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This page was generated on 2021-12-15 12:34:49 -0500 (Wed, 15 Dec 2021).

CHECK results for MesKit on riesling1

To the developers/maintainers of the MesKit package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MesKit.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 1080/2069HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.5.0  (landing page)
Mengni Liu
Snapshot Date: 2021-12-14 13:55:12 -0500 (Tue, 14 Dec 2021)
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: master
git_last_commit: 402cd61
git_last_commit_date: 2021-10-26 13:01:22 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MesKit
Version: 1.5.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MesKit.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MesKit_1.5.0.tar.gz
StartedAt: 2021-12-14 19:34:47 -0500 (Tue, 14 Dec 2021)
EndedAt: 2021-12-14 19:39:51 -0500 (Tue, 14 Dec 2021)
EllapsedTime: 304.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MesKit.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MesKit.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MesKit_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MesKit.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MesKit/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MesKit' version '1.5.0'
* 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 'MesKit' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
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
* 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 ... NOTE
calJSI : processJSI: no visible binding for global variable 'CCF'
cna2gene: no visible global function definition for 'genes'
cna2gene: no visible binding for global variable 'org.Hs.eg.db'
cna2gene: no visible binding for global variable 'seqnames'
cna2gene: no visible binding for global variable 'Chromosome'
cna2gene: no visible binding for global variable 'Hugo_Symbol'
cna2gene: no visible binding for global variable 'Start_Position'
cna2gene: no visible binding for global variable 'End_Position'
cna2gene: no visible binding for global variable 'i.End_Position'
cna2gene: no visible binding for global variable 'i.Start_Position'
cna2gene: no visible binding for global variable 'Patient_ID'
cna2gene: no visible binding for global variable 'Tumor_Sample_Barcode'
cna2gene: no visible binding for global variable 'seg_id'
cna2gene: no visible binding for global variable 'overlap_width'
copyNumberFilter: no visible binding for global variable 'Patient_ID'
drawVAFCombine: no visible binding for global variable 'V'
drawVAFCombineVline: no visible binding for global variable 'V'
fitSignatures : processFitSig: no visible binding for global variable
  'Branch'
fitSignatures : processFitSig: no visible binding for global variable
  'Original'
fitSignatures : processFitSig: no visible binding for global variable
  'Reconstructed'
mutCluster : processVafcluster_sample: no visible binding for global
  variable 'cluster'
plotCNA: no visible binding for global variable 'Cytoband'
plotCNA: no visible binding for global variable 'Cytoband_pos'
plotCNA: no visible binding for global variable 'gene_id'
plotCNA: no visible binding for global variable 'gene_pos'
plotCNA: no visible binding for global variable 'Hugo_Symbol'
plotTree: no visible binding for global variable 'is.match'
plotTree: no visible binding for global variable 'x'
plotTree: no visible binding for global variable 'y'
plotTree: no visible binding for global variable 'xend'
plotTree: no visible binding for global variable 'yend'
Undefined global functions or variables:
  Branch CCF Chromosome Cytoband Cytoband_pos End_Position Hugo_Symbol
  Original Patient_ID Reconstructed Start_Position Tumor_Sample_Barcode
  V cluster gene_id gene_pos genes i.End_Position i.Start_Position
  is.match org.Hs.eg.db overlap_width seg_id seqnames x xend y yend
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
cna2gene             13.72   0.69   14.38
getBinaryMatrix       8.73   0.67    9.39
getMutBranches        8.06   0.06    8.12
calFst                7.66   0.22    7.83
getBootstrapValue     7.22   0.32    7.52
getBranchType         7.50   0.04    7.54
getCCFMatrix          7.33   0.08    7.39
getPhyloTreeRef       7.12   0.00    7.11
getPhyloTreePatient   6.85   0.04    6.89
getTreeMethod         6.84   0.01    6.84
getTree               6.70   0.00    6.70
getPhyloTreeTsbLabel  6.59   0.02    6.60
getPhyloTree          6.58   0.00    6.60
compareCCF            5.50   0.41    5.89
plotMutSigProfile     5.62   0.11    5.73
mutHeatmap            5.11   0.05    5.16
calJSI                5.06   0.01    5.08
* 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/MesKit.Rcheck/00check.log'
for details.



