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BioC 3.4: CHECK report for rols on tokay1

This page was generated on 2017-04-15 16:17:16 -0400 (Sat, 15 Apr 2017).

Package 1072/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rols 2.2.5
Laurent Gatto
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/rols
Last Changed Rev: 126135 / Revision: 128728
Last Changed Date: 2017-01-25 05:15:54 -0500 (Wed, 25 Jan 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  ERROR  OK 

Summary

Package: rols
Version: 2.2.5
Command: rm -rf rols.buildbin-libdir rols.Rcheck && mkdir rols.buildbin-libdir rols.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rols.buildbin-libdir rols_2.2.5.tar.gz >rols.Rcheck\00install.out 2>&1 && cp rols.Rcheck\00install.out rols-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=rols.buildbin-libdir --install="check:rols-install.out" --force-multiarch --no-vignettes --timings rols_2.2.5.tar.gz
StartedAt: 2017-04-15 00:36:20 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:52:28 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 967.9 seconds
RetCode: 1
Status:  ERROR  
CheckDir: rols.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf rols.buildbin-libdir rols.Rcheck && mkdir rols.buildbin-libdir rols.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rols.buildbin-libdir rols_2.2.5.tar.gz >rols.Rcheck\00install.out 2>&1 && cp rols.Rcheck\00install.out rols-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=rols.buildbin-libdir --install="check:rols-install.out" --force-multiarch --no-vignettes --timings rols_2.2.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/rols.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '2.2.5'
* 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 installed files from 'inst/doc' ... 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       79.37   2.03  207.15
Properties-class  1.13   0.05    5.88
CVParam-class     0.73   0.04   13.44
OlsSearch-class   0.27   0.02    5.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
Term-class       100.40   2.08  214.43
Properties-class   1.46   0.03    6.42
CVParam-class      0.57   0.05   13.73
OlsSearch-class    0.26   0.01    5.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386/R" CMD BATCH --vanilla  "testthat.R" "testthat.Rout"' had status 1 
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Testing term SO:1000150 
  Testing term SO:0000246 
  Testing term SO:0002100 
  Testing term SO:1001282 
  Testing term SO:0001465 
  Testing term SO:0000595 
  Testing term SO:0002024 
  Testing term SO:0000697 
  Testing term SO:0001477 
  testthat results ================================================================
  OK: 194 SKIPPED: 0 FAILED: 1
  1. Error: unique terms (@test_Terms.R#109) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64/R" CMD BATCH --vanilla  "testthat.R" "testthat.Rout"' had status 1 
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Testing term SO:0000561 
  Testing term SO:0002118 
  Testing term SO:0001624 
  Testing term SO:0001091 
  Testing term SO:0002076 
  Testing term SO:0001822 
  Testing term SO:0001158 
  Testing term SO:0001576 
  Testing term SO:0001177 
  testthat results ================================================================
  OK: 194 SKIPPED: 0 FAILED: 1
  1. Error: unique terms (@test_Terms.R#109) 
  
  Error: testthat unit tests failed
  Execution halted
* 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: 2 ERRORs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/rols.Rcheck/00check.log'
for details.

testthat.Rout.fail:


R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 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 2.2.5 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 10124)
  response(s): 0 
Object of class 'Ontologies' with 166 entries
   AERO, CMO ... ZFA, ZFS 
Object of class 'Ontologies' with 1 entries
AERO 
Object of class 'Ontologies' with 2 entries
AERO, CMO 
Object of class 'Ontologies' with 3 entries
AERO, CMO, CMPO 
Object of class 'Ontologies' with 4 entries
AERO, CMO, CMPO, CTENO 
Object of class 'Ontologies' with 5 entries
   AERO, CMO ... CTENO, CVDO 
Ontology: Gene Ontology (go)  
  An ontology for describing the function of genes and gene products
   Loaded: 2017-04-14 Updated: 2017-04-14 Version: 2017-04-12 
   48560 terms  68 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 444 entries
 From the UBERON ontology
  exocrine gland, endoderm-derived structure ... liver lobule, hepatobiliary system 
A Property from the UBERON ontology: UBERON:0002365 
 Label: exocrine gland
Object of class 'Terms' with 2378 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.
1. Error: unique terms (@test_Terms.R#109) -------------------------------------
Not Found (HTTP 404).
1: term("nbo", "GO:0005802") at testthat/test_Terms.R:109
2: term("nbo", "GO:0005802")
3: .term(object, id, ...)
4: stop_for_status(x)

Testing term SO:0001351 
Testing term SO:1000150 
Testing term SO:0000246 
Testing term SO:0002100 
Testing term SO:1001282 
Testing term SO:0001465 
Testing term SO:0000595 
Testing term SO:0002024 
Testing term SO:0000697 
Testing term SO:0001477 
testthat results ================================================================
OK: 194 SKIPPED: 0 FAILED: 1
1. Error: unique terms (@test_Terms.R#109) 

Error: testthat unit tests failed
Execution halted

testthat.Rout.fail:


R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 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 2.2.5 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 10124)
  response(s): 0 
Object of class 'Ontologies' with 166 entries
   AERO, CMO ... ZFA, ZFS 
Object of class 'Ontologies' with 1 entries
AERO 
Object of class 'Ontologies' with 2 entries
AERO, CMO 
Object of class 'Ontologies' with 3 entries
AERO, CMO, CMPO 
Object of class 'Ontologies' with 4 entries
AERO, CMO, CMPO, CTENO 
Object of class 'Ontologies' with 5 entries
   AERO, CMO ... CTENO, CVDO 
Ontology: Gene Ontology (go)  
  An ontology for describing the function of genes and gene products
   Loaded: 2017-04-14 Updated: 2017-04-14 Version: 2017-04-12 
   48560 terms  68 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 444 entries
 From the UBERON ontology
  exocrine gland, endoderm-derived structure ... bile, liver lobule 
A Property from the UBERON ontology: UBERON:0002365 
 Label: exocrine gland
Object of class 'Terms' with 2378 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.
1. Error: unique terms (@test_Terms.R#109) -------------------------------------
Not Found (HTTP 404).
1: term("nbo", "GO:0005802") at testthat/test_Terms.R:109
2: term("nbo", "GO:0005802")
3: .term(object, id, ...)
4: stop_for_status(x)

Testing term SO:0000671 
Testing term SO:0000561 
Testing term SO:0002118 
Testing term SO:0001624 
Testing term SO:0001091 
Testing term SO:0002076 
Testing term SO:0001822 
Testing term SO:0001158 
Testing term SO:0001576 
Testing term SO:0001177 
testthat results ================================================================
OK: 194 SKIPPED: 0 FAILED: 1
1. Error: unique terms (@test_Terms.R#109) 

Error: testthat unit tests failed
Execution halted

rols.Rcheck/00install.out:


install for i386

* installing *source* package 'rols' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'lapply' from package 'base' in package 'rols'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'rols' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rols' as rols_2.2.5.zip
* DONE (rols)

rols.Rcheck/examples_i386/rols-Ex.timings:

nameusersystemelapsed
CVParam-class 0.73 0.0413.44
OlsSearch-class0.270.025.16
Ontology-class0.500.003.11
Properties-class1.130.055.88
Term-class 79.37 2.03207.15

rols.Rcheck/examples_x64/rols-Ex.timings:

nameusersystemelapsed
CVParam-class 0.57 0.0513.73
OlsSearch-class0.260.015.47
Ontology-class0.530.023.64
Properties-class1.460.036.42
Term-class100.40 2.08214.43