Laurent Gatto
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/rols |
| Branch: RELEASE_3_9 |
| Last Commit: b191259 |
| Last Changed Date: 2019-10-12 16:19:25 -0400 (Sat, 12 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:50:11 -0400 (Wed, 16 Oct 2019).
| Package 1407/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rols 2.12.2 Laurent Gatto
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: rols |
| Version: 2.12.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rols.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rols_2.12.2.tar.gz |
| StartedAt: 2019-10-16 06:22:38 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:33:50 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 672.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rols.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rols.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rols_2.12.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/rols.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.12.2’
* 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 99.023 3.909 203.962
CVParam-class 1.308 0.084 20.028
Ontology-class 0.600 0.039 5.904
Properties-class 0.520 0.021 5.095
OlsSearch-class 0.343 0.032 8.290
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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
rols.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rols ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 2.12.2
>
> test_check("rols")
[, , Hello, World]
Object of class 'OlsSearch':
ontolgy: GO
query: cell
requested: 20 (out of 10029)
response(s): 0
Object of class 'Ontologies' with 239 entries
AEO, MIAPA ... SEP, SEPIO
Object of class 'Ontologies' with 1 entries
AEO
Object of class 'Ontologies' with 2 entries
AEO, MIAPA
Object of class 'Ontologies' with 3 entries
AEO, MIAPA, MICRO
Object of class 'Ontologies' with 4 entries
AEO, MIAPA, MICRO, MIRNAO
Object of class 'Ontologies' with 5 entries
AEO, MIAPA ... MIRNAO, MIRO
Ontology: Gene Ontology (go)
An ontology for describing the function of genes and gene products
Loaded: 2019-10-10 Updated: 2019-10-15 Version: 2019-10-07
49992 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 lobule, hepatobiliary system
A Property from the UBERON ontology: UBERON:0006925
Label: digestive system gland
Object of class 'Terms' with 2571 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.
Testing term SO:0000299
Testing term SO:1000007
Testing term SO:0001251
Testing term SO:0000798
Testing term SO:0000732
Testing term SO:0000506
Testing term SO:1000026
Testing term SO:0000430
Testing term SO:0000052
Testing term SO:0001341
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 2767 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
103.933 2.604 367.433
rols.Rcheck/rols-Ex.timings
| name | user | system | elapsed | |
| CVParam-class | 1.308 | 0.084 | 20.028 | |
| OlsSearch-class | 0.343 | 0.032 | 8.290 | |
| Ontology-class | 0.600 | 0.039 | 5.904 | |
| Properties-class | 0.520 | 0.021 | 5.095 | |
| Term-class | 99.023 | 3.909 | 203.962 | |