| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:32:27 -0400 (Tue, 09 Apr 2019).
| Package 1380/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rols 2.11.1 Laurent Gatto
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: rols |
| Version: 2.11.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rols.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rols_2.11.1.tar.gz |
| StartedAt: 2019-04-09 03:19:00 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:28:59 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 598.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: rols.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rols.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rols_2.11.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rols.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘2.11.1’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Term-class 72.589 0.688 215.658
CVParam-class 1.179 0.032 23.384
Ontology-class 0.454 0.000 5.420
OlsSearch-class 0.335 0.004 9.029
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Testing term SO:0002160
Testing term SO:0000796
Testing term SO:0001965
Testing term SO:0000653
Testing term SO:0000348
Testing term SO:0000807
Testing term SO:0000170
Testing term SO:0000758
══ 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: 1 ERROR
See
‘/home/biocbuild/bbs-3.9-bioc/meat/rols.Rcheck/00check.log’
for details.
rols.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL rols ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * 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 ** 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 * DONE (rols)
rols.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 2.11.1
>
> 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
AERO, AGRO ... UNIMOD, ZFA
Object of class 'Ontologies' with 1 entries
AERO
Object of class 'Ontologies' with 2 entries
AERO, AGRO
Object of class 'Ontologies' with 3 entries
AERO, AGRO, APOLLO_SV
Object of class 'Ontologies' with 4 entries
AERO, AGRO, APOLLO_SV, ATOL
Object of class 'Ontologies' with 5 entries
AERO, AGRO ... ATOL, BAO
Ontology: Gene Ontology (go)
An ontology for describing the function of genes and gene products
Loaded: 2019-03-20 Updated: 2019-04-05 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 ... hepatobiliary system, bile
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:0001048
Testing term SO:0000894
Testing term SO:0002160
Testing term SO:0000796
Testing term SO:0001965
Testing term SO:0000653
Testing term SO:0000348
Testing term SO:0000807
Testing term SO:0000170
Testing term SO:0000758
══ 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/rols-Ex.timings
| name | user | system | elapsed | |
| CVParam-class | 1.179 | 0.032 | 23.384 | |
| OlsSearch-class | 0.335 | 0.004 | 9.029 | |
| Ontology-class | 0.454 | 0.000 | 5.420 | |
| Properties-class | 0.475 | 0.012 | 4.696 | |
| Term-class | 72.589 | 0.688 | 215.658 | |