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This page was generated on 2024-06-21 17:39 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 399/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVRanger 1.20.0  (landing page)
Ludwig Geistlinger
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/CNVRanger
git_branch: RELEASE_3_19
git_last_commit: dca5773
git_last_commit_date: 2024-04-30 11:12:23 -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
merida1macOS 12.7.4 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


CHECK results for CNVRanger on palomino3

To the developers/maintainers of the CNVRanger package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNVRanger.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: CNVRanger
Version: 1.20.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNVRanger.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings CNVRanger_1.20.0.tar.gz
StartedAt: 2024-06-20 02:12:08 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 02:16:59 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 291.2 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVRanger.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:CNVRanger.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings CNVRanger_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/CNVRanger.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 'CNVRanger/DESCRIPTION' ... OK
* this is package 'CNVRanger' version '1.20.0'
* 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 'CNVRanger' 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 ... OK
* 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 ... NOTE
Unexported object imported by a ':::' call: 'rappdirs:::get_os'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotRecurrentRegions: no visible binding for global variable 'type'
plotRecurrentRegions: no visible binding for global variable 'pvalue'
Undefined global functions or variables:
  pvalue type
* 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
plotEQTL             20.56   2.23   28.59
plotRecurrentRegions 17.47   0.22   20.64
plotManhattan         6.88   0.12    7.17
cnvGWAS               5.75   0.28    6.19
* 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/CNVRanger.Rcheck/00check.log'
for details.


Installation output

CNVRanger.Rcheck/00install.out

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


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'CNVRanger' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CNVRanger)

Tests output


Example timings

CNVRanger.Rcheck/CNVRanger-Ex.timings

nameusersystemelapsed
cnvEQTL2.800.273.11
cnvGWAS5.750.286.19
cnvOncoPrint1.720.871.89
generateGDS1.620.281.47
importLrrBaf0.580.040.64
plotEQTL20.56 2.2328.59
plotManhattan6.880.127.17
plotRecurrentRegions17.47 0.2220.64
populationRanges1.570.001.60
setupCnvGWAS0.000.030.03