Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 267/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CaMutQC 1.0.0 (landing page) Xin Wang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the CaMutQC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CaMutQC.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: CaMutQC |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CaMutQC.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CaMutQC_1.0.0.tar.gz |
StartedAt: 2024-07-21 22:24:23 -0400 (Sun, 21 Jul 2024) |
EndedAt: 2024-07-21 22:28:30 -0400 (Sun, 21 Jul 2024) |
EllapsedTime: 247.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CaMutQC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CaMutQC.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CaMutQC_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CaMutQC.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘CaMutQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CaMutQC’ version ‘1.0.0’ * 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 ‘CaMutQC’ can be installed ... OK * 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 mutFilterNormalDP: no visible binding for global variable ‘Existing_variation’ mutFilterNormalDP: no visible binding for global variable ‘n_depth’ mutFilterNormalDP: no visible binding for global variable ‘rowname’ Undefined global functions or variables: Existing_variation n_depth rowname * 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 mutFilterReg 13.502 0.127 13.632 mutFilterCan 6.791 0.239 7.077 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/CaMutQC.Rcheck/00check.log’ for details.
CaMutQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CaMutQC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘CaMutQC’ ... ** 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 (CaMutQC)
CaMutQC.Rcheck/CaMutQC-Ex.timings
name | user | system | elapsed | |
calTMB | 1.645 | 0.088 | 1.735 | |
mutFilterAdj | 0.780 | 0.056 | 0.837 | |
mutFilterCan | 6.791 | 0.239 | 7.077 | |
mutFilterCom | 0.844 | 0.000 | 0.844 | |
mutFilterDB | 1.366 | 0.076 | 1.443 | |
mutFilterNormalDP | 0.750 | 0.012 | 0.762 | |
mutFilterPON | 0.722 | 0.000 | 0.722 | |
mutFilterQual | 0.775 | 0.000 | 0.775 | |
mutFilterRef | 0.784 | 0.008 | 0.792 | |
mutFilterReg | 13.502 | 0.127 | 13.632 | |
mutFilterSB | 0.745 | 0.019 | 0.765 | |
mutFilterTech | 0.782 | 0.016 | 0.799 | |
mutFilterType | 0.739 | 0.005 | 0.743 | |
mutSelection | 0.761 | 0.007 | 0.768 | |
processMut | 0.432 | 0.016 | 0.448 | |
toMesKit | 0.419 | 0.016 | 0.434 | |
tomaftools | 0.473 | 0.017 | 0.468 | |
vcfToMAF | 0.718 | 0.000 | 0.717 | |