Mengni Liu
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/MesKit |
| Branch: RELEASE_3_12 |
| Last Commit: 5896d35 |
| Last Changed Date: 2021-03-26 21:12:13 -0400 (Fri, 26 Mar 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:10 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the MesKit package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1041/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MesKit 1.0.1 (landing page) Mengni Liu
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MesKit |
| Version: 1.0.1 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MesKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MesKit_1.0.1.tar.gz |
| StartedAt: 2021-05-06 04:24:10 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 04:41:07 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 1017.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MesKit.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MesKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MesKit_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MesKit.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.0.1'
* 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 ... OK
* checking installed package size ... NOTE
installed size is 6.1Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
Documented arguments not in \usage in documentation object 'subMaf':
'min.average.adj.vaf'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cna2gene 27.02 1.07 29.75
getBinaryMatrix 20.03 0.94 20.95
getBootstrapValue 18.34 0.09 18.44
getTreeMethod 17.98 0.02 18.00
getTree 17.89 0.01 17.87
calFst 17.26 0.55 18.39
getBranchType 17.58 0.00 17.58
getPhyloTree 13.92 0.01 13.93
getPhyloTreePatient 13.33 0.03 13.35
getPhyloTreeRef 12.97 0.00 12.97
plotMutSigProfile 12.57 0.08 12.66
getMutBranches 12.61 0.03 12.64
getCCFMatrix 12.14 0.01 12.14
compareCCF 11.06 0.92 11.97
getPhyloTreeTsbLabel 11.89 0.04 11.90
fitSignatures 10.06 0.46 10.50
mutHeatmap 10.23 0.03 10.25
compareTree 9.57 0.43 9.99
calJSI 8.89 0.03 8.92
calNeiDist 8.81 0.08 8.88
ccfAUC 8.21 0.03 8.20
mutCluster 7.60 0.10 7.67
triMatrix 7.36 0.13 7.47
classifyMut 7.37 0.03 7.41
mutTrunkBranch 6.77 0.12 6.89
plotPhyloTree 6.18 0.00 6.17
testNeutral 6.03 0.03 6.06
getMafPatient 5.84 0.00 5.84
mathScore 5.45 0.01 5.46
plotMutProfile 5.35 0.03 5.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cna2gene 27.64 0.72 30.02
calFst 23.78 0.14 23.91
getCCFMatrix 20.00 0.01 20.02
getBranchType 18.10 0.02 18.14
getTreeMethod 17.78 0.05 17.82
getTree 16.58 0.00 16.58
compareCCF 15.94 0.39 16.33
getPhyloTreeTsbLabel 16.00 0.00 16.00
getBinaryMatrix 15.61 0.01 15.62
getMutBranches 15.08 0.01 15.09
getBootstrapValue 14.11 0.03 14.13
getPhyloTreeRef 13.85 0.00 13.84
calNeiDist 13.50 0.06 13.54
compareTree 13.03 0.07 13.60
calJSI 12.77 0.02 12.78
getPhyloTree 12.45 0.00 12.43
getPhyloTreePatient 12.39 0.00 12.38
plotMutSigProfile 12.15 0.12 12.25
fitSignatures 11.53 0.19 12.27
mutHeatmap 10.05 0.00 10.05
ccfAUC 8.97 0.01 8.99
mutCluster 8.67 0.12 8.79
plotMutProfile 8.71 0.00 8.71
classifyMut 7.99 0.05 8.03
testNeutral 6.80 0.04 6.81
mutTrunkBranch 6.52 0.11 6.62
triMatrix 6.34 0.09 6.44
mathScore 6.36 0.00 6.39
plotPhyloTree 5.97 0.00 5.96
readMaf 5.89 0.00 5.89
getMafPatient 5.67 0.00 5.66
* 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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/MesKit.Rcheck/00check.log'
for details.
MesKit.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MesKit_1.0.1.tar.gz && rm -rf MesKit.buildbin-libdir && mkdir MesKit.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MesKit.buildbin-libdir MesKit_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MesKit_1.0.1.zip && rm MesKit_1.0.1.tar.gz MesKit_1.0.1.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1799k 100 1799k 0 0 43.5M 0 --:--:-- --:--:-- --:--:-- 45.0M
install for i386
* installing *source* package 'MesKit' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'MesKit' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MesKit' as MesKit_1.0.1.zip
* DONE (MesKit)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MesKit' successfully unpacked and MD5 sums checked
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MesKit.Rcheck/examples_i386/MesKit-Ex.timings
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MesKit.Rcheck/examples_x64/MesKit-Ex.timings
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