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CHECK report for Onassis on tokay2

This page was generated on 2019-10-16 12:39:05 -0400 (Wed, 16 Oct 2019).

Package 1136/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Onassis 1.6.1
Eugenia Galeota
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/Onassis
Branch: RELEASE_3_9
Last Commit: 8f2beb2
Last Changed Date: 2019-10-01 06:15:22 -0400 (Tue, 01 Oct 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Onassis
Version: 1.6.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Onassis.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Onassis_1.6.1.tar.gz
StartedAt: 2019-10-16 05:42:12 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:48:27 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 375.3 seconds
RetCode: 0
Status:  OK  
CheckDir: Onassis.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Onassis.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Onassis_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Onassis.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Onassis/DESCRIPTION' ... OK
* this is package 'Onassis' version '1.6.1'
* 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 ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
compare      8.39   0.55   14.11
EntityFinder 6.30   1.30   67.42
sim          4.00   0.66    7.91
collapse     3.68   0.57    7.11
annotate     2.50   0.46    5.76
mergeonassis 1.97   0.43    7.29
multisim     1.88   0.39    7.53
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
EntityFinder 21.75   1.66   11.29
compare      11.31   0.61   15.96
collapse      8.44   0.60   22.79
sim           6.42   0.68    8.57
annotate      5.93   0.72    5.56
mergeonassis  2.95   0.33    6.57
multisim      2.54   0.36    6.81
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/Onassis.Rcheck/00check.log'
for details.



Installation output

Onassis.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Onassis_1.6.1.tar.gz && rm -rf Onassis.buildbin-libdir && mkdir Onassis.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Onassis.buildbin-libdir Onassis_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Onassis_1.6.1.zip && rm Onassis_1.6.1.tar.gz Onassis_1.6.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1123k  100 1123k    0     0  7407k      0 --:--:-- --:--:-- --:--:-- 7800k

install for i386

* installing *source* package 'Onassis' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Onassis'
    finding HTML links ... done
    CMdictionary-class                      html  
    CMdictionary                            html  
    CMoptions-class                         html  
    CMoptions                               html  
    CaseMatch                               html  
    EntityFinder-class                      html  
    EntityFinder                            html  
    FindAllMatches                          html  
    GEOHandler-functions                    html  
    Onassis-class                           html  
    Onassis                                 html  
    OrderIndependentLookup                  html  
    SearchStrategy                          html  
    Similarity-class                        html  
    Similarity                              html  
    Stemmer                                 html  
    StopWords                               html  
    SynonymType                             html  
    annotate                                html  
    annotateDF                              html  
    collapse                                html  
    compare                                 html  
    dictInfo                                html  
    dictRef                                 html  
    dictTypes                               html  
    dict_location                           html  
    dictionary                              html  
    entities                                html  
    experiment_types                        html  
    filterTerms                             html  
    filterconcepts                          html  
    findEntities                            html  
    findHealthy                             html  
    getGEOMetadata                          html  
    groupConfig                             html  
    groupsim                                html  
    groupwiseConfigRef                      html  
    icConfig                                html  
    listCMOptions                           html  
    listSimilarities                        html  
    mergeonassis                            html  
    multisim                                html  
    ontology                                html  
    organism_types                          html  
    pairsim                                 html  
    pairwiseConfig                          html  
    pairwiseConfigRef                       html  
    paramValueIndex                         html  
    samplesim                               html  
    scores                                  html  
    sim                                     html  
    simil                                   html  
    similarityInstance                      html  
    typeSystemRef                           html  
** 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

install for x64

* installing *source* package 'Onassis' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Onassis' as Onassis_1.6.1.zip
* DONE (Onassis)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Onassis' successfully unpacked and MD5 sums checked

Tests output


Example timings

Onassis.Rcheck/examples_i386/Onassis-Ex.timings

nameusersystemelapsed
CMdictionary-class000
CMdictionary000
CMoptions-class0.010.000.14
CMoptions0.020.000.02
CaseMatch0.030.000.03
EntityFinder-class0.080.000.59
EntityFinder 6.30 1.3067.42
FindAllMatches0.010.000.02
GEOHandler-functions000
Onassis000
OrderIndependentLookup0.030.000.03
SearchStrategy0.020.000.02
Similarity-class0.000.000.15
Similarity0.470.193.38
Stemmer0.010.010.03
StopWords0.000.020.01
SynonymType0.020.010.04
annotate2.500.465.76
annotateDF0.860.363.94
collapse3.680.577.11
compare 8.39 0.5514.11
dictInfo000
dictRef000
dictTypes000
dict_location000
dictionary000
entities000
experiment_types000
filterTerms0.050.000.05
filterconcepts0.690.173.50
findEntities0.790.173.51
findHealthy0.110.000.11
getGEOMetadata000
groupConfig0.100.000.08
groupsim0.280.000.31
groupwiseConfigRef0.060.000.06
icConfig0.020.000.02
listCMOptions000
listSimilarities0.040.000.05
mergeonassis1.970.437.29
multisim1.880.397.53
ontology000
organism_types000
pairsim0.090.000.10
pairwiseConfig0.090.000.09
pairwiseConfigRef0.050.000.05
paramValueIndex0.020.000.01
samplesim1.220.364.32
scores000
sim4.000.667.91
simil000
similarityInstance000
typeSystemRef0.010.000.01

Onassis.Rcheck/examples_x64/Onassis-Ex.timings

nameusersystemelapsed
CMdictionary-class000
CMdictionary000
CMoptions-class000
CMoptions0.010.000.02
CaseMatch0.020.000.01
EntityFinder-class0.080.030.05
EntityFinder21.75 1.6611.29
FindAllMatches0.030.000.02
GEOHandler-functions000
Onassis000
OrderIndependentLookup0.030.000.02
SearchStrategy0.030.000.01
Similarity-class0.060.000.02
Similarity2.350.193.37
Stemmer0.010.000.02
StopWords0.030.000.03
SynonymType0.040.010.03
annotate5.930.725.56
annotateDF2.030.353.63
collapse 8.44 0.6022.79
compare11.31 0.6115.96
dictInfo000
dictRef000
dictTypes000
dict_location000
dictionary0.000.020.01
entities000
experiment_types000
filterTerms0.050.000.05
filterconcepts1.490.203.55
findEntities1.310.213.29
findHealthy0.060.010.07
getGEOMetadata000
groupConfig0.160.000.07
groupsim0.590.000.36
groupwiseConfigRef0.080.000.08
icConfig000
listCMOptions000
listSimilarities0.050.000.04
mergeonassis2.950.336.57
multisim2.540.366.81
ontology000
organism_types0.060.000.02
pairsim0.250.000.10
pairwiseConfig0.370.010.16
pairwiseConfigRef0.050.000.05
paramValueIndex0.010.000.02
samplesim1.880.363.94
scores000
sim6.420.688.57
simil000
similarityInstance000
typeSystemRef0.010.000.02