Mengni Liu
| Snapshot Date: 2024-07-05 14:00 -0400 (Fri, 05 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/MesKit |
| git_branch: devel |
| git_last_commit: 7ed263d |
| git_last_commit_date: 2024-04-30 11:25:41 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-06 11:40 -0400 (Sat, 06 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
| 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 1173/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MesKit 1.15.0 (landing page) Mengni Liu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. |
| Package: MesKit |
| Version: 1.15.0 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MesKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MesKit_1.15.0.tar.gz |
| StartedAt: 2024-07-06 01:24:37 -0400 (Sat, 06 Jul 2024) |
| EndedAt: 2024-07-06 01:35:57 -0400 (Sat, 06 Jul 2024) |
| EllapsedTime: 679.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MesKit.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MesKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MesKit_1.15.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/MesKit.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MesKit/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MesKit' version '1.15.0'
* 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'
Warning: replacing previous import 'ape::where' by 'dplyr::where' when loading 'MesKit'
See 'C:/Users/biocbuild/bbs-3.20-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 code 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 30.96 2.81 34.79
getCCFMatrix 23.76 0.84 25.93
getBootstrapValue 23.05 0.66 20.42
getTree 19.64 0.75 20.93
getPhyloTreeRef 19.25 0.76 19.92
getBranchType 18.45 1.06 19.50
plotMutSigProfile 16.86 0.35 17.19
calFst 16.08 0.58 16.44
getPhyloTreePatient 15.79 0.69 15.63
compareTree 15.78 0.41 17.81
getTreeMethod 15.30 0.66 16.47
getBinaryMatrix 15.03 0.66 16.11
getPhyloTreeTsbLabel 11.99 3.50 15.41
getPhyloTree 13.96 0.66 14.78
compareCCF 13.36 0.66 14.00
getMutBranches 12.61 0.84 13.45
calJSI 12.97 0.11 12.45
mutCluster 8.08 4.89 12.98
calNeiDist 12.23 0.12 12.47
mutHeatmap 10.79 0.36 13.86
triMatrix 10.33 0.37 10.95
subMaf 10.37 0.14 10.50
mutTrunkBranch 9.60 0.41 9.96
ccfAUC 9.81 0.14 10.39
testNeutral 9.46 0.18 9.69
fitSignatures 9.30 0.32 9.85
getNonSyn_vc 8.56 0.11 8.61
classifyMut 8.27 0.19 8.50
plotMutProfile 8.36 0.04 8.61
plotPhyloTree 7.95 0.18 8.11
getMafRef 7.70 0.05 7.76
getMafPatient 7.61 0.06 7.72
getMafData 7.27 0.08 7.68
getSampleInfo 6.89 0.05 6.94
readMaf 6.47 0.11 7.28
plotCNA 4.03 2.02 4.24
mathScore 5.76 0.07 5.88
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/MesKit.Rcheck/00check.log'
for details.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MesKit ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-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' 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)
MesKit.Rcheck/MesKit-Ex.timings
| name | user | system | elapsed | |
| calFst | 16.08 | 0.58 | 16.44 | |
| calJSI | 12.97 | 0.11 | 12.45 | |
| calNeiDist | 12.23 | 0.12 | 12.47 | |
| ccfAUC | 9.81 | 0.14 | 10.39 | |
| classifyMut | 8.27 | 0.19 | 8.50 | |
| cna2gene | 30.96 | 2.81 | 34.79 | |
| compareCCF | 13.36 | 0.66 | 14.00 | |
| compareTree | 15.78 | 0.41 | 17.81 | |
| fitSignatures | 9.30 | 0.32 | 9.85 | |
| getBinaryMatrix | 15.03 | 0.66 | 16.11 | |
| getBootstrapValue | 23.05 | 0.66 | 20.42 | |
| getBranchType | 18.45 | 1.06 | 19.50 | |
| getCCFMatrix | 23.76 | 0.84 | 25.93 | |
| getMafData | 7.27 | 0.08 | 7.68 | |
| getMafPatient | 7.61 | 0.06 | 7.72 | |
| getMafRef | 7.70 | 0.05 | 7.76 | |
| getMutBranches | 12.61 | 0.84 | 13.45 | |
| getNonSyn_vc | 8.56 | 0.11 | 8.61 | |
| getPhyloTree | 13.96 | 0.66 | 14.78 | |
| getPhyloTreePatient | 15.79 | 0.69 | 15.63 | |
| getPhyloTreeRef | 19.25 | 0.76 | 19.92 | |
| getPhyloTreeTsbLabel | 11.99 | 3.50 | 15.41 | |
| getSampleInfo | 6.89 | 0.05 | 6.94 | |
| getTree | 19.64 | 0.75 | 20.93 | |
| getTreeMethod | 15.30 | 0.66 | 16.47 | |
| mathScore | 5.76 | 0.07 | 5.88 | |
| mutCluster | 8.08 | 4.89 | 12.98 | |
| mutHeatmap | 10.79 | 0.36 | 13.86 | |
| mutTrunkBranch | 9.60 | 0.41 | 9.96 | |
| plotCNA | 4.03 | 2.02 | 4.24 | |
| plotMutProfile | 8.36 | 0.04 | 8.61 | |
| plotMutSigProfile | 16.86 | 0.35 | 17.19 | |
| plotPhyloTree | 7.95 | 0.18 | 8.11 | |
| readMaf | 6.47 | 0.11 | 7.28 | |
| readSegment | 0.39 | 0.02 | 0.40 | |
| runMesKit | 0 | 0 | 0 | |
| subMaf | 10.37 | 0.14 | 10.50 | |
| testNeutral | 9.46 | 0.18 | 9.69 | |
| triMatrix | 10.33 | 0.37 | 10.95 | |