Package: Onassis

Version: 1.5.4

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Onassis.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Onassis_1.5.4.tar.gz

StartedAt: 2019-04-09 02:27:50 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:30:10 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 140.1 seconds

RetCode: 0

Status:  OK

CheckDir: Onassis.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Onassis.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Onassis_1.5.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Onassis.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.5.4’
* 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 17.848  0.735   7.879
compare      10.977  0.286   7.907
collapse      7.782  0.164   3.051
annotate      5.605  0.197   2.094
sim           5.530  0.110   3.542
* 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-3.9-bioc/meat/Onassis.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Onassis
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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	0.001
CMdictionary	0	0	0
CMoptions-class	0.007	0.000	0.020
CMoptions	0.007	0.000	0.007
CaseMatch	0.012	0.000	0.011
EntityFinder-class	0.064	0.008	0.185
EntityFinder	17.848	0.735	7.879
FindAllMatches	0.035	0.000	0.017
GEOHandler-functions	0	0	0
Onassis	0.000	0.001	0.001
OrderIndependentLookup	0.013	0.004	0.017
SearchStrategy	0.017	0.000	0.017
Similarity-class	0.025	0.000	0.029
Similarity	2.108	0.072	0.678
Stemmer	0.013	0.000	0.014
StopWords	0.013	0.000	0.014
SynonymType	0.013	0.000	0.013
annotate	5.605	0.197	2.094
annotateDF	2.299	0.073	0.651
collapse	7.782	0.164	3.051
compare	10.977	0.286	7.907
dictInfo	0.001	0.000	0.002
dictRef	0.003	0.000	0.004
dictTypes	0.003	0.000	0.003
dict_location	0.001	0.000	0.002
dictionary	0.001	0.000	0.002
entities	0.002	0.000	0.002
experiment_types	0.001	0.000	0.000
filterTerms	0.076	0.000	0.076
filterconcepts	1.381	0.088	0.620
findEntities	0.907	0.064	0.491
findHealthy	0.116	0.000	0.068
getGEOMetadata	0	0	0
groupConfig	0.116	0.000	0.060
groupsim	0.310	0.004	0.205
groupwiseConfigRef	0.046	0.000	0.046
icConfig	0.002	0.000	0.001
listCMOptions	0.003	0.000	0.002
listSimilarities	0.354	0.000	0.354
mergeonassis	3.439	0.112	1.166
multisim	3.294	0.123	1.430
ontology	0.048	0.000	0.013
organism_types	0.001	0.000	0.000
pairsim	0.318	0.000	0.154
pairwiseConfig	0.342	0.004	0.150
pairwiseConfigRef	0.066	0.000	0.066
paramValueIndex	0.013	0.004	0.017
samplesim	1.465	0.036	0.737
scores	0.001	0.000	0.001
sim	5.530	0.110	3.542
simil	0	0	0
similarityInstance	0.002	0.000	0.002
typeSystemRef	0.013	0.000	0.013