Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-16 11:37:40 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 2202/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
vulcan 1.22.0  (landing page)
Federico M. Giorgi
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/vulcan
git_branch: RELEASE_3_17
git_last_commit: 4049d1d
git_last_commit_date: 2023-04-25 10:56:56 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for vulcan on merida1


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: 1.22.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:vulcan.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings vulcan_1.22.0.tar.gz
StartedAt: 2023-10-16 08:31:08 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 08:44:50 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 822.3 seconds
RetCode: 0
Status:   OK  
CheckDir: vulcan.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:vulcan.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings vulcan_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/vulcan.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vulcan/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘vulcan’ version ‘1.22.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
average_fragment_length 7.606  0.578   8.237
vulcan                  7.341  0.233   7.585
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/vulcan.Rcheck/00check.log’
for details.



Installation output

vulcan.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL vulcan
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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_length7.6060.5788.237
corr2p0.0030.0010.004
densityauc0.0280.0020.031
dpareto0.0060.0010.008
fisherp0.0000.0010.001
gsea0.2890.0690.358
kmgformat0.0590.0060.064
null_gsea0.0500.0050.056
p2corr0.0010.0000.001
p2z0.0000.0000.001
pareto.fit0.0300.0020.032
plot_gsea0.0740.0100.085
ppareto0.0040.0010.006
rea0.0040.0010.005
slice0.0010.0010.001
stouffer0.0000.0010.001
textplot20.3290.0080.338
val2col0.0130.0030.017
vulcan7.3410.2337.585
vulcan.annotate4.3110.1264.445
vulcan.import0.0290.0050.034
vulcan.normalize0.0000.0010.001
vulcan.pathways4.3040.1484.456
wstouffer0.0010.0000.000
z2p0.0000.0000.001