Mengni Liu
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/MesKit |
| git_branch: RELEASE_3_14 |
| git_last_commit: 0782512 |
| git_last_commit_date: 2021-10-26 13:01:22 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:51 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1087/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MesKit 1.4.0 (landing page) Mengni Liu
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MesKit |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MesKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MesKit_1.4.0.tar.gz |
| StartedAt: 2022-04-12 22:27:21 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 22:47:33 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 1211.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MesKit.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MesKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MesKit_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.4.0'
* 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 'C:/Users/biocbuild/bbs-3.14-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
* 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 ... OK
* 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
getPhyloTree 26.47 0.13 26.58
getCCFMatrix 26.12 0.11 26.22
getPhyloTreePatient 26.04 0.09 26.12
getMutBranches 25.64 0.25 25.89
getBranchType 25.63 0.18 25.81
getBootstrapValue 24.65 0.03 24.67
getBinaryMatrix 24.38 0.29 24.66
getPhyloTreeTsbLabel 24.55 0.06 24.59
getPhyloTreeRef 24.39 0.03 24.43
getTree 24.28 0.12 24.39
getTreeMethod 24.15 0.14 24.28
cna2gene 18.10 0.66 18.89
calFst 13.42 0.40 14.51
triMatrix 12.52 0.09 12.61
compareCCF 11.39 1.10 12.50
calJSI 12.47 0.01 12.47
compareTree 10.73 0.61 11.33
plotMutSigProfile 11.16 0.12 11.28
mutHeatmap 9.58 0.02 9.59
calNeiDist 9.32 0.05 9.35
mutTrunkBranch 8.45 0.15 8.60
fitSignatures 7.83 0.39 8.23
plotPhyloTree 8.06 0.03 8.08
mutCluster 7.43 0.06 7.48
plotMutProfile 7.17 0.05 7.22
ccfAUC 6.43 0.00 6.43
testNeutral 5.89 0.02 5.91
getMafData 5.63 0.02 5.63
classifyMut 5.14 0.03 5.17
subMaf 5.12 0.01 5.12
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getPhyloTree 29.37 0.06 29.44
getPhyloTreePatient 28.83 0.16 28.98
getMutBranches 28.07 0.12 28.17
getBootstrapValue 28.03 0.04 28.07
getBinaryMatrix 27.68 0.18 27.84
getCCFMatrix 27.78 0.07 27.85
getBranchType 27.34 0.07 27.40
getPhyloTreeRef 26.23 0.09 26.33
getPhyloTreeTsbLabel 25.43 0.05 25.47
getTree 24.71 0.15 24.85
getTreeMethod 24.15 0.09 24.25
cna2gene 20.78 0.71 21.49
calFst 16.45 0.08 16.53
compareCCF 14.50 0.49 14.95
compareTree 14.29 0.12 14.46
plotMutSigProfile 13.25 0.19 13.46
calJSI 13.39 0.02 13.39
calNeiDist 11.22 0.03 11.25
mutHeatmap 10.37 0.08 10.46
mutTrunkBranch 9.94 0.10 10.03
fitSignatures 9.46 0.14 9.59
triMatrix 9.12 0.19 9.30
plotPhyloTree 8.03 0.01 8.04
mutCluster 7.94 0.01 7.93
ccfAUC 7.64 0.04 7.68
plotMutProfile 6.62 0.03 6.67
testNeutral 6.58 0.05 6.62
classifyMut 5.96 0.04 5.98
* 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-3.14-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://155.52.207.166/BBS/3.14/bioc/src/contrib/MesKit_1.4.0.tar.gz && rm -rf MesKit.buildbin-libdir && mkdir MesKit.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MesKit.buildbin-libdir MesKit_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MesKit_1.4.0.zip && rm MesKit_1.4.0.tar.gz MesKit_1.4.0.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
51 1801k 51 925k 0 0 1170k 0 0:00:01 --:--:-- 0:00:01 1171k
100 1801k 100 1801k 0 0 1451k 0 0:00:01 0:00:01 --:--:-- 1452k
install for i386
* 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
install for x64
* installing *source* package 'MesKit' ...
** testing if installed package can be loaded
Warning: replacing previous import 'ape::degree' by 'circlize::degree' when loading 'MesKit'
* MD5 sums
packaged installation of 'MesKit' as MesKit_1.4.0.zip
* DONE (MesKit)
* installing to library 'C:/Users/biocbuild/bbs-3.14-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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