Mengni Liu
| Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/MesKit |
| git_branch: devel |
| git_last_commit: 471c27c |
| git_last_commit_date: 2024-10-29 10:48:53 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-25 15:38 -0500 (Sat, 25 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 1194/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MesKit 1.17.0 (landing page) Mengni Liu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | 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: 1.17.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MesKit.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MesKit_1.17.0.tar.gz |
| StartedAt: 2025-01-25 03:10:44 -0500 (Sat, 25 Jan 2025) |
| EndedAt: 2025-01-25 03:21:30 -0500 (Sat, 25 Jan 2025) |
| EllapsedTime: 646.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MesKit.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MesKit.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MesKit_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* 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 '1.17.0'
* 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 'E:/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck/00install.out' for details.
* checking installed package size ... INFO
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 22.60 0.73 23.44
calFst 19.28 0.86 19.42
getBranchType 17.09 0.50 17.62
getBinaryMatrix 16.58 0.58 17.17
getTree 16.56 0.57 17.12
getCCFMatrix 16.58 0.52 17.11
getPhyloTreeTsbLabel 16.37 0.65 17.03
getTreeMethod 16.55 0.47 17.00
plotMutSigProfile 16.30 0.37 16.67
getMutBranches 15.78 0.78 16.55
getBootstrapValue 15.59 0.73 16.35
getPhyloTree 15.65 0.48 16.13
getPhyloTreePatient 15.27 0.61 15.86
getPhyloTreeRef 14.69 0.55 15.22
mutHeatmap 14.70 0.15 14.83
compareCCF 13.39 0.75 14.14
compareTree 13.68 0.35 14.03
calNeiDist 13.74 0.18 13.92
calJSI 12.77 0.10 12.86
ccfAUC 12.33 0.08 12.41
mutCluster 11.94 0.23 12.17
plotMutProfile 11.64 0.05 11.71
fitSignatures 11.10 0.34 11.44
classifyMut 10.87 0.30 11.18
mutTrunkBranch 10.83 0.31 11.14
triMatrix 10.89 0.24 11.11
plotPhyloTree 10.92 0.19 11.12
testNeutral 9.97 0.03 9.98
getMafRef 9.31 0.08 9.38
mathScore 9.22 0.08 9.30
readMaf 8.66 0.26 8.89
subMaf 8.53 0.06 8.56
getNonSyn_vc 8.41 0.08 8.46
getMafData 8.30 0.08 8.38
getMafPatient 7.89 0.06 7.93
getSampleInfo 7.72 0.07 7.78
* 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, 2 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/MesKit.Rcheck/00check.log'
for details.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL MesKit ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'MesKit' ... ** this is package 'MesKit' version '1.17.0' ** 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 | 19.28 | 0.86 | 19.42 | |
| calJSI | 12.77 | 0.10 | 12.86 | |
| calNeiDist | 13.74 | 0.18 | 13.92 | |
| ccfAUC | 12.33 | 0.08 | 12.41 | |
| classifyMut | 10.87 | 0.30 | 11.18 | |
| cna2gene | 22.60 | 0.73 | 23.44 | |
| compareCCF | 13.39 | 0.75 | 14.14 | |
| compareTree | 13.68 | 0.35 | 14.03 | |
| fitSignatures | 11.10 | 0.34 | 11.44 | |
| getBinaryMatrix | 16.58 | 0.58 | 17.17 | |
| getBootstrapValue | 15.59 | 0.73 | 16.35 | |
| getBranchType | 17.09 | 0.50 | 17.62 | |
| getCCFMatrix | 16.58 | 0.52 | 17.11 | |
| getMafData | 8.30 | 0.08 | 8.38 | |
| getMafPatient | 7.89 | 0.06 | 7.93 | |
| getMafRef | 9.31 | 0.08 | 9.38 | |
| getMutBranches | 15.78 | 0.78 | 16.55 | |
| getNonSyn_vc | 8.41 | 0.08 | 8.46 | |
| getPhyloTree | 15.65 | 0.48 | 16.13 | |
| getPhyloTreePatient | 15.27 | 0.61 | 15.86 | |
| getPhyloTreeRef | 14.69 | 0.55 | 15.22 | |
| getPhyloTreeTsbLabel | 16.37 | 0.65 | 17.03 | |
| getSampleInfo | 7.72 | 0.07 | 7.78 | |
| getTree | 16.56 | 0.57 | 17.12 | |
| getTreeMethod | 16.55 | 0.47 | 17.00 | |
| mathScore | 9.22 | 0.08 | 9.30 | |
| mutCluster | 11.94 | 0.23 | 12.17 | |
| mutHeatmap | 14.70 | 0.15 | 14.83 | |
| mutTrunkBranch | 10.83 | 0.31 | 11.14 | |
| plotCNA | 3.23 | 0.15 | 3.38 | |
| plotMutProfile | 11.64 | 0.05 | 11.71 | |
| plotMutSigProfile | 16.30 | 0.37 | 16.67 | |
| plotPhyloTree | 10.92 | 0.19 | 11.12 | |
| readMaf | 8.66 | 0.26 | 8.89 | |
| readSegment | 0.55 | 0.02 | 0.57 | |
| runMesKit | 0 | 0 | 0 | |
| subMaf | 8.53 | 0.06 | 8.56 | |
| testNeutral | 9.97 | 0.03 | 9.98 | |
| triMatrix | 10.89 | 0.24 | 11.11 | |