Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-04 11:41 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 271/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CaMutQC 1.4.5  (landing page)
Xin Wang
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/CaMutQC
git_branch: RELEASE_3_21
git_last_commit: 82ef2e3
git_last_commit_date: 2025-07-20 22:09:36 -0400 (Sun, 20 Jul 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CaMutQC on palomino7

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.

raw results


Summary

Package: CaMutQC
Version: 1.4.5
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CaMutQC.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings CaMutQC_1.4.5.tar.gz
StartedAt: 2025-08-01 00:18:39 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 00:23:08 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 269.6 seconds
RetCode: 0
Status:   OK  
CheckDir: CaMutQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CaMutQC.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings CaMutQC_1.4.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/CaMutQC.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* 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 '1.4.5'
* 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 15.97   0.17   16.14
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/CaMutQC.Rcheck/00check.log'
for details.


Installation output

CaMutQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL CaMutQC
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'CaMutQC' ...
** this is package 'CaMutQC' version '1.4.5'
** 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)

Tests output


Example timings

CaMutQC.Rcheck/CaMutQC-Ex.timings

nameusersystemelapsed
calTMB4.580.114.91
mutFilterAdj0.980.061.04
mutFilterCan1.140.051.20
mutFilterCom0.950.010.97
mutFilterDB0.750.000.75
mutFilterNormalDP1.080.001.08
mutFilterPON0.920.050.97
mutFilterQual1.110.021.12
mutFilterRef0.940.000.94
mutFilterReg15.97 0.1716.14
mutFilterSB0.840.030.88
mutFilterTech1.280.021.29
mutFilterType1.100.011.11
mutSelection1.110.021.13
processMut0.700.030.78
toMesKit0.690.000.72
tomaftools0.700.000.72
vcfToMAF1.220.051.26