Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-22 11:35:28 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 3444
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 267/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CaMutQC 1.0.0  (landing page)
Xin Wang
Snapshot Date: 2024-05-21 14:00:15 -0400 (Tue, 21 May 2024)
git_url: https://git.bioconductor.org/packages/CaMutQC
git_branch: RELEASE_3_19
git_last_commit: 2544c8d
git_last_commit_date: 2024-04-30 11:55:10 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for CaMutQC on palomino3


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: 1.0.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CaMutQC.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings CaMutQC_1.0.0.tar.gz
StartedAt: 2024-05-21 23:50:48 -0400 (Tue, 21 May 2024)
EndedAt: 2024-05-21 23:54:51 -0400 (Tue, 21 May 2024)
EllapsedTime: 243.3 seconds
RetCode: 0
Status:   OK  
CheckDir: CaMutQC.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CaMutQC.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings CaMutQC_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/CaMutQC.Rcheck'
* using R version 4.4.0 (2024-04-24 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 '1.0.0'
* 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 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 13.72   0.22   13.95
mutFilterCan  6.42   0.59   13.23
* 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-3.19-bioc/meat/CaMutQC.Rcheck/00check.log'
for details.


Installation output

CaMutQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL CaMutQC
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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)

Tests output


Example timings

CaMutQC.Rcheck/CaMutQC-Ex.timings

nameusersystemelapsed
calTMB1.690.081.97
mutFilterAdj0.950.111.07
mutFilterCan 6.42 0.5913.23
mutFilterCom1.020.021.05
mutFilterDB1.450.011.48
mutFilterNormalDP0.890.000.89
mutFilterPON0.890.000.89
mutFilterQual1.100.021.11
mutFilterRef0.930.010.97
mutFilterReg13.72 0.2213.95
mutFilterSB0.80.00.8
mutFilterTech0.80.00.8
mutFilterType0.780.000.78
mutSelection0.830.000.86
processMut0.630.030.69
toMesKit0.580.000.64
tomaftools0.520.000.54
vcfToMAF1.030.031.07