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This page was generated on 2022-04-13 12:07:15 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 rols on tokay2


To the developers/maintainers of the rols package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rols.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1644/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rols 2.22.1  (landing page)
Laurent Gatto
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/rols
git_branch: RELEASE_3_14
git_last_commit: c90505b
git_last_commit_date: 2022-03-12 04:39:58 -0400 (Sat, 12 Mar 2022)
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: rols
Version: 2.22.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rols.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings rols_2.22.1.tar.gz
StartedAt: 2022-04-13 01:55:30 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 02:14:45 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 1154.7 seconds
RetCode: 0
Status:   OK  
CheckDir: rols.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rols.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings rols_2.22.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/rols.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rols/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rols' version '2.22.1'
* 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 'rols' can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* 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 (user + system) or elapsed time > 5s
                  user system elapsed
Term-class       94.49   1.91  218.44
CVParam-class     0.89   0.05   17.78
Ontology-class    0.90   0.00    6.39
Properties-class  0.81   0.03    5.23
OlsSearch-class   0.39   0.01   10.18
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
Term-class       94.38   1.63  215.28
Ontology-class    0.76   0.04    5.22
CVParam-class     0.74   0.03   19.36
Properties-class  0.75   0.00    5.27
OlsSearch-class   0.48   0.00    9.15
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: OK

Installation output

rols.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/rols_2.22.1.tar.gz && rm -rf rols.buildbin-libdir && mkdir rols.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rols.buildbin-libdir rols_2.22.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL rols_2.22.1.zip && rm rols_2.22.1.tar.gz rols_2.22.1.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 30569  100 30569    0     0   255k      0 --:--:-- --:--:-- --:--:--  257k

install for i386

* installing *source* package 'rols' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'lapply' from package 'base' in package 'rols'
** help
*** installing help indices
  converting help for package 'rols'
    finding HTML links ... done
    CVParam-class                           html  
    finding level-2 HTML links ... done

    OlsSearch-class                         html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/rols.buildbin-libdir/00LOCK-rols/00new/rols/help/olsSearch.html
    Ontology-class                          html  
    Properties-class                        html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/rols.buildbin-libdir/00LOCK-rols/00new/rols/help/properties.html
    Term-class                              html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/rols.buildbin-libdir/00LOCK-rols/00new/rols/help/terms.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/rols.buildbin-libdir/00LOCK-rols/00new/rols/help/term.html
    dot-properties                          html  
    dot-term                                html  
    dot-terms                               html  
    makeOntologies                          html  
    makeOntology                            html  
    makeProperty                            html  
    makeTerm                                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 'rols' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rols' as rols_2.22.1.zip
* DONE (rols)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'rols' successfully unpacked and MD5 sums checked

Tests output

rols.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> # setting R_TESTS to empty string because of 
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library("testthat")
> library("rols")

This is 'rols' version 2.22.1 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 9658)
  response(s): 0 
Object of class 'Ontologies' with 273 entries
   AEO, CMPO ... SCDO, DISDRIV 
Object of class 'Ontologies' with 1 entries
AEO 
Object of class 'Ontologies' with 2 entries
AEO, CMPO 
Object of class 'Ontologies' with 3 entries
AEO, CMPO, AISM 
Object of class 'Ontologies' with 4 entries
AEO, CMPO, AISM, CO_356 
Object of class 'Ontologies' with 5 entries
   AEO, CMPO ... CO_356, CRO 
Ontology: Gene Ontology (go)  
  The Gene Ontology (GO) provides a framework and set of concepts for
  describing the functions of gene products from all organisms.
   Loaded: 2022-03-21 Updated: 2022-04-06 Version: 2022-03-10 
   50800 terms  67 properties  0 individuals
Object of class 'Properties' with 92 entries
 From the SO ontology
  partial_evidence_for_feature, evidence_for_feature ... variant_of, DBVAR 
Object of class 'Properties' with 146 entries
 From the UBERON ontology
  digestive system gland, abdomen element ... Vertebrata <vertebrates>, hepatobiliary system 
A Property from the UBERON ontology: UBERON:0006925 
 Label: digestive system gland
Object of class 'Terms' with 2729 entries
 From the SO ontology
  SO:0000579, SO:0000833 ... SO:0000071, SO:0000070 
Object of class 'Terms' with 1 entries
 From the SO ontology
SO:0000579 
Object of class 'Terms' with 2 entries
 From the SO ontology
SO:0000579, SO:0000833 
Object of class 'Terms' with 3 entries
 From the SO ontology
SO:0000579, SO:0000833, SO:0000578 
Object of class 'Terms' with 4 entries
 From the SO ontology
SO:0000579, SO:0000833, SO:0000578, SO:0000011 
Object of class 'Terms' with 5 entries
 From the SO ontology
  SO:0000579, SO:0000833 ... SO:0000011, SO:0001430 
A Term from the GO ontology: GO:0032801 
 Label: receptor catabolic process
  No description
Testing term SO:0002152 
Testing term SO:0000526 
Testing term SO:0000246 
Testing term SO:0001927 
Testing term SO:0001550 
Testing term SO:0000750 
Testing term SO:0002370 
Testing term SO:0002277 
Testing term SO:0001581 
Testing term SO:0000915 
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2924 ]

== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2924 ]
> 
> proc.time()
   user  system elapsed 
  86.68    1.37  293.43

rols.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> # setting R_TESTS to empty string because of 
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library("testthat")
> library("rols")

This is 'rols' version 2.22.1 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 9658)
  response(s): 0 
Object of class 'Ontologies' with 273 entries
   AEO, CMPO ... SCDO, DISDRIV 
Object of class 'Ontologies' with 1 entries
AEO 
Object of class 'Ontologies' with 2 entries
AEO, CMPO 
Object of class 'Ontologies' with 3 entries
AEO, CMPO, AISM 
Object of class 'Ontologies' with 4 entries
AEO, CMPO, AISM, CO_356 
Object of class 'Ontologies' with 5 entries
   AEO, CMPO ... CO_356, CRO 
Ontology: Gene Ontology (go)  
  The Gene Ontology (GO) provides a framework and set of concepts for
  describing the functions of gene products from all organisms.
   Loaded: 2022-03-21 Updated: 2022-04-06 Version: 2022-03-10 
   50800 terms  67 properties  0 individuals
Object of class 'Properties' with 92 entries
 From the SO ontology
  partial_evidence_for_feature, evidence_for_feature ... variant_of, DBVAR 
Object of class 'Properties' with 146 entries
 From the UBERON ontology
  digestive system gland, abdomen element ... glycogen catabolic process, Vertebrata <vertebrates> 
A Property from the UBERON ontology: UBERON:0006925 
 Label: digestive system gland
Object of class 'Terms' with 2729 entries
 From the SO ontology
  SO:0000579, SO:0000833 ... SO:0000071, SO:0000070 
Object of class 'Terms' with 1 entries
 From the SO ontology
SO:0000579 
Object of class 'Terms' with 2 entries
 From the SO ontology
SO:0000579, SO:0000833 
Object of class 'Terms' with 3 entries
 From the SO ontology
SO:0000579, SO:0000833, SO:0000578 
Object of class 'Terms' with 4 entries
 From the SO ontology
SO:0000579, SO:0000833, SO:0000578, SO:0000011 
Object of class 'Terms' with 5 entries
 From the SO ontology
  SO:0000579, SO:0000833 ... SO:0000011, SO:0001430 
A Term from the GO ontology: GO:0032801 
 Label: receptor catabolic process
  No description
Testing term SO:0001778 
Testing term SO:0002274 
Testing term SO:0002377 
Testing term SO:0000400 
Testing term SO:0000726 
Testing term SO:0001034 
Testing term SO:0001492 
Testing term SO:0001609 
Testing term SO:0001694 
Testing term SO:0001645 
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2924 ]

== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2924 ]
> 
> proc.time()
   user  system elapsed 
  88.81    1.03  290.06

Example timings

rols.Rcheck/examples_i386/rols-Ex.timings

nameusersystemelapsed
CVParam-class 0.89 0.0517.78
OlsSearch-class 0.39 0.0110.18
Ontology-class0.900.006.39
Properties-class0.810.035.23
Term-class 94.49 1.91218.44

rols.Rcheck/examples_x64/rols-Ex.timings

nameusersystemelapsed
CVParam-class 0.74 0.0319.36
OlsSearch-class0.480.009.15
Ontology-class0.760.045.22
Properties-class0.750.005.27
Term-class 94.38 1.63215.28