Package: maser

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:maser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings maser_1.1.0.tar.gz

StartedAt: 2019-04-09 01:57:14 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:03:27 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 373.1 seconds

RetCode: 0

Status:  OK

CheckDir: maser.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:maser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings maser_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/maser.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maser’ version ‘1.1.0’
* 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 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
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 binding for global variable 'Name'
Undefined global functions or variables:
  ID Name subjectHits
* 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 or elapsed time > 5s
                             user system elapsed
plotUniprotKBFeatures      10.449  0.477  11.256
mapProteinFeaturesToEvents  8.510  0.507  10.183
plotTranscripts             6.950  0.048   7.063
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/maser.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL maser
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘maser’ ...
** 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
* DONE (maser)

name	user	system	elapsed
PSI-Maser-character-method	0.993	0.058	1.058
PSI	0.823	0.012	0.843
annotation-Maser-method	0.799	0.009	0.811
availableFeaturesUniprotKB	0.148	0.007	1.401
boxplot_PSI_levels	2.794	0.106	2.922
counts-Maser-method	0.670	0.006	0.680
display	1.869	0.076	1.973
dotplot	1.477	0.012	1.509
filterByCoverage	1.083	0.007	1.108
filterByEventId	1.014	0.008	1.032
geneEvents	1.037	0.004	1.050
granges-Maser-method	0.795	0.042	0.841
mapProteinFeaturesToEvents	8.510	0.507	10.183
mapTranscriptsToEvents	2.002	0.017	2.038
maser	0.685	0.005	0.703
pca	1.359	0.011	1.390
plotGenePSI	2.149	0.021	2.191
plotTranscripts	6.950	0.048	7.063
plotUniprotKBFeatures	10.449	0.477	11.256
splicingDistribution	1.757	0.009	1.777
summary-Maser-method	1.063	0.007	1.084
topEvents	1.265	0.009	1.287
volcano	1.470	0.007	1.494