samples (8): gbm, hnsc, ..., skcm, thca
  Signatures (8): S1, S2, ..., S7, S8
  Motifs (96): CA A.A, CA A.C, ..., TG T.G, TG T.T
== testthat results  ===========================================================
OK: 35 SKIPPED: 2 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  33.62    2.20   37.07 

SomaticSignatures.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> 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 objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:S4Vectors':

    new2

The following object is masked from 'package:base':

    isFALSE

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 39/40

Attaching package: 'NMF'

The following object is masked from 'package:DelayedArray':

    seed

The following object is masked from 'package:BiocParallel':

    register

The following object is masked from 'package:S4Vectors':

    nrun

The following object is masked from 'package:testthat':

    compare

> 
> test_check("SomaticSignatures")
MutationalSignatures:
  Samples (8): gbm, hnsc, ..., skcm, thca
  Signatures (8): S1, S2, ..., S7, S8
  Motifs (96): CA A.A, CA A.C, ..., TG T.G, TG T.T
== testthat results  ===========================================================
OK: 35 SKIPPED: 2 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  37.14    0.84   37.96 

Example timings

SomaticSignatures.Rcheck/examples_i386/SomaticSignatures-Ex.timings

nameusersystemelapsed
SomaticSignatures-package000
gc0.540.100.76
granges-utils0.110.050.17
hs-chrs000
kmers-data0.000.010.01
kmers0.920.534.39
motif-functions0.040.050.08
mutation-context0.290.050.35
mutation-distribution0.440.000.44
mutational-signatures2.480.002.48
mutect0.060.000.07
number-signatures21.39 0.0021.39
sca-data0.020.000.01
signature-plot-functions1.50.01.5
signatures21-data000

SomaticSignatures.Rcheck/examples_x64/SomaticSignatures-Ex.timings

nameusersystemelapsed
SomaticSignatures-package0.010.000.01
gc0.460.000.50
granges-utils0.100.030.12
hs-chrs000
kmers-data0.010.000.02
kmers1.240.061.97
motif-functions0.070.000.08
mutation-context0.410.000.40
mutation-distribution0.560.000.56
mutational-signatures3.670.073.74
mutect0.070.000.06
number-signatures24.59 0.0024.59
sca-data000
signature-plot-functions1.470.001.47
signatures21-data000