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CHECK report for Onassis on malbec1

This page was generated on 2020-04-15 12:13:02 -0400 (Wed, 15 Apr 2020).

Package 1185/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Onassis 1.8.2
Eugenia Galeota
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/Onassis
Branch: RELEASE_3_10
Last Commit: e66cf3b
Last Changed Date: 2019-12-19 06:12:37 -0400 (Thu, 19 Dec 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Onassis
Version: 1.8.2
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Onassis.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Onassis_1.8.2.tar.gz
StartedAt: 2020-04-15 05:01:29 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:04:10 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 160.5 seconds
RetCode: 0
Status:  OK 
CheckDir: Onassis.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Onassis.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Onassis_1.8.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/Onassis.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.2’
* 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 16.852  0.580   9.047
compare      13.140  0.196   9.994
collapse      8.048  0.264   3.557
sim           6.736  0.156   3.832
annotate      6.180  0.168   2.194
* 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-3.10-bioc/meat/Onassis.Rcheck/00check.log’
for details.



Installation output

Onassis.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL Onassis
###
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* installing to library ‘/home/biocbuild/bbs-3.10-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)

Tests output


Example timings

Onassis.Rcheck/Onassis-Ex.timings

nameusersystemelapsed
CMdictionary-class0.0000.0000.001
CMdictionary000
CMoptions-class0.0080.0000.054
CMoptions0.0040.0000.005
CaseMatch0.0080.0040.014
EntityFinder-class0.0880.0040.449
EntityFinder16.852 0.580 9.047
FindAllMatches0.0360.0040.013
GEOHandler-functions000
Onassis0.0040.0000.001
OrderIndependentLookup0.0560.0000.019
SearchStrategy0.0560.0000.019
Similarity-class0.1240.0000.044
Similarity1.7280.0960.806
Stemmer0.0200.0000.024
StopWords0.0160.0000.019
SynonymType0.0120.0040.019
annotate6.1800.1682.194
annotateDF1.9920.0840.802
collapse8.0480.2643.557
compare13.140 0.196 9.994
dictInfo0.0000.0000.002
dictRef0.0040.0000.003
dictTypes0.0040.0000.004
dict_location0.0040.0000.002
dictionary0.0000.0000.002
entities0.0040.0000.002
experiment_types0.0000.0000.001
filterTerms0.080.000.08
filterconcepts1.2560.0680.594
findEntities1.2600.0680.494
findHealthy0.1320.0000.080
getGEOMetadata0.0000.0000.001
groupConfig0.1520.0040.081
groupsim0.4040.0080.334
groupwiseConfigRef0.0480.0000.045
icConfig000
listCMOptions0.0000.0000.001
listSimilarities0.0440.0000.042
mergeonassis3.3760.1281.319
multisim2.6040.1241.628
ontology0.0480.0000.012
organism_types0.0040.0000.000
pairsim0.2440.0040.162
pairwiseConfig0.3040.0000.113
pairwiseConfigRef0.0440.0000.043
paramValueIndex0.0080.0040.011
samplesim1.4200.0640.763
scores0.0040.0000.000
sim6.7360.1563.832
simil000
similarityInstance0.0040.0000.001
typeSystemRef0.0080.0000.009