Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:36:47 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 1204/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MesKit 1.14.0 (landing page) Mengni Liu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.14.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MesKit_1.14.0.tar.gz |
StartedAt: 2024-05-04 00:47:27 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 00:56:50 -0400 (Sat, 04 May 2024) |
EllapsedTime: 563.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MesKit.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MesKit.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MesKit_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MesKit.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘MesKit/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MesKit’ version ‘1.14.0’ * 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 for sufficient/correct file permissions ... 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/MesKit.Rcheck/00install.out’ for details. * checking installed package size ... OK * 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 loading without being on the library search path ... 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 18.709 0.604 19.153 calFst 15.092 0.328 15.380 getBootstrapValue 13.437 0.244 13.621 getTreeMethod 13.078 0.109 13.133 getBinaryMatrix 12.705 0.120 12.778 getMutBranches 12.521 0.144 12.612 getPhyloTreePatient 12.488 0.100 12.528 getPhyloTreeTsbLabel 12.521 0.016 12.487 getPhyloTreeRef 12.417 0.071 12.444 getCCFMatrix 12.322 0.120 12.383 getTree 12.298 0.055 12.305 getPhyloTree 12.245 0.059 12.257 getBranchType 11.896 0.096 11.946 plotMutSigProfile 11.398 0.196 11.559 compareCCF 10.340 0.952 11.247 mutHeatmap 10.780 0.045 10.777 calNeiDist 10.416 0.123 10.476 mutCluster 9.820 0.403 10.182 calJSI 9.722 0.128 9.800 compareTree 9.518 0.080 9.551 ccfAUC 9.127 0.141 9.221 fitSignatures 8.808 0.136 8.911 triMatrix 8.371 0.116 8.446 classifyMut 7.918 0.520 8.388 testNeutral 8.310 0.036 8.290 mutTrunkBranch 8.073 0.191 8.227 plotMutProfile 7.859 0.064 7.871 plotPhyloTree 7.635 0.044 7.641 subMaf 6.718 0.016 6.688 readMaf 6.692 0.004 6.628 mathScore 6.608 0.024 6.582 getNonSyn_vc 6.475 0.023 6.467 getSampleInfo 6.415 0.032 6.414 getMafData 6.377 0.024 6.367 getMafPatient 6.351 0.000 6.323 getMafRef 6.334 0.000 6.306 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/MesKit.Rcheck/00check.log’ for details.
MesKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MesKit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 | 15.092 | 0.328 | 15.380 | |
calJSI | 9.722 | 0.128 | 9.800 | |
calNeiDist | 10.416 | 0.123 | 10.476 | |
ccfAUC | 9.127 | 0.141 | 9.221 | |
classifyMut | 7.918 | 0.520 | 8.388 | |
cna2gene | 18.709 | 0.604 | 19.153 | |
compareCCF | 10.340 | 0.952 | 11.247 | |
compareTree | 9.518 | 0.080 | 9.551 | |
fitSignatures | 8.808 | 0.136 | 8.911 | |
getBinaryMatrix | 12.705 | 0.120 | 12.778 | |
getBootstrapValue | 13.437 | 0.244 | 13.621 | |
getBranchType | 11.896 | 0.096 | 11.946 | |
getCCFMatrix | 12.322 | 0.120 | 12.383 | |
getMafData | 6.377 | 0.024 | 6.367 | |
getMafPatient | 6.351 | 0.000 | 6.323 | |
getMafRef | 6.334 | 0.000 | 6.306 | |
getMutBranches | 12.521 | 0.144 | 12.612 | |
getNonSyn_vc | 6.475 | 0.023 | 6.467 | |
getPhyloTree | 12.245 | 0.059 | 12.257 | |
getPhyloTreePatient | 12.488 | 0.100 | 12.528 | |
getPhyloTreeRef | 12.417 | 0.071 | 12.444 | |
getPhyloTreeTsbLabel | 12.521 | 0.016 | 12.487 | |
getSampleInfo | 6.415 | 0.032 | 6.414 | |
getTree | 12.298 | 0.055 | 12.305 | |
getTreeMethod | 13.078 | 0.109 | 13.133 | |
mathScore | 6.608 | 0.024 | 6.582 | |
mutCluster | 9.820 | 0.403 | 10.182 | |
mutHeatmap | 10.780 | 0.045 | 10.777 | |
mutTrunkBranch | 8.073 | 0.191 | 8.227 | |
plotCNA | 2.544 | 0.060 | 2.507 | |
plotMutProfile | 7.859 | 0.064 | 7.871 | |
plotMutSigProfile | 11.398 | 0.196 | 11.559 | |
plotPhyloTree | 7.635 | 0.044 | 7.641 | |
readMaf | 6.692 | 0.004 | 6.628 | |
readSegment | 0.456 | 0.000 | 0.396 | |
runMesKit | 0.001 | 0.000 | 0.000 | |
subMaf | 6.718 | 0.016 | 6.688 | |
testNeutral | 8.310 | 0.036 | 8.290 | |
triMatrix | 8.371 | 0.116 | 8.446 | |