Package: Onassis

Version: 1.4.5

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Onassis.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Onassis_1.4.5.tar.gz

StartedAt: 2019-04-16 01:52:11 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:54:56 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 165.7 seconds

RetCode: 0

Status:  OK

CheckDir: Onassis.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Onassis.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Onassis_1.4.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/Onassis.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 34.312  0.828  35.149
EntityFinder       16.536  0.568   7.103
compare             9.064  0.224   6.140
sim                 6.204  0.124   3.986
collapse            6.000  0.168   2.950
annotate            5.964  0.136   2.032
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/Onassis.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Onassis
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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	0.000	0.000	0.001
CMdictionary	0.000	0.000	0.001
CMoptions-class	0.008	0.000	0.023
CMoptions	0.004	0.000	0.006
CaseMatch	0.024	0.000	0.021
EntityFinder-class	0.088	0.000	0.160
EntityFinder	16.536	0.568	7.103
FindAllMatches	0.036	0.004	0.019
GEOHandler-functions	0.004	0.000	0.001
Onassis	0.004	0.000	0.001
OrderIndependentLookup	0.04	0.00	0.02
SearchStrategy	0.036	0.004	0.020
Similarity-class	0.092	0.004	0.125
Similarity	2.632	0.072	1.042
Stemmer	0.036	0.004	0.019
StopWords	0.036	0.004	0.019
SynonymType	0.040	0.000	0.019
annotate	5.964	0.136	2.032
annotateDF	2.168	0.088	0.757
annotateTissueDisease	0.008	0.000	0.001
collapse	6.000	0.168	2.950
compare	9.064	0.224	6.140
createScoreMatrix	3.636	0.016	3.665
dictInfo	0.004	0.000	0.003
dictRef	0.000	0.004	0.004
dictTypes	0.004	0.000	0.003
dict_location	0.004	0.000	0.002
dictionary	0.000	0.000	0.001
entities	0.000	0.000	0.003
experiment_types	0.000	0.000	0.001
filterTerms	0.096	0.004	0.101
filterconcepts	1.712	0.080	0.656
findEntities	1.604	0.060	0.563
findHealthy	0.232	0.000	0.096
getGEOMetadata	0.004	0.000	0.001
groupConfig	0.224	0.000	0.077
groupsim	0.916	0.004	0.515
groupwiseConfigRef	0.068	0.000	0.067
icConfig	0.000	0.000	0.001
listCMOptions	0.000	0.000	0.002
listSimilarities	0.060	0.004	0.061
mergeonassis	3.180	0.140	1.271
multisim	2.452	0.116	1.604
ontology	0.048	0.004	0.013
organism_types	0.000	0.000	0.001
pairsim	0.240	0.000	0.178
pairwiseConfig	0.364	0.000	0.163
pairwiseConfigRef	0.076	0.000	0.073
paramValueIndex	0.02	0.00	0.02
samplesim	1.688	0.076	0.905
scores	0.000	0.000	0.001
semanticdifference	34.312	0.828	35.149
sim	6.204	0.124	3.986
simil	0	0	0
similarityInstance	0.000	0.000	0.002
typeSystemRef	0.016	0.000	0.016