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This page was generated on 2023-10-16 11:35:29 -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 1120/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maser 1.18.0  (landing page)
Diogo F.T. Veiga
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/maser
git_branch: RELEASE_3_17
git_last_commit: 32d84cc
git_last_commit_date: 2023-04-25 11:02:11 -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 maser on nebbiolo1


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: 1.18.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:maser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings maser_1.18.0.tar.gz
StartedAt: 2023-10-15 22:29:27 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 22:38:15 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 528.9 seconds
RetCode: 0
Status:   OK  
CheckDir: maser.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:maser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings maser_1.18.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/maser.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maser’ version ‘1.18.0’
* 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 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 loading without being on the library search path ... OK
* checking 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            7.086  0.384   7.469
plotUniprotKBFeatures      6.204  0.559  10.826
mapProteinFeaturesToEvents 4.061  0.360   8.810
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Introduction.Rmd’ using ‘UTF-8’... OK
  ‘Protein_mapping.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/maser.Rcheck/00check.log’
for details.



Installation output

maser.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL maser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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-method0.6780.0770.759
PSI0.5400.0590.599
annotation-Maser-method0.5180.0040.522
availableFeaturesUniprotKB0.1250.0130.344
boxplot_PSI_levels1.4800.0311.512
counts-Maser-method0.5330.0120.546
display1.7800.1521.933
dotplot1.1790.1001.279
filterByCoverage2.0360.2762.312
filterByEventId0.810.040.85
geneEvents0.7780.0120.789
granges-Maser-method0.6170.0160.633
mapProteinFeaturesToEvents4.0610.3608.810
mapTranscriptsToEvents1.7470.1701.916
maser0.5740.0330.608
pca1.0940.0211.114
plotGenePSI1.7810.0711.852
plotTranscripts7.0860.3847.469
plotUniprotKBFeatures 6.204 0.55910.826
splicingDistribution1.1970.0521.249
summary-Maser-method0.6550.0480.702
topEvents0.8430.1400.983
volcano1.0440.0761.120