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This page was generated on 2021-09-20 15:05:10 -0400 (Mon, 20 Sep 2021).

CHECK results for decompTumor2Sig on tokay2

To the developers/maintainers of the decompTumor2Sig package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decompTumor2Sig.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 457/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decompTumor2Sig 2.8.0  (landing page)
Rosario M. Piro
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/decompTumor2Sig
git_branch: RELEASE_3_13
git_last_commit: 974c2b7
git_last_commit_date: 2021-05-19 12:39:46 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: decompTumor2Sig
Version: 2.8.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:decompTumor2Sig.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings decompTumor2Sig_2.8.0.tar.gz
StartedAt: 2021-09-19 21:19:18 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 21:28:07 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 529.0 seconds
RetCode: 0
Status:   OK  
CheckDir: decompTumor2Sig.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:decompTumor2Sig.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings decompTumor2Sig_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/decompTumor2Sig.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'decompTumor2Sig/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'decompTumor2Sig' version '2.8.0'
* package encoding: UTF-8
* 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 'decompTumor2Sig' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  inst/LICENSE
will install at top-level and is not mentioned in the DESCRIPTION file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plotExplainedVariance     59.59   0.01   59.61
convertGenomesFromVRanges  6.85   1.11    7.97
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plotExplainedVariance     68.19   0.03   68.23
convertGenomesFromVRanges  6.19   0.51    6.70
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/decompTumor2Sig.Rcheck/00check.log'
for details.



Installation output

decompTumor2Sig.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/decompTumor2Sig_2.8.0.tar.gz && rm -rf decompTumor2Sig.buildbin-libdir && mkdir decompTumor2Sig.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=decompTumor2Sig.buildbin-libdir decompTumor2Sig_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL decompTumor2Sig_2.8.0.zip && rm decompTumor2Sig_2.8.0.tar.gz decompTumor2Sig_2.8.0.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
  0 2034k    0  1135    0     0  13870      0  0:02:30 --:--:--  0:02:30 13841
100 2034k  100 2034k    0     0  4460k      0 --:--:-- --:--:-- --:--:-- 4461k

install for i386

* installing *source* package 'decompTumor2Sig' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'decompTumor2Sig'
    finding HTML links ... done
    QPforSig                                html  
    addBestSignatureToSubset                html  
    adjustAlexandrovSignature               html  
    adjustShiraishiSignature                html  
    adjustSignaturesForRegionSet            html  
    buildGenomesFromMutationData            html  
    buildSortedAlexandrovSignaturePatternList
                                            html  
    compNucFreq                             html  
    composeGenomesFromExposures             html  
    computeExplainedVariance                html  
    computeFrobeniusNorm                    html  
    computeRSS                              html  
    convAlx2Shi                             html  
    convertAlexandrov2Shiraishi             html  
    convertGenomesFromVRanges               html  
    convertSeqFreqToBaseFreq                html  
    decompTumor2Sig-package                 html  
    decomposeTumorGenomes                   html  
    determineSignatureDistances             html  
    determineTypeNumBasesAndTrDir           html  
    downgradeShiraishiSignatures            html  
    evaluateDecompositionQuality            html  
    getBestDecomp4Ksignatures               html  
    getCountData                            html  
    getFeatVectList                         html  
    getGenomesFromMutFeatData               html  
    getNumFlankingBases                     html  
    getNumSignatures                        html  
    getSampleList                           html  
    getSigFeatDist                          html  
    getSigFromEstParam                      html  
    getSigType                              html  
    getSignaturesFromEstParam               html  
    haveTrDir                               html  
    is.probability.data.frame               html  
    is.probability.data.frame.list          html  
    is.probability.matrix                   html  
    is.probability.matrix.list              html  
    is.probability.object                   html  
    is.probability.vector                   html  
    is.probability.vector.list              html  
    isAlexandrovSet                         html  
    isBackGround                            html  
    isEstParamObject                        html  
    isExposureSet                           html  
    isMutFeatDataObject                     html  
    isShiraishiSet                          html  
    isSignatureSet                          html  
    mapSignatureSets                        html  
    plotAlexandrovModel                     html  
    plotDecomposedContribution              html  
    plotExplainedVariance                   html  
    plotMutationDistribution                html  
    plotShiraishiModel                      html  
    processMultipleSigSets                  html  
    readAlexandrovSignatures                html  
    readGenomesFromMPF                      html  
    readGenomesFromVCF                      html  
    readShiraishiSignatures                 html  
    roundIntegerSum                         html  
    sameSignatureFormat                     html  
    setNames4ShiraishiTable                 html  
    setNumFlankingBases                     html  
    setSigFeatDist                          html  
    setSigType                              html  
    setTrDir                                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 'decompTumor2Sig' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'decompTumor2Sig' as decompTumor2Sig_2.8.0.zip
* DONE (decompTumor2Sig)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'decompTumor2Sig' successfully unpacked and MD5 sums checked

Tests output


Example timings

decompTumor2Sig.Rcheck/examples_i386/decompTumor2Sig-Ex.timings

nameusersystemelapsed
adjustSignaturesForRegionSet2.450.423.64
composeGenomesFromExposures0.440.030.58
computeExplainedVariance0.490.060.64
convertAlexandrov2Shiraishi0.230.000.34
convertGenomesFromVRanges6.851.117.97
decomposeTumorGenomes3.290.393.80
determineSignatureDistances0.220.000.33
downgradeShiraishiSignatures000
evaluateDecompositionQuality0.40.00.5
getGenomesFromMutFeatData0.640.000.69
getSignaturesFromEstParam0.190.000.20
isAlexandrovSet0.170.020.28
isExposureSet3.820.284.21
isShiraishiSet0.210.000.32
isSignatureSet0.180.000.27
mapSignatureSets0.310.000.40
plotDecomposedContribution0.680.000.78
plotExplainedVariance59.59 0.0159.61
plotMutationDistribution1.750.022.17
readAlexandrovSignatures0.170.000.29
readGenomesFromMPF3.210.273.46
readGenomesFromVCF3.120.263.39
readShiraishiSignatures000
sameSignatureFormat0.250.000.34

decompTumor2Sig.Rcheck/examples_x64/decompTumor2Sig-Ex.timings

nameusersystemelapsed
adjustSignaturesForRegionSet2.870.253.65
composeGenomesFromExposures0.440.000.60
computeExplainedVariance0.470.010.60
convertAlexandrov2Shiraishi0.220.020.33
convertGenomesFromVRanges6.190.516.70
decomposeTumorGenomes4.500.194.80
determineSignatureDistances0.210.000.31
downgradeShiraishiSignatures0.020.000.01
evaluateDecompositionQuality0.390.000.49
getGenomesFromMutFeatData0.530.000.53
getSignaturesFromEstParam0.130.000.13
isAlexandrovSet0.140.000.25
isExposureSet3.220.283.60
isShiraishiSet0.180.000.30
isSignatureSet0.140.000.25
mapSignatureSets0.290.000.39
plotDecomposedContribution0.590.020.71
plotExplainedVariance68.19 0.0368.23
plotMutationDistribution1.860.022.31
readAlexandrovSignatures0.140.000.25
readGenomesFromMPF2.780.313.09
readGenomesFromVCF4.360.304.66
readShiraishiSignatures0.020.000.01
sameSignatureFormat0.190.000.28