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CHECK report for vulcan on malbec2

This page was generated on 2020-10-17 11:56:00 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE vulcan PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1879/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
vulcan 1.10.0
Federico M. Giorgi
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/vulcan
Branch: RELEASE_3_11
Last Commit: 3077052
Last Changed Date: 2020-04-27 15:10:51 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: vulcan
Version: 1.10.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:vulcan.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings vulcan_1.10.0.tar.gz
StartedAt: 2020-10-17 06:26:02 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:33:54 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 471.7 seconds
RetCode: 0
Status:  OK 
CheckDir: vulcan.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:vulcan.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings vulcan_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/vulcan.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vulcan/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘vulcan’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'ChIPpeakAnno', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'zoo',
  'GenomicRanges', 'S4Vectors', 'viper', 'DiffBind', 'locfit'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘vulcan’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
average_fragment_length 8.278  0.292   8.814
vulcan                  5.857  0.036   5.956
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/vulcan.Rcheck/00check.log’
for details.



Installation output

vulcan.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL vulcan
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘vulcan’ ...
** 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 (vulcan)

Tests output


Example timings

vulcan.Rcheck/vulcan-Ex.timings

nameusersystemelapsed
average_fragment_length8.2780.2928.814
corr2p0.0010.0000.002
densityauc0.0270.0000.028
dpareto0.0070.0000.008
fisherp0.0000.0000.001
gsea0.2140.0120.435
kmgformat0.1290.0000.129
null_gsea0.0420.0000.042
p2corr0.0010.0000.000
p2z000
pareto.fit0.0280.0000.029
plot_gsea0.050.000.05
ppareto0.0030.0030.006
rea0.0050.0000.004
slice0.0000.0000.001
stouffer0.0010.0000.000
textplot20.310.000.31
val2col0.0230.0000.023
vulcan5.8570.0365.956
vulcan.annotate1.6770.0001.677
vulcan.import0.0250.0040.029
vulcan.normalize000
vulcan.pathways2.9430.0042.953
wstouffer000
z2p000