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CHECK report for rols on tokay2

This page was generated on 2018-10-17 08:36:19 -0400 (Wed, 17 Oct 2018).

Package 1268/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rols 2.8.2
Laurent Gatto
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/rols
Branch: RELEASE_3_7
Last Commit: c437df8
Last Changed Date: 2018-10-07 11:50:00 -0400 (Sun, 07 Oct 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rols
Version: 2.8.2
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rols.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings rols_2.8.2.tar.gz
StartedAt: 2018-10-17 04:30:55 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:53:45 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 1370.4 seconds
RetCode: 0
Status:  OK  
CheckDir: rols.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rols.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings rols_2.8.2.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/rols.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.8.2'
* 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 or elapsed time > 5s
                 user system elapsed
Term-class      90.00   2.54  214.08
CVParam-class    0.97   0.07   20.38
Ontology-class   0.69   0.03    6.14
OlsSearch-class  0.28   0.00    8.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
Term-class      106.53   2.14  415.11
CVParam-class     0.72   0.04   19.05
Ontology-class    0.76   0.00    6.02
OlsSearch-class   0.36   0.00    7.56
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/rols_2.8.2.tar.gz && rm -rf rols.buildbin-libdir && mkdir rols.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rols.buildbin-libdir rols_2.8.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL rols_2.8.2.zip && rm rols_2.8.2.tar.gz rols_2.8.2.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 30182  100 30182    0     0   539k      0 --:--:-- --:--:-- --:--:--  601k

install for i386

* installing *source* package 'rols' ...
** 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  
    Ontology-class                          html  
    Properties-class                        html  
    Term-class                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'rols' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rols' as rols_2.8.2.zip
* DONE (rols)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'rols' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

rols.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 2.8.2 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 10054)
  response(s): 0 
Object of class 'Ontologies' with 215 entries
   NCBITAXON, XCO ... MS, NBO 
Object of class 'Ontologies' with 1 entries
NCBITAXON 
Object of class 'Ontologies' with 2 entries
NCBITAXON, XCO 
Object of class 'Ontologies' with 3 entries
NCBITAXON, XCO, AEO 
Object of class 'Ontologies' with 4 entries
NCBITAXON, XCO, AEO, AERO 
Object of class 'Ontologies' with 5 entries
   NCBITAXON, XCO ... AERO, AGRO 
Ontology: Gene Ontology (go)  
  An ontology for describing the function of genes and gene products
   Loaded: 2018-10-09 Updated: 2018-10-16 Version: 2018-10-07 
   49709 terms  60 properties  0 individuals
Object of class 'Properties' with 89 entries
 From the SO ontology
  partial_evidence_for_feature, evidence_for_feature ... variant_of, DBVAR 
Object of class 'Properties' with 112 entries
 From the UBERON ontology
  digestive system gland, abdomen element ... septum transversum, liver bud 
A Property from the UBERON ontology: UBERON:0006925 
 Label: digestive system gland
Object of class 'Terms' with 2434 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:0000577 
A Term from the GO ontology: GO:0032801 
 Label: receptor catabolic process
  The chemical reactions and pathways resulting in the breakdown of a
  receptor molecule, a macromolecule that undergoes combination with a
  hormone, neurotransmitter, drug or intracellular messenger to initiate
  a change in cell function.
Testing term SO:0000236 
Testing term SO:0000981 
Testing term SO:0000631 
Testing term SO:0001586 
Testing term SO:0000610 
Testing term SO:0000809 
Testing term SO:0001511 
Testing term SO:0002038 
Testing term SO:0001259 
Testing term SO:0000228 
== testthat results  ===========================================================
OK: 2632 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  80.81    1.10  283.48

rols.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 2.8.2 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 10054)
  response(s): 0 
Object of class 'Ontologies' with 215 entries
   NCBITAXON, XCO ... MS, NBO 
Object of class 'Ontologies' with 1 entries
NCBITAXON 
Object of class 'Ontologies' with 2 entries
NCBITAXON, XCO 
Object of class 'Ontologies' with 3 entries
NCBITAXON, XCO, AEO 
Object of class 'Ontologies' with 4 entries
NCBITAXON, XCO, AEO, AERO 
Object of class 'Ontologies' with 5 entries
   NCBITAXON, XCO ... AERO, AGRO 
Ontology: Gene Ontology (go)  
  An ontology for describing the function of genes and gene products
   Loaded: 2018-10-09 Updated: 2018-10-16 Version: 2018-10-07 
   49709 terms  60 properties  0 individuals
Object of class 'Properties' with 89 entries
 From the SO ontology
  partial_evidence_for_feature, evidence_for_feature ... variant_of, DBVAR 
Object of class 'Properties' with 112 entries
 From the UBERON ontology
  digestive system gland, abdomen element ... hepatobiliary system, bile 
A Property from the UBERON ontology: UBERON:0006925 
 Label: digestive system gland
Object of class 'Terms' with 2434 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:0000577 
A Term from the GO ontology: GO:0032801 
 Label: receptor catabolic process
  The chemical reactions and pathways resulting in the breakdown of a
  receptor molecule, a macromolecule that undergoes combination with a
  hormone, neurotransmitter, drug or intracellular messenger to initiate
  a change in cell function.
Testing term SO:0000765 
Testing term SO:0000263 
Testing term SO:1000012 
Testing term SO:0002125 
Testing term SO:0000051 
Testing term SO:0000164 
Testing term SO:0000795 
Testing term SO:0000580 
Testing term SO:0000753 
Testing term SO:0001210 
== testthat results  ===========================================================
OK: 2632 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  85.54    1.07  332.21

Example timings

rols.Rcheck/examples_i386/rols-Ex.timings

nameusersystemelapsed
CVParam-class 0.97 0.0720.38
OlsSearch-class0.280.008.19
Ontology-class0.690.036.14
Properties-class0.610.004.78
Term-class 90.00 2.54214.08

rols.Rcheck/examples_x64/rols-Ex.timings

nameusersystemelapsed
CVParam-class 0.72 0.0419.05
OlsSearch-class0.360.007.56
Ontology-class0.760.006.02
Properties-class0.550.024.25
Term-class106.53 2.14415.11