Mengni Liu
| Snapshot Date: 2022-03-16 13:55:23 -0400 (Wed, 16 Mar 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 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-17 11:08:10 -0400 (Thu, 17 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4060 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 1091/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MesKit 1.5.0 (landing page) Mengni Liu
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MesKit |
| Version: 1.5.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MesKit.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MesKit_1.5.0.tar.gz |
| StartedAt: 2022-03-16 19:29:21 -0400 (Wed, 16 Mar 2022) |
| EndedAt: 2022-03-16 19:37:32 -0400 (Wed, 16 Mar 2022) |
| EllapsedTime: 492.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MesKit.Rcheck |
| Warnings: 1 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MesKit.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MesKit_1.5.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MesKit.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... 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'
See 'D:/biocbuild/bbs-3.15-bioc/meat/MesKit.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 6.2Mb
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
getTreeMethod 21.66 0.09 21.75
getBinaryMatrix 20.08 0.92 20.98
getTree 20.56 0.16 20.77
getCCFMatrix 20.56 0.09 20.66
getPhyloTree 20.22 0.11 20.30
getMutBranches 19.16 0.16 19.31
getPhyloTreeTsbLabel 17.63 0.15 17.80
getBootstrapValue 17.52 0.25 17.75
getPhyloTreeRef 17.37 0.06 17.43
getBranchType 16.92 0.05 16.97
getPhyloTreePatient 16.16 0.12 16.27
cna2gene 13.22 1.10 14.28
calFst 9.86 0.11 9.96
calJSI 9.36 0.05 9.39
plotMutSigProfile 9.22 0.19 9.39
compareCCF 8.75 0.54 9.30
compareTree 7.58 0.38 7.94
mutHeatmap 7.30 0.02 7.31
triMatrix 7.00 0.13 7.12
calNeiDist 6.73 0.05 6.77
plotPhyloTree 6.72 0.03 6.75
fitSignatures 6.07 0.33 6.39
mutCluster 5.84 0.11 5.94
mutTrunkBranch 5.70 0.14 5.84
testNeutral 5.16 0.03 5.18
ccfAUC 5.03 0.09 5.11
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/MesKit.Rcheck/00check.log'
for details.
MesKit.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MesKit
###
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* installing to library 'D:/biocbuild/bbs-3.15-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'
** help
*** installing help indices
converting help for package 'MesKit'
finding HTML links ... done
Maf-class html
MafList-class html
calFst html
calJSI html
calNeiDist html
ccfAUC html
classifyMut html
cna2gene html
compareCCF html
compareTree html
fitSignatures html
getBinaryMatrix html
getBootstrapValue html
getBranchType html
getCCFMatrix html
getMafData html
getMafPatient html
getMafRef html
getMutBranches html
getNonSyn_vc html
getPhyloTree html
getPhyloTreePatient html
getPhyloTreeRef html
getPhyloTreeTsbLabel html
getSampleInfo html
getTree html
getTreeMethod html
mathScore html
mutCluster html
mutHeatmap html
mutTrunkBranch html
phyloTree-class html
phyloTreeList-class html
plotCNA html
plotMutProfile html
plotMutSigProfile html
plotPhyloTree html
readMaf html
readSegment html
runMesKit html
subMaf html
testNeutral html
triMatrix html
** 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)
Making 'packages.html' ... done
MesKit.Rcheck/MesKit-Ex.timings
| name | user | system | elapsed | |
| calFst | 9.86 | 0.11 | 9.96 | |
| calJSI | 9.36 | 0.05 | 9.39 | |
| calNeiDist | 6.73 | 0.05 | 6.77 | |
| ccfAUC | 5.03 | 0.09 | 5.11 | |
| classifyMut | 3.69 | 0.09 | 3.78 | |
| cna2gene | 13.22 | 1.10 | 14.28 | |
| compareCCF | 8.75 | 0.54 | 9.30 | |
| compareTree | 7.58 | 0.38 | 7.94 | |
| fitSignatures | 6.07 | 0.33 | 6.39 | |
| getBinaryMatrix | 20.08 | 0.92 | 20.98 | |
| getBootstrapValue | 17.52 | 0.25 | 17.75 | |
| getBranchType | 16.92 | 0.05 | 16.97 | |
| getCCFMatrix | 20.56 | 0.09 | 20.66 | |
| getMafData | 2.97 | 0.02 | 2.96 | |
| getMafPatient | 3.25 | 0.01 | 3.27 | |
| getMafRef | 3.17 | 0.00 | 3.16 | |
| getMutBranches | 19.16 | 0.16 | 19.31 | |
| getNonSyn_vc | 4.53 | 0.00 | 4.51 | |
| getPhyloTree | 20.22 | 0.11 | 20.30 | |
| getPhyloTreePatient | 16.16 | 0.12 | 16.27 | |
| getPhyloTreeRef | 17.37 | 0.06 | 17.43 | |
| getPhyloTreeTsbLabel | 17.63 | 0.15 | 17.80 | |
| getSampleInfo | 2.73 | 0.01 | 2.75 | |
| getTree | 20.56 | 0.16 | 20.77 | |
| getTreeMethod | 21.66 | 0.09 | 21.75 | |
| mathScore | 2.92 | 0.02 | 2.92 | |
| mutCluster | 5.84 | 0.11 | 5.94 | |
| mutHeatmap | 7.30 | 0.02 | 7.31 | |
| mutTrunkBranch | 5.70 | 0.14 | 5.84 | |
| plotCNA | 2.20 | 0.03 | 2.23 | |
| plotMutProfile | 4.95 | 0.01 | 4.96 | |
| plotMutSigProfile | 9.22 | 0.19 | 9.39 | |
| plotPhyloTree | 6.72 | 0.03 | 6.75 | |
| readMaf | 3.48 | 0.00 | 3.49 | |
| readSegment | 0.36 | 0.00 | 0.34 | |
| runMesKit | 0 | 0 | 0 | |
| subMaf | 3.03 | 0.03 | 3.06 | |
| testNeutral | 5.16 | 0.03 | 5.18 | |
| triMatrix | 7.00 | 0.13 | 7.12 | |