Package: Onassis

Version: 1.9.2

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_1.9.2.tar.gz

StartedAt: 2020-01-16 07:07:20 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:11:06 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 225.9 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_1.9.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Onassis.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.9.2’
* 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’ ‘Rtsne’ ‘clusteval’ ‘dendextend’ ‘ggfortify’ ‘ggplot2’ ‘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 (user + system) or elapsed time > 5s
               user system elapsed
EntityFinder 24.361  6.940  10.215
compare      18.830  2.470  15.451
annotate     10.326  2.331   3.824
collapse      7.964  1.883   5.075
sim           8.292  1.216   5.596
mergeonassis  4.365  1.444   2.229
multisim      5.065  0.727   2.728
annotateDF    3.896  1.763   1.434
* 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-3.11-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/4.0/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	0	0
CMoptions-class	0.010	0.002	0.012
CMoptions	0.008	0.001	0.009
CaseMatch	0.022	0.003	0.025
EntityFinder-class	0.101	0.038	0.098
EntityFinder	24.361	6.940	10.215
FindAllMatches	0.059	0.002	0.021
GEOHandler-functions	0.001	0.001	0.001
Onassis	0.001	0.001	0.002
OrderIndependentLookup	0.077	0.002	0.022
SearchStrategy	0.057	0.004	0.022
Similarity-class	0.067	0.003	0.017
Similarity	3.093	0.604	1.281
Stemmer	0.022	0.002	0.024
StopWords	0.018	0.002	0.020
SynonymType	0.015	0.002	0.017
annotate	10.326	2.331	3.824
annotateDF	3.896	1.763	1.434
collapse	7.964	1.883	5.075
compare	18.830	2.470	15.451
dictInfo	0.002	0.000	0.002
dictRef	0.003	0.001	0.003
dictTypes	0.003	0.000	0.003
dict_location	0.001	0.000	0.001
dictionary	0.001	0.000	0.002
entities	0.002	0.000	0.003
experiment_types	0.001	0.001	0.001
filterTerms	0.061	0.001	0.062
filterconcepts	1.858	0.859	1.196
findEntities	1.766	0.731	1.111
findHealthy	0.058	0.001	0.059
getGEOMetadata	0.001	0.000	0.002
groupConfig	0.144	0.001	0.075
groupsim	0.545	0.017	0.408
groupwiseConfigRef	0.105	0.000	0.106
icConfig	0.001	0.000	0.002
listCMOptions	0.002	0.001	0.003
listSimilarities	0.105	0.001	0.105
mergeonassis	4.365	1.444	2.229
multisim	5.065	0.727	2.728
ontology	0.055	0.003	0.019
organism_types	0.001	0.001	0.001
pairsim	0.246	0.005	0.181
pairwiseConfig	0.525	0.008	0.238
pairwiseConfigRef	0.078	0.000	0.078
paramValueIndex	0.013	0.001	0.015
samplesim	2.908	0.478	1.570
scores	0.001	0.000	0.001
sim	8.292	1.216	5.596
simil	0.001	0.000	0.002
similarityInstance	0.003	0.000	0.003
typeSystemRef	0.020	0.001	0.021