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This page was generated on 2024-06-24 11:38 -0400 (Mon, 24 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2213/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
vulcan 1.27.0  (landing page)
Federico M. Giorgi
Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 Jun 2024)
git_url: https://git.bioconductor.org/packages/vulcan
git_branch: devel
git_last_commit: cb667e0
git_last_commit_date: 2024-04-30 11:01:07 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for vulcan on nebbiolo2

To the developers/maintainers of the vulcan package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: vulcan
Version: 1.27.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:vulcan.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings vulcan_1.27.0.tar.gz
StartedAt: 2024-06-24 04:38:39 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 04:45:56 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 436.7 seconds
RetCode: 0
Status:   OK  
CheckDir: vulcan.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:vulcan.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings vulcan_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/vulcan.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘vulcan/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘vulcan’ version ‘1.27.0’
* 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 code 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 loading without being on the library search path ... 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
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
vulcan 5.585  0.208   5.794
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/vulcan.Rcheck/00check.log’
for details.


Installation output

vulcan.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL vulcan
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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_length4.1570.2284.401
corr2p0.0020.0000.001
densityauc0.0210.0040.024
dpareto0.0090.0000.009
fisherp0.0010.0000.001
gsea0.1780.0120.189
kmgformat0.0580.0000.058
null_gsea0.0220.0000.022
p2corr000
p2z000
pareto.fit0.0210.0000.021
plot_gsea0.0280.0000.028
ppareto0.0040.0000.004
rea0.0030.0000.003
slice000
stouffer000
textplot20.1310.0040.135
val2col0.0160.0000.016
vulcan5.5850.2085.794
vulcan.annotate1.8220.0961.918
vulcan.import0.0240.0000.024
vulcan.normalize000
vulcan.pathways2.9080.0522.960
wstouffer0.0000.0000.001
z2p000