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This page was generated on 2022-04-13 12:05:34 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MesKit on nebbiolo2


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? 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 1087/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.4.0  (landing page)
Mengni Liu
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: RELEASE_3_14
git_last_commit: 0782512
git_last_commit_date: 2021-10-26 13:01:22 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MesKit
Version: 1.4.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MesKit_1.4.0.tar.gz
StartedAt: 2022-04-12 08:07:22 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:16:21 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 539.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MesKit_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.4.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘ape::degree’ by ‘circlize::degree’ when loading ‘MesKit’
See ‘/home/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.0Mb
  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
getPhyloTreeTsbLabel 22.760  0.161  22.856
getPhyloTreeRef      22.635  0.116  22.693
getBinaryMatrix      22.188  0.228  22.352
getBootstrapValue    22.269  0.056  22.256
getBranchType        22.173  0.124  22.236
getCCFMatrix         22.096  0.196  22.234
getPhyloTreePatient  21.489  0.088  21.516
getPhyloTree         21.509  0.044  21.491
getMutBranches       21.073  0.144  21.159
getTreeMethod        20.711  0.076  20.726
getTree              20.429  0.152  20.526
cna2gene             17.898  0.636  18.377
calFst               12.888  0.211  13.051
calJSI               11.582  0.117  11.649
compareCCF           10.822  0.444  11.217
compareTree           9.680  0.092   9.728
plotMutSigProfile     9.492  0.068   9.512
calNeiDist            8.540  0.120   8.612
fitSignatures         7.864  0.096   7.912
triMatrix             7.702  0.056   7.801
mutHeatmap            7.569  0.032   7.550
mutTrunkBranch        7.026  0.060   7.041
ccfAUC                6.432  0.104   6.484
plotPhyloTree         6.458  0.076   6.482
mutCluster            5.891  0.076   5.918
testNeutral           5.832  0.012   5.784
plotMutProfile        5.004  0.052   5.003
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck/00check.log’
for details.



Installation output

MesKit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL MesKit
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘MesKit’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘ape::degree’ by ‘circlize::degree’ when loading ‘MesKit’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘ape::degree’ by ‘circlize::degree’ when loading ‘MesKit’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘ape::degree’ by ‘circlize::degree’ when loading ‘MesKit’
** testing if installed package keeps a record of temporary installation path
* DONE (MesKit)

Tests output


Example timings

MesKit.Rcheck/MesKit-Ex.timings

nameusersystemelapsed
calFst12.888 0.21113.051
calJSI11.582 0.11711.649
calNeiDist8.5400.1208.612
ccfAUC6.4320.1046.484
classifyMut4.8610.0684.869
cna2gene17.898 0.63618.377
compareCCF10.822 0.44411.217
compareTree9.6800.0929.728
fitSignatures7.8640.0967.912
getBinaryMatrix22.188 0.22822.352
getBootstrapValue22.269 0.05622.256
getBranchType22.173 0.12422.236
getCCFMatrix22.096 0.19622.234
getMafData3.4730.0153.459
getMafPatient3.5380.0043.507
getMafRef3.5170.0443.526
getMutBranches21.073 0.14421.159
getNonSyn_vc3.5170.0683.553
getPhyloTree21.509 0.04421.491
getPhyloTreePatient21.489 0.08821.516
getPhyloTreeRef22.635 0.11622.693
getPhyloTreeTsbLabel22.760 0.16122.856
getSampleInfo3.5060.0073.480
getTree20.429 0.15220.526
getTreeMethod20.711 0.07620.726
mathScore3.6620.0093.617
mutCluster5.8910.0765.918
mutHeatmap7.5690.0327.550
mutTrunkBranch7.0260.0607.041
plotCNA2.6050.0122.492
plotMutProfile5.0040.0525.003
plotMutSigProfile9.4920.0689.512
plotPhyloTree6.4580.0766.482
readMaf4.3220.0044.260
readSegment0.5060.0040.449
runMesKit000
subMaf4.0240.0003.982
testNeutral5.8320.0125.784
triMatrix7.7020.0567.801