Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-05 11:41 -0400 (Fri, 05 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4593 |
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" | 4399 |
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" | 3688 |
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 264/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CaMutQC 1.1.0 (landing page) Xin Wang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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: 1.1.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CaMutQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CaMutQC_1.1.0.tar.gz |
StartedAt: 2024-07-04 19:14:23 -0400 (Thu, 04 Jul 2024) |
EndedAt: 2024-07-04 19:18:24 -0400 (Thu, 04 Jul 2024) |
EllapsedTime: 240.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CaMutQC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CaMutQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CaMutQC_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CaMutQC.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CaMutQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CaMutQC’ version ‘1.1.0’ * 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 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 15.629 0.155 15.87 mutFilterCan 7.715 0.545 8.67 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/CaMutQC.Rcheck/00check.log’ for details.
CaMutQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CaMutQC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 | 1.219 | 0.120 | 1.359 | |
mutFilterAdj | 0.949 | 0.013 | 0.967 | |
mutFilterCan | 7.715 | 0.545 | 8.670 | |
mutFilterCom | 1.007 | 0.013 | 1.025 | |
mutFilterDB | 0.969 | 0.014 | 0.986 | |
mutFilterNormalDP | 1.006 | 0.011 | 1.023 | |
mutFilterPON | 0.984 | 0.011 | 1.000 | |
mutFilterQual | 0.977 | 0.009 | 0.992 | |
mutFilterRef | 1.031 | 0.011 | 1.049 | |
mutFilterReg | 15.629 | 0.155 | 15.870 | |
mutFilterSB | 0.968 | 0.010 | 0.983 | |
mutFilterTech | 0.968 | 0.011 | 0.984 | |
mutFilterType | 0.884 | 0.008 | 0.896 | |
mutSelection | 0.971 | 0.010 | 0.986 | |
processMut | 0.554 | 0.010 | 0.567 | |
toMesKit | 0.496 | 0.010 | 0.509 | |
tomaftools | 0.557 | 0.012 | 0.572 | |
vcfToMAF | 0.930 | 0.009 | 0.943 | |