Package: Onassis

Version: 1.4.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Onassis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Onassis_1.4.5.tar.gz

StartedAt: 2019-04-16 01:41:13 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:44:31 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 198.1 seconds

RetCode: 0

Status:  OK

CheckDir: Onassis.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:Onassis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Onassis_1.4.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Onassis.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Onassis/DESCRIPTION’ ... OK
* this is package ‘Onassis’ version ‘1.4.5’
* 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 ‘Onassis’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘data.table’
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘DT’ ‘knitr’
  All declared Imports should be used.
':::' call which should be '::': ‘tools:::file_path_as_absolute’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotate,data.frame-character-character: no visible binding for global
  variable ‘sample_id’
annotateDF,EntityFinder-data.frame-character-CMoptions: no visible
  binding for global variable ‘ID’
annotateDF,EntityFinder-data.frame-character-CMoptions: no visible
  binding for global variable ‘NEW’
compare,Onassis: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  ID NEW p.adjust sample_id
Consider adding
  importFrom("stats", "p.adjust")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
semanticdifference 44.418  3.151  47.950
EntityFinder       20.831  2.897   6.355
compare            11.103  1.541   7.731
annotate            9.388  0.696   2.656
sim                 7.329  1.828   4.587
collapse            6.579  1.394   3.222
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/Onassis.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 Onassis
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Onassis’ ...
** 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 (Onassis)

name	user	system	elapsed
CMdictionary-class	0.001	0.000	0.002
CMdictionary	0.001	0.000	0.001
CMoptions-class	0.005	0.001	0.006
CMoptions	0.005	0.000	0.005
CaseMatch	0.014	0.001	0.016
EntityFinder-class	0.075	0.015	0.085
EntityFinder	20.831	2.897	6.355
FindAllMatches	0.038	0.002	0.016
GEOHandler-functions	0.006	0.000	0.001
Onassis	0.002	0.000	0.001
OrderIndependentLookup	0.041	0.002	0.019
SearchStrategy	0.037	0.002	0.019
Similarity-class	0.035	0.001	0.014
Similarity	1.259	0.174	0.597
Stemmer	0.011	0.001	0.012
StopWords	0.012	0.001	0.013
SynonymType	0.012	0.001	0.012
annotate	9.388	0.696	2.656
annotateDF	3.396	1.048	0.867
annotateTissueDisease	0.002	0.000	0.002
collapse	6.579	1.394	3.222
compare	11.103	1.541	7.731
createScoreMatrix	3.265	0.031	3.326
dictInfo	0.002	0.000	0.003
dictRef	0.004	0.000	0.004
dictTypes	0.003	0.000	0.003
dict_location	0.001	0.000	0.002
dictionary	0.002	0.000	0.002
entities	0.002	0.000	0.003
experiment_types	0.001	0.000	0.001
filterTerms	0.078	0.000	0.079
filterconcepts	1.468	0.881	0.773
findEntities	1.672	0.804	0.745
findHealthy	0.083	0.001	0.073
getGEOMetadata	0.001	0.000	0.001
groupConfig	0.178	0.002	0.093
groupsim	0.662	0.009	0.604
groupwiseConfigRef	0.068	0.001	0.070
icConfig	0.001	0.000	0.001
listCMOptions	0.002	0.001	0.002
listSimilarities	0.073	0.004	0.079
mergeonassis	3.791	1.038	1.511
multisim	3.321	0.452	1.825
ontology	0.035	0.001	0.013
organism_types	0.000	0.001	0.001
pairsim	0.273	0.003	0.164
pairwiseConfig	0.439	0.006	0.180
pairwiseConfigRef	0.066	0.000	0.067
paramValueIndex	0.017	0.001	0.018
samplesim	2.229	0.686	1.129
scores	0.001	0.000	0.000
semanticdifference	44.418	3.151	47.950
sim	7.329	1.828	4.587
simil	0.001	0.000	0.001
similarityInstance	0.002	0.000	0.003
typeSystemRef	0.012	0.001	0.013