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This page was generated on 2022-01-21 13:08:02 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 machv2


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 1087/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.4.0  (landing page)
Mengni Liu
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 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 -0500 (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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MesKit.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MesKit_1.4.0.tar.gz
StartedAt: 2022-01-20 14:47:02 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 14:58:40 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 697.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MesKit.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MesKit_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘/Users/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
cna2gene             23.855  0.891  24.770
getMutBranches       21.137  0.384  21.544
getBranchType        20.534  0.251  20.803
calFst               20.457  0.270  20.756
getBinaryMatrix      19.750  0.362  20.130
getPhyloTree         19.703  0.162  19.880
getBootstrapValue    19.596  0.229  19.840
getPhyloTreeTsbLabel 19.278  0.231  19.526
getTree              19.291  0.176  19.481
getPhyloTreePatient  19.249  0.161  19.422
getCCFMatrix         18.991  0.281  19.294
getPhyloTreeRef      18.446  0.168  18.625
getTreeMethod        18.176  0.195  18.391
plotMutSigProfile    15.317  0.118  15.443
compareCCF           13.216  1.710  15.082
mutHeatmap           13.671  0.126  13.808
calNeiDist           13.329  0.091  13.432
calJSI               12.971  0.080  13.062
compareTree          12.278  0.212  12.506
fitSignatures        11.073  0.227  11.310
mutCluster           10.255  0.791  11.059
mutTrunkBranch       10.551  0.117  10.679
plotPhyloTree        10.045  0.058  10.113
plotMutProfile        9.514  0.035   9.560
ccfAUC                9.307  0.073   9.390
triMatrix             8.984  0.120   9.109
testNeutral           8.800  0.040   8.849
classifyMut           7.664  0.043   7.711
getMafRef             6.771  0.100   6.880
mathScore             6.297  0.019   6.318
getNonSyn_vc          6.252  0.048   6.305
subMaf                6.231  0.043   6.277
readMaf               6.135  0.048   6.188
getMafPatient         5.835  0.040   5.878
getSampleInfo         5.701  0.017   5.721
getMafData            5.654  0.039   5.696
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck/00check.log’
for details.



Installation output

MesKit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MesKit
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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
calFst20.457 0.27020.756
calJSI12.971 0.08013.062
calNeiDist13.329 0.09113.432
ccfAUC9.3070.0739.390
classifyMut7.6640.0437.711
cna2gene23.855 0.89124.770
compareCCF13.216 1.71015.082
compareTree12.278 0.21212.506
fitSignatures11.073 0.22711.310
getBinaryMatrix19.750 0.36220.130
getBootstrapValue19.596 0.22919.840
getBranchType20.534 0.25120.803
getCCFMatrix18.991 0.28119.294
getMafData5.6540.0395.696
getMafPatient5.8350.0405.878
getMafRef6.7710.1006.880
getMutBranches21.137 0.38421.544
getNonSyn_vc6.2520.0486.305
getPhyloTree19.703 0.16219.880
getPhyloTreePatient19.249 0.16119.422
getPhyloTreeRef18.446 0.16818.625
getPhyloTreeTsbLabel19.278 0.23119.526
getSampleInfo5.7010.0175.721
getTree19.291 0.17619.481
getTreeMethod18.176 0.19518.391
mathScore6.2970.0196.318
mutCluster10.255 0.79111.059
mutHeatmap13.671 0.12613.808
mutTrunkBranch10.551 0.11710.679
plotCNA4.0520.0484.107
plotMutProfile9.5140.0359.560
plotMutSigProfile15.317 0.11815.443
plotPhyloTree10.045 0.05810.113
readMaf6.1350.0486.188
readSegment0.8470.0080.857
runMesKit000
subMaf6.2310.0436.277
testNeutral8.8000.0408.849
triMatrix8.9840.1209.109