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This page was generated on 2021-10-15 15:05:44 -0400 (Fri, 15 Oct 2021).

CHECK results for MesKit on nebbiolo1

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 1074/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.2.0  (landing page)
Mengni Liu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: RELEASE_3_13
git_last_commit: faa3f2a
git_last_commit_date: 2021-05-19 12:54:10 -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: MesKit
Version: 1.2.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MesKit_1.2.0.tar.gz
StartedAt: 2021-10-14 10:30:08 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:36:16 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 367.9 seconds
RetCode: 0
Status:   OK  
CheckDir: MesKit.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MesKit_1.2.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MesKit.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MesKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MesKit’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MesKit’ 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
  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             18.552  0.640  19.027
calFst               10.831  0.076  10.862
getCCFMatrix         10.549  0.116  10.596
getBinaryMatrix       9.996  0.112  10.044
getBootstrapValue    10.037  0.056  10.023
getBranchType         9.626  0.068   9.640
getTree               9.350  0.020   9.315
getPhyloTreeTsbLabel  9.236  0.068   9.248
getMutBranches        9.154  0.139   9.238
getPhyloTreeRef       9.145  0.056   9.150
getPhyloTreePatient   9.127  0.032   9.100
getTreeMethod         9.022  0.020   8.988
getPhyloTree          8.965  0.044   8.945
compareCCF            6.331  1.140   7.424
calNeiDist            7.238  0.108   7.288
plotMutSigProfile     6.969  0.188   7.108
mutHeatmap            6.941  0.036   6.928
calJSI                6.702  0.040   6.693
compareTree           6.003  0.068   6.022
fitSignatures         5.463  0.192   5.624
mutCluster            5.319  0.280   5.554
mutTrunkBranch        5.116  0.192   5.272
plotMutProfile        5.194  0.084   5.231
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/MesKit.Rcheck/00check.log’
for details.



Installation output

MesKit.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MesKit
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘MesKit’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (MesKit)

Tests output


Example timings

MesKit.Rcheck/MesKit-Ex.timings

nameusersystemelapsed
calFst10.831 0.07610.862
calJSI6.7020.0406.693
calNeiDist7.2380.1087.288
ccfAUC4.7540.0164.724
classifyMut3.8800.0483.881
cna2gene18.552 0.64019.027
compareCCF6.3311.1407.424
compareTree6.0030.0686.022
fitSignatures5.4630.1925.624
getBinaryMatrix 9.996 0.11210.044
getBootstrapValue10.037 0.05610.023
getBranchType9.6260.0689.640
getCCFMatrix10.549 0.11610.596
getMafData2.6690.0042.639
getMafPatient2.6080.0002.571
getMafRef2.5970.0002.566
getMutBranches9.1540.1399.238
getNonSyn_vc2.6530.0322.654
getPhyloTree8.9650.0448.945
getPhyloTreePatient9.1270.0329.100
getPhyloTreeRef9.1450.0569.150
getPhyloTreeTsbLabel9.2360.0689.248
getSampleInfo2.7960.0082.773
getTree9.3500.0209.315
getTreeMethod9.0220.0208.988
mathScore2.9590.0402.951
mutCluster5.3190.2805.554
mutHeatmap6.9410.0366.928
mutTrunkBranch5.1160.1925.272
plotCNA2.6510.0122.567
plotMutProfile5.1940.0845.231
plotMutSigProfile6.9690.1887.108
plotPhyloTree3.7220.0403.725
readMaf2.5730.0002.512
readSegment0.4320.0000.379
runMesKit000
subMaf2.6450.0002.608
testNeutral4.0470.0204.013
triMatrix4.8310.1364.930