Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

This page was generated on 2021-10-14 12:05:23 -0400 (Thu, 14 Oct 2021).

CHECK results for vulcan on nebbiolo2

To the developers/maintainers of the vulcan package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/vulcan.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2030/2056HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
vulcan 1.15.0  (landing page)
Federico M. Giorgi
Snapshot Date: 2021-10-13 14:50:09 -0400 (Wed, 13 Oct 2021)
git_url: https://git.bioconductor.org/packages/vulcan
git_branch: master
git_last_commit: 7a47a6c
git_last_commit_date: 2021-05-19 12:30:45 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: vulcan
Version: 1.15.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:vulcan.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings vulcan_1.15.0.tar.gz
StartedAt: 2021-10-13 22:20:16 -0400 (Wed, 13 Oct 2021)
EndedAt: 2021-10-13 22:25:26 -0400 (Wed, 13 Oct 2021)
EllapsedTime: 310.0 seconds
RetCode: 0
Status:   OK  
CheckDir: vulcan.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:vulcan.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings vulcan_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/vulcan.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.15.0’
* 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 ... NOTE
vulcan.normalize: no visible global function definition for 'assay'
Undefined global functions or variables:
  assay
* 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
* 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-3.14-bioc/meat/vulcan.Rcheck/00check.log’
for details.



Installation output

vulcan.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL vulcan
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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_length4.0410.2244.280
corr2p0.0020.0000.001
densityauc0.0160.0000.016
dpareto0.0050.0000.005
fisherp000
gsea0.1110.0120.124
kmgformat0.0420.0040.046
null_gsea0.0160.0000.016
p2corr0.0000.0000.001
p2z000
pareto.fit0.0170.0000.017
plot_gsea0.0200.0000.019
ppareto0.0000.0030.003
rea0.0010.0010.002
slice0.0000.0000.001
stouffer000
textplot20.1120.0000.113
val2col0.0130.0000.013
vulcan4.7490.0564.806
vulcan.annotate1.4030.0481.451
vulcan.import0.0140.0000.015
vulcan.normalize0.0000.0000.001
vulcan.pathways3.0030.0323.035
wstouffer000
z2p000