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This page was generated on 2023-02-07 11:06:54 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4511
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4289
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4318
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 lconway


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 1136/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.8.0  (landing page)
Mengni Liu
Snapshot Date: 2023-02-06 14:00:04 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: RELEASE_3_16
git_last_commit: f2c7a2f
git_last_commit_date: 2022-11-01 11:22:30 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MesKit
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2023-02-06 21:35:29 -0500 (Mon, 06 Feb 2023)
EndedAt: 2023-02-06 21:52:55 -0500 (Mon, 06 Feb 2023)
EllapsedTime: 1045.7 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/MesKit.Rcheck’
* using R version 4.2.2 (2022-10-31)
* 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 ‘1.8.0’
* 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 ‘/Users/biocbuild/bbs-3.16-bioc/meat/MesKit.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.9Mb
  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               59.451  0.354  60.007
getTree              35.785  0.486  36.506
getPhyloTreePatient  35.180  0.572  35.981
getPhyloTreeRef      34.580  0.513  35.504
getBootstrapValue    34.545  0.479  35.187
getPhyloTree         34.624  0.376  35.161
getBranchType        34.492  0.495  35.158
getCCFMatrix         34.044  0.494  34.721
getPhyloTreeTsbLabel 33.988  0.441  34.639
getMutBranches       32.836  0.528  33.529
getTreeMethod        32.804  0.481  33.508
getBinaryMatrix      32.037  0.614  32.788
compareCCF           24.250  0.925  25.281
plotMutSigProfile    23.364  0.333  23.831
compareTree          23.323  0.220  23.645
fitSignatures        22.337  0.466  22.949
calJSI               21.759  0.108  21.925
calNeiDist           21.595  0.154  21.872
mutHeatmap           20.539  0.203  20.828
mutTrunkBranch       19.642  0.216  19.979
triMatrix            19.162  0.205  19.437
classifyMut          18.764  0.448  19.288
plotPhyloTree        18.809  0.133  19.029
mutCluster           18.449  0.462  19.037
ccfAUC               18.647  0.132  18.842
testNeutral          18.166  0.155  18.403
cna2gene             17.539  0.739  18.372
plotMutProfile       18.074  0.112  18.265
getNonSyn_vc         16.735  0.191  17.019
readMaf              16.715  0.177  16.966
getMafData           16.592  0.191  16.860
getSampleInfo        16.637  0.109  16.855
subMaf               16.364  0.094  16.514
getMafPatient        16.155  0.107  16.332
mathScore            15.842  0.177  16.099
getMafRef            15.517  0.139  15.726
* 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-3.16-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/4.2/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’
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
calFst59.451 0.35460.007
calJSI21.759 0.10821.925
calNeiDist21.595 0.15421.872
ccfAUC18.647 0.13218.842
classifyMut18.764 0.44819.288
cna2gene17.539 0.73918.372
compareCCF24.250 0.92525.281
compareTree23.323 0.22023.645
fitSignatures22.337 0.46622.949
getBinaryMatrix32.037 0.61432.788
getBootstrapValue34.545 0.47935.187
getBranchType34.492 0.49535.158
getCCFMatrix34.044 0.49434.721
getMafData16.592 0.19116.860
getMafPatient16.155 0.10716.332
getMafRef15.517 0.13915.726
getMutBranches32.836 0.52833.529
getNonSyn_vc16.735 0.19117.019
getPhyloTree34.624 0.37635.161
getPhyloTreePatient35.180 0.57235.981
getPhyloTreeRef34.580 0.51335.504
getPhyloTreeTsbLabel33.988 0.44134.639
getSampleInfo16.637 0.10916.855
getTree35.785 0.48636.506
getTreeMethod32.804 0.48133.508
mathScore15.842 0.17716.099
mutCluster18.449 0.46219.037
mutHeatmap20.539 0.20320.828
mutTrunkBranch19.642 0.21619.979
plotCNA2.6720.0522.738
plotMutProfile18.074 0.11218.265
plotMutSigProfile23.364 0.33323.831
plotPhyloTree18.809 0.13319.029
readMaf16.715 0.17716.966
readSegment0.4310.0070.441
runMesKit0.0000.0010.000
subMaf16.364 0.09416.514
testNeutral18.166 0.15518.403
triMatrix19.162 0.20519.437