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This page was generated on 2022-01-19 11:06:22 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 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 1084/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.5.0  (landing page)
Mengni Liu
Snapshot Date: 2022-01-18 13:55:18 -0500 (Tue, 18 Jan 2022)
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 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  ERROR    ERROR  skippedskipped
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'Biostrings' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MesKit
Version: 1.5.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MesKit_1.5.0.tar.gz
StartedAt: 2022-01-18 19:52:06 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 19:58:10 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 364.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/MesKit.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.5.0’
* 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 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-3.15-bioc/meat/MesKit.Rcheck/00install.out’ for details.
* 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             20.336  0.835  21.014
calFst               10.920  0.209  11.093
getBootstrapValue     9.588  0.092   9.623
getCCFMatrix          9.534  0.129   9.606
compareCCF            8.152  1.428   9.533
getTree               9.470  0.068   9.469
getBranchType         9.445  0.092   9.483
getBinaryMatrix       9.349  0.140   9.434
getMutBranches        9.264  0.196   9.405
getTreeMethod         9.367  0.023   9.333
getPhyloTree          9.282  0.059   9.277
getPhyloTreeTsbLabel  9.162  0.032   9.129
getPhyloTreeRef       9.086  0.080   9.101
getPhyloTreePatient   9.034  0.040   9.012
plotMutSigProfile     7.509  0.184   7.649
calNeiDist            6.975  0.140   7.062
mutCluster            6.545  0.476   6.975
mutHeatmap            6.752  0.048   6.749
calJSI                6.458  0.136   6.542
fitSignatures         6.201  0.303   6.464
compareTree           5.873  0.056   5.865
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/MesKit.Rcheck/00check.log’
for details.



Installation output

MesKit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL MesKit
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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
calFst10.920 0.20911.093
calJSI6.4580.1366.542
calNeiDist6.9750.1407.062
ccfAUC4.9340.0404.925
classifyMut3.3420.0603.351
cna2gene20.336 0.83521.014
compareCCF8.1521.4289.533
compareTree5.8730.0565.865
fitSignatures6.2010.3036.464
getBinaryMatrix9.3490.1409.434
getBootstrapValue9.5880.0929.623
getBranchType9.4450.0929.483
getCCFMatrix9.5340.1299.606
getMafData2.6080.0282.605
getMafPatient2.7450.0002.715
getMafRef2.6870.0202.675
getMutBranches9.2640.1969.405
getNonSyn_vc2.6930.0482.713
getPhyloTree9.2820.0599.277
getPhyloTreePatient9.0340.0409.012
getPhyloTreeRef9.0860.0809.101
getPhyloTreeTsbLabel9.1620.0329.129
getSampleInfo2.7560.0362.758
getTree9.4700.0689.469
getTreeMethod9.3670.0239.333
mathScore2.9440.0002.898
mutCluster6.5450.4766.975
mutHeatmap6.7520.0486.749
mutTrunkBranch4.6490.1444.742
plotCNA2.6330.0282.552
plotMutProfile4.2510.0044.206
plotMutSigProfile7.5090.1847.649
plotPhyloTree4.7130.0324.704
readMaf3.1730.0043.105
readSegment0.5130.0000.451
runMesKit000
subMaf2.9490.0202.931
testNeutral4.3030.0164.262
triMatrix4.7170.1324.814