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 02:37:41 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:40:15 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 154.3 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) (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 ‘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 18.485  2.554   5.874
compare      11.555  3.107   8.026
annotate     11.093  1.255   2.919
collapse      6.786  1.756   3.127
sim           6.742  1.235   4.104
mergeonassis  4.590  1.582   1.442
* 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’ ...
** 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	0.001
CMdictionary	0	0	0
CMoptions-class	0.006	0.001	0.007
CMoptions	0.007	0.001	0.008
CaseMatch	0.016	0.002	0.019
EntityFinder-class	0.071	0.014	0.051
EntityFinder	18.485	2.554	5.874
FindAllMatches	0.055	0.002	0.020
GEOHandler-functions	0.001	0.000	0.001
Onassis	0.010	0.001	0.001
OrderIndependentLookup	0.049	0.001	0.015
SearchStrategy	0.078	0.002	0.026
Similarity-class	0.048	0.002	0.016
Similarity	2.285	0.210	0.758
Stemmer	0.037	0.001	0.021
StopWords	0.039	0.002	0.022
SynonymType	0.040	0.001	0.024
annotate	11.093	1.255	2.919
annotateDF	2.660	1.059	0.917
collapse	6.786	1.756	3.127
compare	11.555	3.107	8.026
dictInfo	0.002	0.000	0.002
dictRef	0.003	0.001	0.004
dictTypes	0.003	0.000	0.004
dict_location	0.002	0.001	0.002
dictionary	0.001	0.000	0.002
entities	0.003	0.001	0.003
experiment_types	0.000	0.000	0.001
filterTerms	0.065	0.001	0.065
filterconcepts	1.660	0.685	0.750
findEntities	1.466	0.741	0.641
findHealthy	0.109	0.000	0.067
getGEOMetadata	0.000	0.001	0.001
groupConfig	0.170	0.001	0.091
groupsim	0.369	0.007	0.303
groupwiseConfigRef	0.066	0.000	0.067
icConfig	0.002	0.000	0.002
listCMOptions	0.002	0.000	0.003
listSimilarities	0.064	0.000	0.064
mergeonassis	4.590	1.582	1.442
multisim	3.430	0.853	2.086
ontology	0.047	0.001	0.010
organism_types	0.007	0.001	0.001
pairsim	0.269	0.003	0.172
pairwiseConfig	0.386	0.005	0.175
pairwiseConfigRef	0.064	0.000	0.064
paramValueIndex	0.015	0.001	0.017
samplesim	2.288	0.881	1.045
scores	0.001	0.000	0.001
sim	6.742	1.235	4.104
simil	0.001	0.000	0.002
similarityInstance	0.002	0.000	0.003
typeSystemRef	0.015	0.000	0.015