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This page was generated on 2017-04-15 16:17:16 -0400 (Sat, 15 Apr 2017).
| Package 1072/1296 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| rols 2.2.5 Laurent Gatto
| 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 |
| 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 |
##############################################################################
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###
### 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
###
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##############################################################################
* 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:
| name | user | system | elapsed | |
| CVParam-class | 0.73 | 0.04 | 13.44 | |
| OlsSearch-class | 0.27 | 0.02 | 5.16 | |
| Ontology-class | 0.50 | 0.00 | 3.11 | |
| Properties-class | 1.13 | 0.05 | 5.88 | |
| Term-class | 79.37 | 2.03 | 207.15 | |
rols.Rcheck/examples_x64/rols-Ex.timings:
| name | user | system | elapsed | |
| CVParam-class | 0.57 | 0.05 | 13.73 | |
| OlsSearch-class | 0.26 | 0.01 | 5.47 | |
| Ontology-class | 0.53 | 0.02 | 3.64 | |
| Properties-class | 1.46 | 0.03 | 6.42 | |
| Term-class | 100.40 | 2.08 | 214.43 | |