Back to Multiple platform build/check report for BioC 3.13 experimental data
ABCDEFGHIJKLMNOP[Q]RSTUVWXYZ

CHECK report for QDNAseq.hg19 on malbec2

This page was generated on 2021-01-14 15:59:04 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE QDNAseq.hg19 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 284/385HostnameOS / ArchINSTALLBUILDCHECK
QDNAseq.hg19 1.21.0
Daoud Sie
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/QDNAseq.hg19
Branch: master
Last Commit: ee8d568
Last Changed Date: 2020-10-27 10:14:40 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK 

Summary

Package: QDNAseq.hg19
Version: 1.21.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:QDNAseq.hg19.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings QDNAseq.hg19_1.21.0.tar.gz
StartedAt: 2021-01-14 12:38:17 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 12:40:45 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 148.2 seconds
RetCode: 0
Status:  OK 
CheckDir: QDNAseq.hg19.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:QDNAseq.hg19.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings QDNAseq.hg19_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/QDNAseq.hg19.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QDNAseq.hg19/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QDNAseq.hg19’ version ‘1.21.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘QDNAseq.hg19’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 35.4Mb
  sub-directories of 1Mb or more:
    data  35.3Mb
* checking package 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
hg19.1kbp.SR50 19.006  0.308  19.313
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/QDNAseq.hg19.Rcheck/00check.log’
for details.



Installation output

QDNAseq.hg19.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL QDNAseq.hg19
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘QDNAseq.hg19’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (QDNAseq.hg19)

Tests output


Example timings

QDNAseq.hg19.Rcheck/QDNAseq.hg19-Ex.timings

nameusersystemelapsed
QDNAseq.hg19-package0.8240.0120.836
hg19.1000kbp.SR500.0220.0030.024
hg19.100kbp.SR500.1780.0080.186
hg19.10kbp.SR501.8270.0441.871
hg19.15kbp.SR501.5930.0241.618
hg19.1kbp.SR5019.006 0.30819.313
hg19.30kbp.SR500.5590.0200.578
hg19.500kbp.SR500.0440.0000.043
hg19.50kbp.SR500.3970.0200.417
hg19.5kbp.SR503.4120.0963.508