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This page was generated on 2025-01-25 15:37 -0500 (Sat, 25 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4658
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4455
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4408
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 1194/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.17.0  (landing page)
Mengni Liu
Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025)
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: devel
git_last_commit: 471c27c
git_last_commit_date: 2024-10-29 10:48:53 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for MesKit on nebbiolo1

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: 1.17.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MesKit_1.17.0.tar.gz
StartedAt: 2025-01-24 23:50:31 -0500 (Fri, 24 Jan 2025)
EndedAt: 2025-01-25 00:00:12 -0500 (Sat, 25 Jan 2025)
EllapsedTime: 580.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MesKit_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MesKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MesKit’ version ‘1.17.0’
* 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-3.21-bioc/meat/MesKit.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 loading without being on the library search path ... 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             18.841  0.523  19.191
calFst               14.985  0.167  15.103
getBinaryMatrix      14.438  0.119  14.507
getPhyloTree         14.010  0.310  14.268
getPhyloTreeRef      13.599  0.062  13.610
getMutBranches       13.432  0.160  13.541
getPhyloTreeTsbLabel 13.154  0.116  13.206
getTreeMethod        13.133  0.001  13.078
getTree              13.005  0.055  13.001
getCCFMatrix         12.889  0.085  12.920
getBranchType        12.819  0.033  12.801
getBootstrapValue    12.708  0.020  12.676
getPhyloTreePatient  12.566  0.051  12.569
plotMutSigProfile    11.961  0.215  12.138
compareCCF           11.026  0.881  11.850
mutHeatmap           11.447  0.023  11.421
calJSI               10.679  0.049  10.684
compareTree          10.515  0.083  10.561
calNeiDist           10.388  0.056  10.404
plotPhyloTree         9.378  0.162   9.502
fitSignatures         9.242  0.166   9.389
mutCluster            8.994  0.293   9.247
ccfAUC                8.982  0.048   8.983
mutTrunkBranch        8.829  0.181   8.958
triMatrix             8.802  0.179   8.932
plotMutProfile        8.681  0.030   8.655
testNeutral           8.416  0.017   8.381
classifyMut           7.626  0.453   8.036
getNonSyn_vc          6.917  0.003   6.887
getMafRef             6.898  0.019   6.885
mathScore             6.861  0.004   6.803
getMafData            6.779  0.070   6.817
getSampleInfo         6.736  0.024   6.727
getMafPatient         6.667  0.050   6.684
subMaf                6.573  0.031   6.563
readMaf               6.546  0.036   6.516
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck/00check.log’
for details.


Installation output

MesKit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MesKit
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘MesKit’ ...
** this is package ‘MesKit’ version ‘1.17.0’
** 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
calFst14.985 0.16715.103
calJSI10.679 0.04910.684
calNeiDist10.388 0.05610.404
ccfAUC8.9820.0488.983
classifyMut7.6260.4538.036
cna2gene18.841 0.52319.191
compareCCF11.026 0.88111.850
compareTree10.515 0.08310.561
fitSignatures9.2420.1669.389
getBinaryMatrix14.438 0.11914.507
getBootstrapValue12.708 0.02012.676
getBranchType12.819 0.03312.801
getCCFMatrix12.889 0.08512.920
getMafData6.7790.0706.817
getMafPatient6.6670.0506.684
getMafRef6.8980.0196.885
getMutBranches13.432 0.16013.541
getNonSyn_vc6.9170.0036.887
getPhyloTree14.010 0.31014.268
getPhyloTreePatient12.566 0.05112.569
getPhyloTreeRef13.599 0.06213.610
getPhyloTreeTsbLabel13.154 0.11613.206
getSampleInfo6.7360.0246.727
getTree13.005 0.05513.001
getTreeMethod13.133 0.00113.078
mathScore6.8610.0046.803
mutCluster8.9940.2939.247
mutHeatmap11.447 0.02311.421
mutTrunkBranch8.8290.1818.958
plotCNA2.8020.0042.711
plotMutProfile8.6810.0308.655
plotMutSigProfile11.961 0.21512.138
plotPhyloTree9.3780.1629.502
readMaf6.5460.0366.516
readSegment0.4420.0020.382
runMesKit000
subMaf6.5730.0316.563
testNeutral8.4160.0178.381
triMatrix8.8020.1798.932