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This page was generated on 2022-01-21 11:11:43 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 merida1


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? here 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 1084/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.5.0  (landing page)
Mengni Liu
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: master
git_last_commit: 402cd61
git_last_commit_date: 2021-10-26 13:01:22 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  ERROR    ERROR  skippedskipped
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'Biostrings' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MesKit
Version: 1.5.0
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_1.5.0.tar.gz
StartedAt: 2022-01-21 02:36:50 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 02:49:57 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 787.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/MesKit.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.5.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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’
See ‘/Users/biocbuild/bbs-3.15-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
cna2gene             26.692  0.705  27.436
calFst               23.621  0.209  23.879
getCCFMatrix         22.711  0.139  23.310
getBranchType        22.606  0.127  23.253
getBootstrapValue    22.249  0.162  22.454
getMutBranches       22.060  0.182  22.382
getBinaryMatrix      21.852  0.207  22.093
getPhyloTreePatient  21.789  0.117  22.315
getPhyloTree         21.686  0.125  22.257
getTree              21.348  0.121  21.501
getTreeMethod        21.229  0.115  21.374
getPhyloTreeTsbLabel 21.196  0.107  21.326
getPhyloTreeRef      21.016  0.191  21.235
plotMutSigProfile    17.125  0.127  17.274
compareCCF           15.282  1.056  16.385
mutHeatmap           15.963  0.064  16.055
calNeiDist           15.323  0.082  15.422
calJSI               14.236  0.087  14.351
compareTree          13.928  0.212  14.165
mutCluster           12.846  0.281  13.156
ccfAUC               12.268  0.074  12.362
fitSignatures        11.999  0.275  12.293
mutTrunkBranch       11.447  0.115  11.577
triMatrix            11.053  0.128  11.192
testNeutral          10.533  0.074  10.978
plotMutProfile       10.337  0.041  10.395
plotPhyloTree         9.986  0.039  10.039
getNonSyn_vc          8.618  0.039   9.045
classifyMut           8.216  0.050   8.278
getMafData            7.489  0.101   7.901
subMaf                7.475  0.035   7.848
getMafPatient         7.043  0.028   7.186
mathScore             6.967  0.027   7.005
readMaf               6.874  0.038   6.920
getMafRef             6.830  0.029   6.866
getSampleInfo         6.794  0.022   6.826
plotCNA               5.018  0.031   5.061
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-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’
** 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’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘ape::degree’ by ‘circlize::degree’ 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
calFst23.621 0.20923.879
calJSI14.236 0.08714.351
calNeiDist15.323 0.08215.422
ccfAUC12.268 0.07412.362
classifyMut8.2160.0508.278
cna2gene26.692 0.70527.436
compareCCF15.282 1.05616.385
compareTree13.928 0.21214.165
fitSignatures11.999 0.27512.293
getBinaryMatrix21.852 0.20722.093
getBootstrapValue22.249 0.16222.454
getBranchType22.606 0.12723.253
getCCFMatrix22.711 0.13923.310
getMafData7.4890.1017.901
getMafPatient7.0430.0287.186
getMafRef6.8300.0296.866
getMutBranches22.060 0.18222.382
getNonSyn_vc8.6180.0399.045
getPhyloTree21.686 0.12522.257
getPhyloTreePatient21.789 0.11722.315
getPhyloTreeRef21.016 0.19121.235
getPhyloTreeTsbLabel21.196 0.10721.326
getSampleInfo6.7940.0226.826
getTree21.348 0.12121.501
getTreeMethod21.229 0.11521.374
mathScore6.9670.0277.005
mutCluster12.846 0.28113.156
mutHeatmap15.963 0.06416.055
mutTrunkBranch11.447 0.11511.577
plotCNA5.0180.0315.061
plotMutProfile10.337 0.04110.395
plotMutSigProfile17.125 0.12717.274
plotPhyloTree 9.986 0.03910.039
readMaf6.8740.0386.920
readSegment0.9580.0070.967
runMesKit000
subMaf7.4750.0357.848
testNeutral10.533 0.07410.978
triMatrix11.053 0.12811.192