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This page was generated on 2022-01-26 13:07:02 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ontoProc on tokay2


To the developers/maintainers of the ontoProc package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ontoProc.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1337/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 1.16.0  (landing page)
VJ Carey
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: RELEASE_3_14
git_last_commit: 45a31ef
git_last_commit_date: 2021-10-26 12:39:25 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ontoProc
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ontoProc_1.16.0.tar.gz
StartedAt: 2022-01-26 00:03:28 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 00:17:15 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 827.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ontoProc_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ontoProc.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.16.0'
* 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  7.4Mb
  sub-directories of 1Mb or more:
    app       1.9Mb
    data      2.0Mb
    ontoRda   2.8Mb
* 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'
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<- 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 LazyData ... OK
* 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
getCellOnto       32.05   1.71   35.11
CLfeats           26.49   2.28   30.47
siblings_TAG      26.22   1.36   29.05
common_classes    25.30   1.47   34.16
fastGrep          21.31   1.26   23.72
getLeavesFromTerm 20.36   0.71   21.55
sym2CellOnto      13.40   0.51   14.59
TermSet-class      9.54   0.94   10.99
secLevGen          8.23   0.44    9.18
nomenCheckup       7.46   0.36    8.31
cleanCLOnames      7.09   0.59    8.24
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
getCellOnto       32.72   1.19   35.40
siblings_TAG      27.27   1.22   29.90
CLfeats           24.63   1.17   27.05
common_classes    23.27   1.48   25.95
fastGrep          17.78   0.50   18.78
getLeavesFromTerm 17.41   0.71   18.46
sym2CellOnto      11.94   0.51   12.90
nomenCheckup       8.30   0.43    9.23
secLevGen          8.05   0.56    9.14
TermSet-class      7.97   0.59    9.05
cleanCLOnames      6.00   0.55    7.06
* 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-3.14-bioc/meat/ontoProc.Rcheck/00check.log'
for details.



Installation output

ontoProc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ontoProc_1.16.0.tar.gz && rm -rf ontoProc.buildbin-libdir && mkdir ontoProc.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ontoProc.buildbin-libdir ontoProc_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ontoProc_1.16.0.zip && rm ontoProc_1.16.0.tar.gz ontoProc_1.16.0.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
 20 8330k   20 1740k    0     0  2632k      0  0:00:03 --:--:--  0:00:03 2632k
 71 8330k   71 5939k    0     0  3552k      0  0:00:02  0:00:01  0:00:01 3552k
100 8330k  100 8330k    0     0  3844k      0  0:00:02  0:00:02 --:--:-- 3846k

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'ontoProc/vignettes/ontoProc.Rmd' to 'ontoProc/README.md'
* 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  
    findCommonAncestors                     html  
    finding level-2 HTML links ... done

    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) :
  failed to copy 'ontoProc/vignettes/ontoProc.Rmd' to 'ontoProc/README.md'
* installing *source* package 'ontoProc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ontoProc' as ontoProc_1.16.0.zip
* DONE (ontoProc)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ontoProc' successfully unpacked and MD5 sums checked

Tests output

ontoProc.Rcheck/tests_i386/test.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 8 ]

[ FAIL 0 | WARN 9 | SKIP 0 | PASS 8 ]
> 
> 
> proc.time()
   user  system elapsed 
  77.70    4.76   86.89 

ontoProc.Rcheck/tests_x64/test.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 8 ]

[ FAIL 0 | WARN 9 | SKIP 0 | PASS 8 ]
> 
> 
> proc.time()
   user  system elapsed 
  83.04    3.26  100.93 

Example timings

ontoProc.Rcheck/examples_i386/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats26.49 2.2830.47
PROSYM000
TermSet-class 9.54 0.9410.99
allGOterms0.050.000.04
cellTypeToGO1.550.131.67
cleanCLOnames7.090.598.24
common_classes25.30 1.4734.16
cyclicSigset0.010.000.01
demoApp000
dropStop0.020.000.02
fastGrep21.31 1.2623.72
findCommonAncestors3.111.114.21
getCellOnto32.05 1.7135.11
getLeavesFromTerm20.36 0.7121.55
humrna0.010.000.02
ldfToTerms0.110.000.11
liberalMap2.030.042.06
makeSelectInput000
make_graphNEL_from_ontology_plot2.570.042.61
mapOneNaive1.930.172.11
minicorpus000
nomenCheckup7.460.368.31
onto_plot22.170.022.19
onto_roots000
packDesc2019000
recognizedPredicates000
secLevGen8.230.449.18
selectFromMap2.470.282.75
seur3kTab0.020.000.02
siblings_TAG26.22 1.3629.05
stopWords000
sym2CellOnto13.40 0.5114.59

ontoProc.Rcheck/examples_x64/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats24.63 1.1727.05
PROSYM000
TermSet-class7.970.599.05
allGOterms0.030.000.03
cellTypeToGO1.330.051.38
cleanCLOnames6.000.557.06
common_classes23.27 1.4825.95
cyclicSigset000
demoApp000
dropStop0.000.020.01
fastGrep17.78 0.5018.78
findCommonAncestors2.910.072.99
getCellOnto32.72 1.1935.40
getLeavesFromTerm17.41 0.7118.46
humrna000
ldfToTerms0.150.000.15
liberalMap2.040.042.09
makeSelectInput000
make_graphNEL_from_ontology_plot2.250.082.35
mapOneNaive1.750.021.76
minicorpus000
nomenCheckup8.300.439.23
onto_plot21.950.021.97
onto_roots000
packDesc2019000
recognizedPredicates000
secLevGen8.050.569.14
selectFromMap1.900.051.95
seur3kTab000
siblings_TAG27.27 1.2229.90
stopWords000
sym2CellOnto11.94 0.5112.90