Package: Onassis

Version: 1.0.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Onassis_1.0.1.tar.gz

StartedAt: 2018-04-12 01:33:28 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:35:44 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 136.4 seconds

RetCode: 0

Status:  OK

CheckDir: Onassis.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Onassis_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/Onassis.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
':::' 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: no visible global function definition for ‘is’
annotateTissueDisease: no visible global function definition for
  ‘as.dist’
annotateTissueDisease: no visible global function definition for
  ‘hclust’
annotateTissueDisease: no visible global function definition for
  ‘quantile’
annotateTissueDisease: no visible global function definition for
  ‘cutree’
annotateTissueDisease: no visible global function definition for
  ‘aggregate’
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’
multisim,list-list-character-character : <anonymous>: no visible global
  function definition for ‘is’
Undefined global functions or variables:
  ID NEW aggregate as.dist cutree hclust is quantile
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "aggregate", "as.dist", "cutree", "hclust",
             "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
semanticdifference 30.468  0.356  30.822
EntityFinder-class 10.416  0.384   3.968
Similarity-class    9.616  0.352   3.819
annotate            7.248  0.140   1.694
* 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-3.6-bioc/meat/Onassis.Rcheck/00check.log’
for details.

* installing *source* package ‘Onassis’ ...
** R
** inst
** preparing 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	1.968	0.104	1.955
CMoptions-class	0.056	0.016	0.072
EntityFinder-class	10.416	0.384	3.968
GEOHandler-functions	0	0	0
Similarity-class	9.616	0.352	3.819
Similarity-methods	0.052	0.000	0.043
annotate	7.248	0.140	1.694
annotateTissueDisease	0.004	0.000	0.001
connectToSRADB	0	0	0
createScoreMatrix	2.676	0.016	2.636
experiment_types	0.004	0.000	0.001
filterTerms	0.068	0.000	0.068
findHealthy	0.076	0.000	0.076
getGEOMetadata	0.004	0.000	0.001
getSRAMetadata	0.000	0.000	0.001
library_sources	0.000	0.000	0.001
library_strategies	0.004	0.000	0.000
organism_types	0.000	0.000	0.001
semanticdifference	30.468	0.356	30.822