Package: Onassis

Version: 1.5.4

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_1.5.4.tar.gz

StartedAt: 2019-04-09 04:05:17 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:08:39 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 201.5 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_1.5.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Onassis.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.5.4’
* 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’ ‘stats’
  All declared Imports should be used.
* 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’
collapse,Onassis: no visible global function definition for ‘as.dist’
collapse,Onassis: no visible global function definition for ‘hclust’
collapse,Onassis: no visible global function definition for ‘cutree’
compare,Onassis: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  ID NEW as.dist cutree hclust p.adjust sample_id
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust", "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
EntityFinder 20.279  6.808   9.679
compare      16.184  2.767  13.483
annotate     11.418  2.577   4.083
collapse      8.562  1.365   5.087
sim           8.471  0.897   5.258
mergeonassis  5.304  0.981   2.259
* 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-3.9-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/3.6/Resources/library’
* installing *source* package ‘Onassis’ ...
** 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 (Onassis)

name	user	system	elapsed
CMdictionary-class	0.002	0.000	0.002
CMdictionary	0.000	0.000	0.001
CMoptions-class	0.010	0.002	0.014
CMoptions	0.005	0.001	0.005
CaseMatch	0.022	0.004	0.026
EntityFinder-class	0.097	0.034	0.090
EntityFinder	20.279	6.808	9.679
FindAllMatches	0.016	0.003	0.019
GEOHandler-functions	0.001	0.000	0.001
Onassis	0.002	0.000	0.001
OrderIndependentLookup	0.016	0.004	0.021
SearchStrategy	0.012	0.002	0.014
Similarity-class	0.031	0.004	0.018
Similarity	1.838	0.665	1.315
Stemmer	0.018	0.002	0.020
StopWords	0.016	0.002	0.018
SynonymType	0.020	0.001	0.022
annotate	11.418	2.577	4.083
annotateDF	3.163	0.968	1.530
collapse	8.562	1.365	5.087
compare	16.184	2.767	13.483
dictInfo	0.001	0.000	0.002
dictRef	0.004	0.000	0.004
dictTypes	0.002	0.000	0.003
dict_location	0.001	0.000	0.002
dictionary	0.002	0.001	0.002
entities	0.003	0.000	0.003
experiment_types	0.001	0.000	0.001
filterTerms	0.085	0.001	0.087
filterconcepts	1.738	0.658	1.156
findEntities	1.393	0.408	1.171
findHealthy	0.123	0.001	0.090
getGEOMetadata	0.002	0.001	0.002
groupConfig	0.225	0.003	0.118
groupsim	0.570	0.020	0.474
groupwiseConfigRef	0.105	0.000	0.106
icConfig	0.002	0.000	0.002
listCMOptions	0.002	0.000	0.003
listSimilarities	0.060	0.000	0.061
mergeonassis	5.304	0.981	2.259
multisim	3.523	0.982	2.533
ontology	0.069	0.002	0.019
organism_types	0.001	0.000	0.002
pairsim	0.253	0.004	0.155
pairwiseConfig	0.487	0.005	0.236
pairwiseConfigRef	0.090	0.001	0.090
paramValueIndex	0.024	0.003	0.026
samplesim	2.477	0.752	1.538
scores	0.001	0.000	0.001
sim	8.471	0.897	5.258
simil	0.001	0.000	0.001
similarityInstance	0.003	0.000	0.004
typeSystemRef	0.018	0.001	0.019