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This page was generated on 2023-02-07 11:06:16 -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 palomino4


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: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MesKit.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MesKit_1.8.0.tar.gz
StartedAt: 2023-02-07 02:56:35 -0500 (Tue, 07 Feb 2023)
EndedAt: 2023-02-07 03:14:24 -0500 (Tue, 07 Feb 2023)
EllapsedTime: 1068.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MesKit.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MesKit_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/MesKit.Rcheck'
* using R version 4.2.2 (2022-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (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 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 'F:/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               64.09   0.53   64.93
getMutBranches       36.16   0.39   36.54
getTree              36.16   0.39   36.60
getBranchType        35.80   0.33   36.14
getBinaryMatrix      34.85   0.67   35.51
getPhyloTreeTsbLabel 34.85   0.44   35.29
getCCFMatrix         34.56   0.45   35.03
getPhyloTreePatient  34.20   0.39   34.61
getTreeMethod        34.22   0.27   34.50
getPhyloTree         34.10   0.30   34.39
getBootstrapValue    33.45   0.24   33.77
getPhyloTreeRef      32.31   0.33   32.65
calJSI               25.34   0.30   25.64
compareCCF           24.67   0.89   25.56
calNeiDist           23.46   0.20   23.69
plotMutSigProfile    22.85   0.30   23.18
compareTree          22.47   0.33   22.78
fitSignatures        21.31   0.39   21.70
mutHeatmap           21.57   0.11   21.72
mutTrunkBranch       20.23   0.27   20.50
mutCluster           20.15   0.26   20.47
triMatrix            19.92   0.26   20.22
ccfAUC               19.82   0.17   20.00
plotPhyloTree        19.34   0.14   19.49
plotMutProfile       19.31   0.11   19.41
cna2gene             18.39   0.53   18.91
classifyMut          18.24   0.28   18.51
testNeutral          18.20   0.13   18.34
getMafData           17.81   0.13   17.94
readMaf              16.86   0.14   17.00
subMaf               16.71   0.12   16.83
mathScore            16.42   0.11   16.51
getNonSyn_vc         16.39   0.06   16.47
getSampleInfo        15.70   0.09   15.79
getMafRef            15.64   0.08   15.71
getMafPatient        15.58   0.04   15.62
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/MesKit.Rcheck/00check.log'
for details.



Installation output

MesKit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL MesKit
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-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
calFst64.09 0.5364.93
calJSI25.34 0.3025.64
calNeiDist23.46 0.2023.69
ccfAUC19.82 0.1720.00
classifyMut18.24 0.2818.51
cna2gene18.39 0.5318.91
compareCCF24.67 0.8925.56
compareTree22.47 0.3322.78
fitSignatures21.31 0.3921.70
getBinaryMatrix34.85 0.6735.51
getBootstrapValue33.45 0.2433.77
getBranchType35.80 0.3336.14
getCCFMatrix34.56 0.4535.03
getMafData17.81 0.1317.94
getMafPatient15.58 0.0415.62
getMafRef15.64 0.0815.71
getMutBranches36.16 0.3936.54
getNonSyn_vc16.39 0.0616.47
getPhyloTree34.10 0.3034.39
getPhyloTreePatient34.20 0.3934.61
getPhyloTreeRef32.31 0.3332.65
getPhyloTreeTsbLabel34.85 0.4435.29
getSampleInfo15.70 0.0915.79
getTree36.16 0.3936.60
getTreeMethod34.22 0.2734.50
mathScore16.42 0.1116.51
mutCluster20.15 0.2620.47
mutHeatmap21.57 0.1121.72
mutTrunkBranch20.23 0.2720.50
plotCNA2.890.043.00
plotMutProfile19.31 0.1119.41
plotMutSigProfile22.85 0.3023.18
plotPhyloTree19.34 0.1419.49
readMaf16.86 0.1417.00
readSegment0.480.020.50
runMesKit000
subMaf16.71 0.1216.83
testNeutral18.20 0.1318.34
triMatrix19.92 0.2620.22