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CHECK report for ontoProc on tokay2

This page was generated on 2020-10-17 11:57:19 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ontoProc PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1235/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 1.10.1
VJ Carey
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ontoProc
Branch: RELEASE_3_11
Last Commit: 2c91e8e
Last Changed Date: 2020-08-18 23:10:00 -0400 (Tue, 18 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR  OK 

Summary

Package: ontoProc
Version: 1.10.1
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ontoProc_1.10.1.tar.gz
StartedAt: 2020-10-17 06:37:38 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:44:05 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 387.3 seconds
RetCode: 0
Status:  OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ontoProc_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ontoProc.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ontoProc/DESCRIPTION' ... OK
* this is package 'ontoProc' version '1.10.1'
* 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 'ontoProc' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 37.9Mb
  sub-directories of 1Mb or more:
    app       1.9Mb
    data      2.0Mb
    ontoRda  33.5Mb
* 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CLfeat : prupdate: no visible binding for global variable 'PRID'
CLfeat : prupdate: no visible binding for global variable 'SYMBOL'
bind_formal_tags: no visible global function definition for 'colData'
bind_formal_tags: no visible global function definition for 'colData<-'
common_classes: no visible global function definition for 'colData'
connect_classes: no visible global function definition for 'colData'
ctmarks: no visible binding for '<<-' assignment to 'pr'
ctmarks: no visible binding for '<<-' assignment to 'go'
ctmarks : server: no visible binding for global variable 'text'
cyclicSigset: no visible binding for global variable 'sigels'
ldfToTerm: no visible binding for global variable 'PROSYM'
subset_descendants: no visible global function definition for 'colData'
sym2CellOnto: no visible binding for global variable 'SYMBOL'
Undefined global functions or variables:
  PRID PROSYM SYMBOL colData colData<- sigels text
Consider adding
  importFrom("graphics", "text")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 162 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
common_classes    21.39   1.71   60.57
CLfeats           15.40   0.96   16.57
fastGrep          14.28   0.76   16.47
getLeavesFromTerm 10.65   1.48   12.14
sym2CellOnto       5.41   0.63    6.06
getCellOnto        4.38   0.71    6.96
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
common_classes    21.30   1.48   27.56
CLfeats           14.67   0.19   14.86
fastGrep          13.60   0.22   13.82
getLeavesFromTerm  9.78   0.09    9.90
sym2CellOnto       6.14   0.07    6.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R'
 OK
** running tests for arch 'x64' ...
  Running 'test.R'
 OK
* 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-3.11-bioc/meat/ontoProc.Rcheck/00check.log'
for details.



Installation output

ontoProc.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ontoProc_1.10.1.tar.gz && rm -rf ontoProc.buildbin-libdir && mkdir ontoProc.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ontoProc.buildbin-libdir ontoProc_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ontoProc_1.10.1.zip && rm ontoProc_1.10.1.tar.gz ontoProc_1.10.1.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
 73 37.0M   73 27.1M    0     0  58.2M      0 --:--:-- --:--:-- --:--:-- 59.0M
100 37.0M  100 37.0M    0     0  49.4M      0 --:--:-- --:--:-- --:--:-- 49.8M

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'ontoProc' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ontoProc'
    finding HTML links ... done
    CLfeats                                 html  
    PROSYM                                  html  
    TermSet-class                           html  
    allGOterms                              html  
    bind_formal_tags                        html  
    c-TermSet-method                        html  
    cellTypeToGO                            html  
    cleanCLOnames                           html  
    common_classes                          html  
    connect_classes                         html  
    ctmarks                                 html  
    cyclicSigset                            html  
    demoApp                                 html  
    dropStop                                html  
    fastGrep                                html  
    getCellOnto                             html  
    getLeavesFromTerm                       html  
    humrna                                  html  
    improveNodes                            html  
    ldfToTerms                              html  
    liberalMap                              html  
    makeSelectInput                         html  
    make_graphNEL_from_ontology_plot        html  
    map2prose                               html  
    mapOneNaive                             html  
    minicorpus                              html  
    nomenCheckup                            html  
    onto_plot2                              html  
    onto_roots                              html  
    packDesc2019                            html  
    recognizedPredicates                    html  
    secLevGen                               html  
    selectFromMap                           html  
    seur3kTab                               html  
    siblings_TAG                            html  
    stopWords                               html  
    subset_descendants                      html  
    sym2CellOnto                            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

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'ontoProc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ontoProc' as ontoProc_1.10.1.zip
* DONE (ontoProc)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ontoProc' successfully unpacked and MD5 sums checked

Tests output

ontoProc.Rcheck/tests_i386/test.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> library(ontoProc)
Loading required package: ontologyIndex
> library(testthat)
> 
> test_check("ontoProc")
== testthat results  ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
  14.01    0.51   14.53 

ontoProc.Rcheck/tests_x64/test.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> library(ontoProc)
Loading required package: ontologyIndex
> library(testthat)
> 
> test_check("ontoProc")
== testthat results  ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
  12.84    0.45   13.29 

Example timings

ontoProc.Rcheck/examples_i386/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats15.40 0.9616.57
PROSYM000
TermSet-class0.420.110.55
allGOterms0.080.000.08
cellTypeToGO2.020.322.34
cleanCLOnames0.990.091.19
common_classes21.39 1.7160.57
cyclicSigset0.020.000.01
demoApp000
dropStop0.010.000.02
fastGrep14.28 0.7616.47
getCellOnto4.380.716.96
getLeavesFromTerm10.65 1.4812.14
humrna000
ldfToTerms0.160.000.15
liberalMap0.330.130.46
makeSelectInput000
make_graphNEL_from_ontology_plot0.670.060.73
mapOneNaive0.310.000.31
minicorpus000
nomenCheckup1.300.011.32
onto_plot20.540.030.57
onto_roots000
packDesc2019000
recognizedPredicates000
secLevGen0.220.000.22
selectFromMap0.310.020.33
seur3kTab000
siblings_TAG0.540.030.56
stopWords0.010.000.02
sym2CellOnto5.410.636.06

ontoProc.Rcheck/examples_x64/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats14.67 0.1914.86
PROSYM0.020.000.01
TermSet-class0.230.000.24
allGOterms0.050.020.06
cellTypeToGO1.620.071.70
cleanCLOnames1.510.021.53
common_classes21.30 1.4827.56
cyclicSigset0.010.000.02
demoApp000
dropStop0.010.000.02
fastGrep13.60 0.2213.82
getCellOnto3.980.024.00
getLeavesFromTerm9.780.099.90
humrna0.020.000.01
ldfToTerms0.150.000.16
liberalMap0.550.000.54
makeSelectInput000
make_graphNEL_from_ontology_plot0.590.000.59
mapOneNaive0.640.000.64
minicorpus000
nomenCheckup1.330.081.43
onto_plot20.560.020.57
onto_roots000
packDesc2019000
recognizedPredicates000
secLevGen0.240.000.24
selectFromMap0.370.000.37
seur3kTab000
siblings_TAG0.80.00.8
stopWords000
sym2CellOnto6.140.076.22