Package: Onassis

Version: 1.8.2

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_1.8.2.tar.gz

StartedAt: 2020-04-15 04:20:47 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:23:28 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 161.0 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_1.8.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/Onassis.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.2’
* 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 or elapsed time > 5s
               user system elapsed
EntityFinder 18.382  3.017   6.171
compare      15.110  2.448  10.811
annotate     13.246  0.906   2.884
collapse      7.433  2.090   3.431
sim           6.679  1.971   4.026
mergeonassis  5.139  2.089   1.490
annotateDF    3.390  1.714   0.840
* 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-3.10-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	0.001	0.000	0.002
CMdictionary	0.000	0.000	0.001
CMoptions-class	0.009	0.001	0.009
CMoptions	0.006	0.001	0.007
CaseMatch	0.017	0.002	0.019
EntityFinder-class	0.074	0.016	0.058
EntityFinder	18.382	3.017	6.171
FindAllMatches	0.058	0.001	0.020
GEOHandler-functions	0.007	0.000	0.001
Onassis	0.001	0.000	0.001
OrderIndependentLookup	0.046	0.001	0.018
SearchStrategy	0.058	0.001	0.019
Similarity-class	0.055	0.002	0.016
Similarity	2.013	0.233	0.717
Stemmer	0.032	0.001	0.017
StopWords	0.036	0.001	0.019
SynonymType	0.025	0.001	0.016
annotate	13.246	0.906	2.884
annotateDF	3.390	1.714	0.840
collapse	7.433	2.090	3.431
compare	15.110	2.448	10.811
dictInfo	0.001	0.000	0.001
dictRef	0.003	0.000	0.003
dictTypes	0.002	0.001	0.002
dict_location	0.001	0.000	0.002
dictionary	0.001	0.001	0.001
entities	0.002	0.000	0.003
experiment_types	0.001	0.000	0.001
filterTerms	0.087	0.000	0.088
filterconcepts	1.485	1.138	0.672
findEntities	1.560	1.097	0.759
findHealthy	0.110	0.002	0.086
getGEOMetadata	0.001	0.000	0.001
groupConfig	0.179	0.003	0.094
groupsim	0.358	0.010	0.316
groupwiseConfigRef	0.060	0.001	0.060
icConfig	0.001	0.000	0.001
listCMOptions	0.002	0.001	0.002
listSimilarities	0.055	0.000	0.054
mergeonassis	5.139	2.089	1.490
multisim	3.202	1.012	1.841
ontology	0.039	0.002	0.013
organism_types	0.004	0.000	0.001
pairsim	0.236	0.005	0.161
pairwiseConfig	0.383	0.007	0.137
pairwiseConfigRef	0.076	0.002	0.079
paramValueIndex	0.019	0.001	0.020
samplesim	2.207	1.000	1.096
scores	0.001	0.000	0.001
sim	6.679	1.971	4.026
simil	0.001	0.000	0.001
similarityInstance	0.002	0.000	0.002
typeSystemRef	0.015	0.000	0.015