Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:40 -0400 (Wed, 21 Aug 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" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 267/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CaMutQC 1.1.1 (landing page) Xin Wang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | 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 | 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: 1.1.1 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CaMutQC.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CaMutQC_1.1.1.tar.gz |
StartedAt: 2024-08-20 23:03:58 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 23:08:21 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 262.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CaMutQC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CaMutQC.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CaMutQC_1.1.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/CaMutQC.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 'CaMutQC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CaMutQC' version '1.1.1' * 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 '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 16.00 0.1 16.13 mutFilterCan 7.72 0.6 13.50 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/CaMutQC.Rcheck/00check.log' for details.
CaMutQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CaMutQC ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 | 1.84 | 0.11 | 2.19 | |
mutFilterAdj | 0.97 | 0.04 | 1.02 | |
mutFilterCan | 7.72 | 0.60 | 13.50 | |
mutFilterCom | 0.90 | 0.03 | 0.94 | |
mutFilterDB | 1.55 | 0.03 | 1.58 | |
mutFilterNormalDP | 0.94 | 0.00 | 0.94 | |
mutFilterPON | 1.07 | 0.02 | 1.09 | |
mutFilterQual | 1.18 | 0.00 | 1.17 | |
mutFilterRef | 1.06 | 0.02 | 1.08 | |
mutFilterReg | 16.00 | 0.10 | 16.13 | |
mutFilterSB | 0.80 | 0.05 | 0.84 | |
mutFilterTech | 0.89 | 0.00 | 0.89 | |
mutFilterType | 0.82 | 0.02 | 0.85 | |
mutSelection | 1.22 | 0.00 | 1.21 | |
processMut | 0.61 | 0.01 | 0.63 | |
toMesKit | 0.56 | 0.03 | 0.64 | |
tomaftools | 0.65 | 0.00 | 0.75 | |
vcfToMAF | 0.76 | 0.00 | 0.76 | |