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This page was generated on 2023-02-23 01:34:09 -0000 (Thu, 23 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4245
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CHECK results for MesKit on kunpeng1


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 1122/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.9.0  (landing page)
Mengni Liu
Snapshot Date: 2023-02-21 12:29:53 -0000 (Tue, 21 Feb 2023)
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: master
git_last_commit: 09f7690
git_last_commit_date: 2022-11-01 15:22:30 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    WARNINGS  

Summary

Package: MesKit
Version: 1.9.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MesKit_1.9.0.tar.gz
StartedAt: 2023-02-22 07:41:11 -0000 (Wed, 22 Feb 2023)
EndedAt: 2023-02-22 08:10:53 -0000 (Wed, 22 Feb 2023)
EllapsedTime: 1782.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MesKit_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MesKit.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MesKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MesKit’ version ‘1.9.0’
* 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’
  Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘MesKit’
See ‘/home/biocbuild/bbs-3.17-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
calFst               106.304  0.751 107.075
getBootstrapValue     55.646  0.283  55.916
getMutBranches        55.450  0.456  55.893
getPhyloTreeTsbLabel  54.878  0.332  55.199
getPhyloTreeRef       54.638  0.248  54.873
getPhyloTreePatient   54.092  0.308  54.386
getCCFMatrix          54.055  0.268  54.310
getTree               53.865  0.268  54.120
getPhyloTree          53.837  0.264  54.088
getBinaryMatrix       53.585  0.248  53.820
getBranchType         53.253  0.260  53.499
getTreeMethod         53.172  0.280  53.439
calJSI                38.547  0.116  38.648
compareCCF            37.965  0.540  38.491
plotMutSigProfile     37.693  0.284  37.969
compareTree           36.857  0.108  36.958
calNeiDist            35.171  0.060  35.217
mutHeatmap            33.967  0.112  34.066
fitSignatures         32.991  0.124  33.110
mutTrunkBranch        32.241  0.240  32.472
triMatrix             31.745  0.560  32.299
mutCluster            31.789  0.264  32.045
plotPhyloTree         31.892  0.156  32.039
ccfAUC                31.545  0.120  31.650
testNeutral           29.593  1.168  30.752
classifyMut           29.639  0.208  29.833
plotMutProfile        29.603  0.092  29.681
subMaf                28.748  0.220  28.954
readMaf               27.837  0.056  27.878
getMafPatient         27.307  0.044  27.343
getMafRef             27.167  0.092  27.250
mathScore             26.819  0.124  26.928
getNonSyn_vc          26.734  0.148  26.874
getMafData            26.617  0.132  26.740
getSampleInfo         26.264  0.052  26.309
cna2gene              23.045  0.592  23.595
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MesKit.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MesKit.Rcheck/00check.log’
for details.



Installation output

MesKit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MesKit
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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’
Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ 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’
Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ 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’
Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ 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
calFst106.304 0.751107.075
calJSI38.547 0.11638.648
calNeiDist35.171 0.06035.217
ccfAUC31.545 0.12031.650
classifyMut29.639 0.20829.833
cna2gene23.045 0.59223.595
compareCCF37.965 0.54038.491
compareTree36.857 0.10836.958
fitSignatures32.991 0.12433.110
getBinaryMatrix53.585 0.24853.820
getBootstrapValue55.646 0.28355.916
getBranchType53.253 0.26053.499
getCCFMatrix54.055 0.26854.310
getMafData26.617 0.13226.740
getMafPatient27.307 0.04427.343
getMafRef27.167 0.09227.250
getMutBranches55.450 0.45655.893
getNonSyn_vc26.734 0.14826.874
getPhyloTree53.837 0.26454.088
getPhyloTreePatient54.092 0.30854.386
getPhyloTreeRef54.638 0.24854.873
getPhyloTreeTsbLabel54.878 0.33255.199
getSampleInfo26.264 0.05226.309
getTree53.865 0.26854.120
getTreeMethod53.172 0.28053.439
mathScore26.819 0.12426.928
mutCluster31.789 0.26432.045
mutHeatmap33.967 0.11234.066
mutTrunkBranch32.241 0.24032.472
plotCNA4.1950.0284.204
plotMutProfile29.603 0.09229.681
plotMutSigProfile37.693 0.28437.969
plotPhyloTree31.892 0.15632.039
readMaf27.837 0.05627.878
readSegment0.6870.0240.703
runMesKit000
subMaf28.748 0.22028.954
testNeutral29.593 1.16830.752
triMatrix31.745 0.56032.299