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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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

Package 1173/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.15.0  (landing page)
Mengni Liu
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: devel
git_last_commit: 7ed263d
git_last_commit_date: 2024-04-30 11:25:41 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


CHECK results for MesKit on palomino6

To the developers/maintainers of the MesKit package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MesKit
Version: 1.15.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MesKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MesKit_1.15.0.tar.gz
StartedAt: 2024-07-16 01:31:20 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 01:39:13 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 472.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MesKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MesKit_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/MesKit.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MesKit/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MesKit' version '1.15.0'
* 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 'C:/Users/biocbuild/bbs-3.20-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 code 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             22.02   0.73   23.03
getBootstrapValue    13.00   0.44   13.17
calFst               12.60   0.75   12.90
getBranchType        12.06   1.03   15.45
getBinaryMatrix      11.88   0.77   12.63
getCCFMatrix         11.30   0.73   12.05
plotMutSigProfile    11.00   0.51   11.50
getPhyloTree         11.00   0.48   11.43
getPhyloTreeTsbLabel 10.50   0.90   11.31
getTreeMethod        10.72   0.52   11.22
getTree              10.45   0.73   11.20
getPhyloTreePatient  10.25   0.75   11.04
getMutBranches       10.15   0.84   11.07
getPhyloTreeRef      10.25   0.69   10.93
compareCCF           10.23   0.54   10.83
mutHeatmap            9.92   0.16   10.08
calNeiDist            8.88   0.45    9.50
compareTree           9.05   0.28    9.32
ccfAUC                9.21   0.11    9.39
calJSI                8.96   0.09    9.07
fitSignatures         8.29   0.28    8.60
mutCluster            7.95   0.23    8.19
mutTrunkBranch        7.42   0.30    7.77
classifyMut           6.25   0.92    7.17
plotMutProfile        6.93   0.14    7.11
testNeutral           6.88   0.16    7.05
triMatrix             6.75   0.25    7.00
plotPhyloTree         6.22   0.07    6.33
mathScore             5.61   0.09    5.67
getSampleInfo         5.36   0.13    5.50
getNonSyn_vc          5.21   0.10    5.32
subMaf                5.08   0.05    5.12
getMafPatient         5.03   0.06    5.11
getMafData            5.01   0.07    5.08
readMaf               5.00   0.06    5.08
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/MesKit.Rcheck/00check.log'
for details.


Installation output

MesKit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MesKit
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-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
calFst12.60 0.7512.90
calJSI8.960.099.07
calNeiDist8.880.459.50
ccfAUC9.210.119.39
classifyMut6.250.927.17
cna2gene22.02 0.7323.03
compareCCF10.23 0.5410.83
compareTree9.050.289.32
fitSignatures8.290.288.60
getBinaryMatrix11.88 0.7712.63
getBootstrapValue13.00 0.4413.17
getBranchType12.06 1.0315.45
getCCFMatrix11.30 0.7312.05
getMafData5.010.075.08
getMafPatient5.030.065.11
getMafRef4.930.064.97
getMutBranches10.15 0.8411.07
getNonSyn_vc5.210.105.32
getPhyloTree11.00 0.4811.43
getPhyloTreePatient10.25 0.7511.04
getPhyloTreeRef10.25 0.6910.93
getPhyloTreeTsbLabel10.50 0.9011.31
getSampleInfo5.360.135.50
getTree10.45 0.7311.20
getTreeMethod10.72 0.5211.22
mathScore5.610.095.67
mutCluster7.950.238.19
mutHeatmap 9.92 0.1610.08
mutTrunkBranch7.420.307.77
plotCNA2.160.112.31
plotMutProfile6.930.147.11
plotMutSigProfile11.00 0.5111.50
plotPhyloTree6.220.076.33
readMaf5.000.065.08
readSegment0.390.010.41
runMesKit000
subMaf5.080.055.12
testNeutral6.880.167.05
triMatrix6.750.257.00