Package: maser

Version: 1.2.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:maser.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings maser_1.2.0.tar.gz

StartedAt: 2019-10-16 02:52:33 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:58:02 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 328.7 seconds

RetCode: 0

Status:  OK

CheckDir: maser.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:maser.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings maser_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/maser.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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      6.996  0.060   8.556
plotTranscripts            6.954  0.000   6.954
mapProteinFeaturesToEvents 5.786  0.044   7.874
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/maser.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL maser
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

name	user	system	elapsed
PSI-Maser-character-method	0.609	0.016	0.653
PSI	0.462	0.004	0.467
annotation-Maser-method	0.452	0.000	0.452
availableFeaturesUniprotKB	0.122	0.000	0.658
boxplot_PSI_levels	3.279	0.052	3.331
counts-Maser-method	0.774	0.036	0.811
display	2.104	0.052	2.183
dotplot	1.277	0.000	1.277
filterByCoverage	1.194	0.002	1.197
filterByEventId	0.701	0.000	0.701
geneEvents	0.798	0.000	0.798
granges-Maser-method	0.529	0.000	0.529
mapProteinFeaturesToEvents	5.786	0.044	7.874
mapTranscriptsToEvents	1.681	0.011	1.714
maser	0.703	0.020	0.724
pca	1.417	0.004	1.421
plotGenePSI	2.100	0.016	2.118
plotTranscripts	6.954	0.000	6.954
plotUniprotKBFeatures	6.996	0.060	8.556
splicingDistribution	1.569	0.000	1.569
summary-Maser-method	1.040	0.004	1.045
topEvents	1.114	0.000	1.113
volcano	1.685	0.008	1.693