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This page was generated on 2023-10-16 11:35:30 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1162/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.10.0  (landing page)
Mengni Liu
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: RELEASE_3_17
git_last_commit: b2526ca
git_last_commit_date: 2023-04-25 11:20:51 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

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: 1.10.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MesKit_1.10.0.tar.gz
StartedAt: 2023-10-15 22:36:16 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 22:46:22 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 605.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MesKit_1.10.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MesKit.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MesKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MesKit’ version ‘1.10.0’
* 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-3.17-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 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 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             18.745  0.792  19.396
calFst               16.144  0.268  16.367
getBootstrapValue    15.732  0.204  15.887
getTreeMethod        15.532  0.240  15.726
getPhyloTreeRef      15.327  0.116  15.396
getPhyloTreeTsbLabel 15.271  0.072  15.287
getTree              15.197  0.092  15.240
getPhyloTree         15.168  0.048  15.166
getPhyloTreePatient  14.956  0.123  15.033
getBinaryMatrix      14.573  0.164  14.676
getMutBranches       14.377  0.212  14.539
getCCFMatrix         14.218  0.128  14.295
getBranchType        13.759  0.052  13.749
compareCCF           11.943  1.040  12.934
plotMutSigProfile    12.313  0.160  12.442
calJSI               12.310  0.112  12.367
calNeiDist           12.111  0.124  12.187
mutHeatmap           11.458  0.056  11.467
compareTree          10.361  0.212  10.523
mutTrunkBranch        9.264  0.152   9.378
mutCluster            9.049  0.304   9.314
fitSignatures         9.123  0.212   9.303
ccfAUC                9.040  0.100   9.096
triMatrix             8.629  0.172   8.757
plotPhyloTree         8.510  0.060   8.519
plotMutProfile        8.412  0.052   8.418
testNeutral           8.405  0.012   8.360
classifyMut           7.774  0.508   8.239
getSampleInfo         7.188  0.016   7.159
getNonSyn_vc          7.100  0.012   7.084
readMaf               6.808  0.008   6.724
getMafData            6.731  0.044   6.743
subMaf                6.677  0.044   6.687
getMafPatient         6.669  0.000   6.641
mathScore             6.589  0.040   6.587
getMafRef             6.553  0.076   6.592
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MesKit.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MesKit.Rcheck/00check.log’
for details.



Installation output

MesKit.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MesKit
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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
calFst16.144 0.26816.367
calJSI12.310 0.11212.367
calNeiDist12.111 0.12412.187
ccfAUC9.0400.1009.096
classifyMut7.7740.5088.239
cna2gene18.745 0.79219.396
compareCCF11.943 1.04012.934
compareTree10.361 0.21210.523
fitSignatures9.1230.2129.303
getBinaryMatrix14.573 0.16414.676
getBootstrapValue15.732 0.20415.887
getBranchType13.759 0.05213.749
getCCFMatrix14.218 0.12814.295
getMafData6.7310.0446.743
getMafPatient6.6690.0006.641
getMafRef6.5530.0766.592
getMutBranches14.377 0.21214.539
getNonSyn_vc7.1000.0127.084
getPhyloTree15.168 0.04815.166
getPhyloTreePatient14.956 0.12315.033
getPhyloTreeRef15.327 0.11615.396
getPhyloTreeTsbLabel15.271 0.07215.287
getSampleInfo7.1880.0167.159
getTree15.197 0.09215.240
getTreeMethod15.532 0.24015.726
mathScore6.5890.0406.587
mutCluster9.0490.3049.314
mutHeatmap11.458 0.05611.467
mutTrunkBranch9.2640.1529.378
plotCNA2.8810.0402.804
plotMutProfile8.4120.0528.418
plotMutSigProfile12.313 0.16012.442
plotPhyloTree8.5100.0608.519
readMaf6.8080.0086.724
readSegment0.4890.0040.439
runMesKit0.0010.0000.001
subMaf6.6770.0446.687
testNeutral8.4050.0128.360
triMatrix8.6290.1728.757