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This page was generated on 2021-07-30 15:06:02 -0400 (Fri, 30 Jul 2021).

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 1311/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 1.14.0  (landing page)
VJ Carey
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/ontoProc
Branch: RELEASE_3_13
Last Commit: 2ba1033
Last Changed Date: 2021-05-19 12:31:28 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.14.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ontoProc_1.14.0.tar.gz
StartedAt: 2021-07-30 03:14:54 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 03:22:06 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 431.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ontoProc_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ontoProc.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.14.0'
* 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 41.7Mb
  sub-directories of 1Mb or more:
    app       1.9Mb
    data      2.0Mb
    ontoRda  37.2Mb
* 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
common_classes    25.03   2.11   31.65
CLfeats           16.20   1.03   17.71
fastGrep          11.44   0.42   11.86
getLeavesFromTerm  9.73   0.00    9.73
sym2CellOnto       8.01   0.15    8.17
getCellOnto        5.80   0.02    5.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
common_classes    22.65   1.80   25.91
CLfeats           14.53   0.38   14.90
fastGrep          11.62   0.09   11.72
getLeavesFromTerm  9.89   0.03    9.93
sym2CellOnto       5.82   0.11    5.93
* 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-3.13-bioc/meat/ontoProc.Rcheck/00check.log'
for details.



Installation output

ontoProc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ontoProc_1.14.0.tar.gz && rm -rf ontoProc.buildbin-libdir && mkdir ontoProc.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ontoProc.buildbin-libdir ontoProc_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ontoProc_1.14.0.zip && rm ontoProc_1.14.0.tar.gz ontoProc_1.14.0.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
  4 40.7M    4 1860k    0     0  3407k      0  0:00:12 --:--:--  0:00:12 3407k
 19 40.7M   19 7932k    0     0  5004k      0  0:00:08  0:00:01  0:00:07 5004k
 37 40.7M   37 15.4M    0     0  6222k      0  0:00:06  0:00:02  0:00:04 6221k
 62 40.7M   62 25.6M    0     0  7411k      0  0:00:05  0:00:03  0:00:02 7410k
 93 40.7M   93 38.0M    0     0  8566k      0  0:00:04  0:00:04 --:--:-- 8566k
100 40.7M  100 40.7M    0     0  8795k      0  0:00:04  0:00:04 --:--:-- 9496k

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  
    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) :
  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_1.14.0.zip
* DONE (ontoProc)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ontoProc' successfully unpacked and MD5 sums checked

Tests output

ontoProc.Rcheck/tests_i386/test.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 5 | SKIP 0 | PASS 8 ]
> 
> 
> proc.time()
   user  system elapsed 
  22.95    1.21   24.14 

ontoProc.Rcheck/tests_x64/test.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 5 | SKIP 0 | PASS 8 ]
> 
> 
> proc.time()
   user  system elapsed 
  26.17    1.26   43.57 

Example timings

ontoProc.Rcheck/examples_i386/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats16.20 1.0317.71
PROSYM000
TermSet-class0.280.000.28
allGOterms0.630.000.63
cellTypeToGO2.210.062.28
cleanCLOnames0.660.000.66
common_classes25.03 2.1131.65
cyclicSigset0.080.000.08
demoApp000
dropStop000
fastGrep11.44 0.4211.86
findCommonAncestors2.640.583.22
getCellOnto5.800.025.92
getLeavesFromTerm9.730.009.73
humrna0.020.000.02
ldfToTerms0.140.000.14
liberalMap3.540.043.59
makeSelectInput0.020.000.02
make_graphNEL_from_ontology_plot1.940.072.00
mapOneNaive1.920.041.97
minicorpus000
nomenCheckup0.890.000.89
onto_plot22.230.042.27
onto_roots000
packDesc2019000
recognizedPredicates000
secLevGen0.20.00.2
selectFromMap1.990.032.02
seur3kTab000
siblings_TAG0.610.000.61
stopWords000
sym2CellOnto8.010.158.17

ontoProc.Rcheck/examples_x64/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats14.53 0.3814.90
PROSYM000
TermSet-class0.170.030.20
allGOterms0.030.010.05
cellTypeToGO1.390.101.48
cleanCLOnames0.580.010.59
common_classes22.65 1.8025.91
cyclicSigset0.020.000.01
demoApp000
dropStop000
fastGrep11.62 0.0911.72
findCommonAncestors4.850.064.96
getCellOnto4.200.054.25
getLeavesFromTerm9.890.039.93
humrna0.020.000.02
ldfToTerms0.120.000.12
liberalMap1.770.031.80
makeSelectInput000
make_graphNEL_from_ontology_plot2.080.042.11
mapOneNaive1.960.062.03
minicorpus000
nomenCheckup1.330.011.35
onto_plot21.820.051.85
onto_roots000
packDesc2019000
recognizedPredicates000
secLevGen0.350.000.36
selectFromMap2.250.052.30
seur3kTab000
siblings_TAG0.580.010.59
stopWords000
sym2CellOnto5.820.115.93