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This page was generated on 2024-05-18 11:37:58 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 1163/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maser 1.22.0  (landing page)
Diogo F.T. Veiga
Snapshot Date: 2024-05-17 14:00:11 -0400 (Fri, 17 May 2024)
git_url: https://git.bioconductor.org/packages/maser
git_branch: RELEASE_3_19
git_last_commit: 8be4c56
git_last_commit_date: 2024-04-30 11:06:52 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for maser on lconway


To the developers/maintainers of the maser package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maser.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: maser
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maser_1.22.0.tar.gz
StartedAt: 2024-05-17 21:55:59 -0400 (Fri, 17 May 2024)
EndedAt: 2024-05-17 22:03:35 -0400 (Fri, 17 May 2024)
EllapsedTime: 455.6 seconds
RetCode: 0
Status:   OK  
CheckDir: maser.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maser_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/maser.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maser’ version ‘1.22.0’
* package encoding: UTF-8
* 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 ‘maser’ 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 whether startup messages can be suppressed ... 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
availableFeaturesUniprotKB: no visible global function definition for
  'read.csv'
availableFeaturesUniprotKB: no visible binding for global variable
  'Category'
availableFeaturesUniprotKB: no visible binding for global variable
  'Name'
filterByIds: no visible binding for global variable 'ID'
mapTranscriptsA3SSevent: no visible global function definition for
  'subjectHits'
mapTranscriptsA5SSevent: no visible global function definition for
  'subjectHits'
mapTranscriptsMXEevent: no visible global function definition for
  'subjectHits'
mapTranscriptsRIevent: no visible global function definition for
  'subjectHits'
mapTranscriptsSEevent: no visible global function definition for
  'subjectHits'
overlappingFeatures: no visible global function definition for
  'subjectHits'
urlTracksUniprotKB: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  Category ID Name read.csv subjectHits
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
plotTranscripts            7.927  0.132   8.140
plotUniprotKBFeatures      7.115  0.189   8.333
mapProteinFeaturesToEvents 4.061  0.122  10.292
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/maser.Rcheck/00check.log’
for details.


Installation output

maser.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘maser’ ...
** 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 (maser)

Tests output


Example timings

maser.Rcheck/maser-Ex.timings

nameusersystemelapsed
PSI-Maser-character-method0.7880.0260.825
PSI0.6960.0440.748
annotation-Maser-method0.6990.0120.718
availableFeaturesUniprotKB0.0400.0060.159
boxplot_PSI_levels2.0420.0522.120
counts-Maser-method1.8670.0251.914
display1.7980.1211.943
dotplot1.5470.0921.655
filterByCoverage1.0990.0171.125
filterByEventId2.3740.0292.423
geneEvents1.0840.0171.114
granges-Maser-method0.7720.0130.791
mapProteinFeaturesToEvents 4.061 0.12210.292
mapTranscriptsToEvents1.8920.0311.945
maser0.7400.0150.763
pca1.3540.0211.390
plotGenePSI2.0060.0342.060
plotTranscripts7.9270.1328.140
plotUniprotKBFeatures7.1150.1898.333
splicingDistribution1.3880.0241.431
summary-Maser-method0.8050.0150.827
topEvents1.0290.0141.054
volcano1.3830.0221.418