| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:11 -0400 (Sat, 13 Apr 2019).
| Package 1339/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rols 2.10.1 Laurent Gatto
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: rols |
| Version: 2.10.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rols.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rols_2.10.1.tar.gz |
| StartedAt: 2019-04-13 05:09:28 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 05:26:12 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 1004.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: rols.Rcheck |
| Warnings: NA |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rols.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rols_2.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/rols.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '2.10.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 67.28 1.31 156.52
CVParam-class 0.61 0.05 17.97
OlsSearch-class 0.20 0.01 7.00
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Term-class 75.27 1.53 168.67
CVParam-class 0.54 0.03 17.99
Ontology-class 0.42 0.03 6.36
OlsSearch-class 0.18 0.00 7.79
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
Testing term SO:0001530
Testing term SO:0001882
Testing term SO:0001331
Testing term SO:0000217
Testing term SO:1001255
Testing term SO:0001209
Testing term SO:0000128
Testing term SO:1000048
== testthat results ===========================================================
OK: 2766 SKIPPED: 0 FAILED: 2
1. Failure: accessors (@test_Terms.R#84)
2. Failure: accessors (@test_Terms.R#85)
Error: testthat unit tests failed
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
Testing term SO:0001230
Testing term SO:0001911
Testing term SO:0000188
Testing term SO:0000792
Testing term SO:0100014
Testing term SO:0000878
Testing term SO:0000426
Testing term SO:0001927
== testthat results ===========================================================
OK: 2766 SKIPPED: 0 FAILED: 2
1. Failure: accessors (@test_Terms.R#84)
2. Failure: accessors (@test_Terms.R#85)
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-3.8-bioc/meat/rols.Rcheck/00check.log'
for details.
rols.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/rols_2.10.1.tar.gz && rm -rf rols.buildbin-libdir && mkdir rols.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rols.buildbin-libdir rols_2.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL rols_2.10.1.zip && rm rols_2.10.1.tar.gz rols_2.10.1.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
100 32448 100 32448 0 0 785k 0 --:--:-- --:--:-- --:--:-- 880k
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
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
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_2.10.1.zip
* DONE (rols)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'rols' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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rols.Rcheck/tests_i386/testthat.Rout.fail
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 2.10.1
>
> test_check("rols")
[, , Hello, World]
Object of class 'OlsSearch':
ontolgy: GO
query: cell
requested: 20 (out of 10060)
response(s): 0
Object of class 'Ontologies' with 227 entries
AEO, AERO ... XPO, ZECO
Object of class 'Ontologies' with 1 entries
AEO
Object of class 'Ontologies' with 2 entries
AEO, AERO
Object of class 'Ontologies' with 3 entries
AEO, AERO, AGRO
Object of class 'Ontologies' with 4 entries
AEO, AERO, AGRO, ancestro
Object of class 'Ontologies' with 5 entries
AEO, AERO ... ancestro, APOLLO_SV
Ontology: Gene Ontology (go)
An ontology for describing the function of genes and gene products
Loaded: 2019-03-20 Updated: 2019-04-12 Version: 2019-03-19
49801 terms 60 properties 0 individuals
Object of class 'Properties' with 90 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 2569 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
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. Failure: accessors (@test_Terms.R#84) -----------------------------------
sum(isObsolete(trms)) not equal to `k`.
1/1 mismatches
[1] 335 - 204 == 131
-- 2. Failure: accessors (@test_Terms.R#85) -----------------------------------
sum(!isObsolete(trms)) not equal to length(trms) - k.
1/1 mismatches
[1] 2234 - 2365 == -131
Testing term SO:0000984
Testing term SO:1001280
Testing term SO:0001530
Testing term SO:0001882
Testing term SO:0001331
Testing term SO:0000217
Testing term SO:1001255
Testing term SO:0001209
Testing term SO:0000128
Testing term SO:1000048
== testthat results ===========================================================
OK: 2766 SKIPPED: 0 FAILED: 2
1. Failure: accessors (@test_Terms.R#84)
2. Failure: accessors (@test_Terms.R#85)
Error: testthat unit tests failed
Execution halted
|
rols.Rcheck/tests_x64/testthat.Rout.fail
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 2.10.1
>
> test_check("rols")
[, , Hello, World]
Object of class 'OlsSearch':
ontolgy: GO
query: cell
requested: 20 (out of 10060)
response(s): 0
Object of class 'Ontologies' with 227 entries
AEO, AERO ... XPO, ZECO
Object of class 'Ontologies' with 1 entries
AEO
Object of class 'Ontologies' with 2 entries
AEO, AERO
Object of class 'Ontologies' with 3 entries
AEO, AERO, AGRO
Object of class 'Ontologies' with 4 entries
AEO, AERO, AGRO, ancestro
Object of class 'Ontologies' with 5 entries
AEO, AERO ... ancestro, APOLLO_SV
Ontology: Gene Ontology (go)
An ontology for describing the function of genes and gene products
Loaded: 2019-03-20 Updated: 2019-04-12 Version: 2019-03-19
49801 terms 60 properties 0 individuals
Object of class 'Properties' with 90 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 ... liver bud, hepatobiliary system
A Property from the UBERON ontology: UBERON:0006925
Label: digestive system gland
Object of class 'Terms' with 2569 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
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. Failure: accessors (@test_Terms.R#84) -----------------------------------
sum(isObsolete(trms)) not equal to `k`.
1/1 mismatches
[1] 335 - 204 == 131
-- 2. Failure: accessors (@test_Terms.R#85) -----------------------------------
sum(!isObsolete(trms)) not equal to length(trms) - k.
1/1 mismatches
[1] 2234 - 2365 == -131
Testing term SO:0000391
Testing term SO:0000479
Testing term SO:0001230
Testing term SO:0001911
Testing term SO:0000188
Testing term SO:0000792
Testing term SO:0100014
Testing term SO:0000878
Testing term SO:0000426
Testing term SO:0001927
== testthat results ===========================================================
OK: 2766 SKIPPED: 0 FAILED: 2
1. Failure: accessors (@test_Terms.R#84)
2. Failure: accessors (@test_Terms.R#85)
Error: testthat unit tests failed
Execution halted
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rols.Rcheck/examples_i386/rols-Ex.timings
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rols.Rcheck/examples_x64/rols-Ex.timings
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