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CHECK report for QDNAseq.hg19 on malbec1

This page was generated on 2020-04-14 17:46:24 -0400 (Tue, 14 Apr 2020).

Package 287/384HostnameOS / ArchINSTALLBUILDCHECK
QDNAseq.hg19 1.16.0
Daoud Sie
Snapshot Date: 2020-04-14 09:30:11 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/QDNAseq.hg19
Branch: RELEASE_3_10
Last Commit: d0b9b3f
Last Changed Date: 2019-10-29 13:29:44 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: QDNAseq.hg19
Version: 1.16.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:QDNAseq.hg19.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings QDNAseq.hg19_1.16.0.tar.gz
StartedAt: 2020-04-14 13:29:32 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 13:31:45 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 133.4 seconds
RetCode: 0
Status:  OK 
CheckDir: QDNAseq.hg19.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:QDNAseq.hg19.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings QDNAseq.hg19_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/QDNAseq.hg19.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 ‘QDNAseq.hg19/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QDNAseq.hg19’ version ‘1.16.0’
* 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 ... OK
* 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 or elapsed time > 5s
                 user system elapsed
hg19.1kbp.SR50 17.464    0.3  17.769
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.10-data-experiment/meat/QDNAseq.hg19.Rcheck/00check.log’
for details.



Installation output

QDNAseq.hg19.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL QDNAseq.hg19
###
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* installing to library ‘/home/biocbuild/bbs-3.10-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-package0.4480.0160.462
hg19.1000kbp.SR500.0240.0000.023
hg19.100kbp.SR500.1360.0000.136
hg19.10kbp.SR501.7200.0441.765
hg19.15kbp.SR501.320.041.36
hg19.1kbp.SR5017.464 0.30017.769
hg19.30kbp.SR500.4440.0240.469
hg19.500kbp.SR500.0400.0000.039
hg19.50kbp.SR500.3240.0120.335
hg19.5kbp.SR502.9880.0843.073