Back to Multiple platform build/check report for BioC 3.10
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for CNVRanger on malbec1

This page was generated on 2020-04-15 12:15:13 -0400 (Wed, 15 Apr 2020).

Package 328/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVRanger 1.2.2
Ludwig Geistlinger
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CNVRanger
Branch: RELEASE_3_10
Last Commit: 556ffbf
Last Changed Date: 2019-11-13 18:37:25 -0400 (Wed, 13 Nov 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNVRanger
Version: 1.2.2
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CNVRanger.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CNVRanger_1.2.2.tar.gz
StartedAt: 2020-04-15 06:17:49 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:22:04 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 255.2 seconds
RetCode: 0
Status:  OK 
CheckDir: CNVRanger.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CNVRanger.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CNVRanger_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CNVRanger.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVRanger/DESCRIPTION’ ... OK
* this is package ‘CNVRanger’ version ‘1.2.2’
* 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 ‘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 R 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 or elapsed time > 5s
                       user system elapsed
plotRecurrentRegions 20.048  0.020  33.712
plotEQTL             18.444  0.268  35.202
plotManhattan         6.544  0.160   6.943
cnvGWAS               5.836  0.136   6.551
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/CNVRanger.Rcheck/00check.log’
for details.



Installation output

CNVRanger.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CNVRanger
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-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
cnvEQTL3.4280.1163.559
cnvGWAS5.8360.1366.551
generateGDS0.9320.0080.940
importLrrBaf0.0280.0040.031
plotEQTL18.444 0.26835.202
plotManhattan6.5440.1606.943
plotRecurrentRegions20.048 0.02033.712
populationRanges2.0280.0042.033
setupCnvGWAS0.0120.0000.014