Installation output

MesKit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.15/bioc/src/contrib/MesKit_1.5.0.tar.gz && rm -rf MesKit.buildbin-libdir && mkdir MesKit.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=MesKit.buildbin-libdir MesKit_1.5.0.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MesKit_1.5.0.zip && rm MesKit_1.5.0.tar.gz MesKit_1.5.0.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
 81 1802k   81 1460k    0     0  2340k      0 --:--:-- --:--:-- --:--:-- 2336k
100 1802k  100 1802k    0     0  2552k      0 --:--:-- --:--:-- --:--:-- 2549k
* installing *source* package 'MesKit' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MesKit'
    finding HTML links ... done
    Maf-class                               html  
    MafList-class                           html  
    calFst                                  html  
    calJSI                                  html  
    calNeiDist                              html  
    ccfAUC                                  html  
    classifyMut                             html  
    cna2gene                                html  
    compareCCF                              html  
    compareTree                             html  
    fitSignatures                           html  
    getBinaryMatrix                         html  
    getBootstrapValue                       html  
    getBranchType                           html  
    getCCFMatrix                            html  
    getMafData                              html  
    getMafPatient                           html  
    getMafRef                               html  
    getMutBranches                          html  
    getNonSyn_vc                            html  
    getPhyloTree                            html  
    getPhyloTreePatient                     html  
    getPhyloTreeRef                         html  
    getPhyloTreeTsbLabel                    html  
    getSampleInfo                           html  
    getTree                                 html  
    getTreeMethod                           html  
    mathScore                               html  
    mutCluster                              html  
    mutHeatmap                              html  
    mutTrunkBranch                          html  
    phyloTree-class                         html  
    phyloTreeList-class                     html  
    plotCNA                                 html  
    plotMutProfile                          html  
    plotMutSigProfile                       html  
    plotPhyloTree                           html  
    readMaf                                 html  
    readSegment                             html  
    runMesKit                               html  
    subMaf                                  html  
    testNeutral                             html  
    triMatrix                               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
* MD5 sums
packaged installation of 'MesKit' as MesKit_1.5.0.zip
* DONE (MesKit)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'MesKit' successfully unpacked and MD5 sums checked

Tests output


Example timings

MesKit.Rcheck/MesKit-Ex.timings

nameusersystemelapsed
calFst7.660.227.83
calJSI5.060.015.08
calNeiDist4.850.074.90
ccfAUC4.260.064.32
classifyMut2.690.012.71
cna2gene13.72 0.6914.38
compareCCF5.500.415.89
compareTree4.370.254.61
fitSignatures4.460.314.75
getBinaryMatrix8.730.679.39
getBootstrapValue7.220.327.52
getBranchType7.500.047.54
getCCFMatrix7.330.087.39
getMafData1.900.051.96
getMafPatient1.910.011.92
getMafRef2.390.022.39
getMutBranches8.060.068.12
getNonSyn_vc1.890.051.94
getPhyloTree6.580.006.60
getPhyloTreePatient6.850.046.89
getPhyloTreeRef7.120.007.11
getPhyloTreeTsbLabel6.590.026.60
getSampleInfo1.960.021.96
getTree6.70.06.7
getTreeMethod6.840.016.84
mathScore2.540.022.54
mutCluster4.320.154.48
mutHeatmap5.110.055.16
mutTrunkBranch4.170.194.36
plotCNA1.820.111.90
plotMutProfile3.060.033.08
plotMutSigProfile5.620.115.73
plotPhyloTree2.970.033.00
readMaf2.010.062.06
readSegment0.290.050.33
runMesKit000
subMaf1.950.011.97
testNeutral3.010.023.02
triMatrix3.470.093.56