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 12:26:33 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rols.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rols_2.12.2.tar.gz |
| StartedAt: 2019-10-16 06:45:50 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:04:08 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1097.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rols.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rols.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rols_2.12.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/rols.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '2.12.2'
* 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 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 89.72 2.11 198.20
CVParam-class 0.78 0.02 20.20
OlsSearch-class 0.32 0.00 8.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Term-class 95.87 1.95 218.50
CVParam-class 0.79 0.05 19.39
Ontology-class 0.75 0.01 5.06
OlsSearch-class 0.36 0.00 7.87
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/rols_2.12.2.tar.gz && rm -rf rols.buildbin-libdir && mkdir rols.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rols.buildbin-libdir rols_2.12.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL rols_2.12.2.zip && rm rols_2.12.2.tar.gz rols_2.12.2.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 31676 100 31676 0 0 204k 0 --:--:-- --:--:-- --:--:-- 542k
install for i386
* 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
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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'rols' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rols' as rols_2.12.2.zip
* DONE (rols)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'rols' successfully unpacked and MD5 sums checked
|
rols.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 2.12.2
>
> 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 ... hepatobiliary system, bile
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:1000108
Testing term SO:1000115
Testing term SO:0000593
Testing term SO:1001265
Testing term SO:0001634
Testing term SO:0000705
Testing term SO:0005841
Testing term SO:0002129
Testing term SO:0002111
Testing term SO:0000753
== testthat results ===========================================================
[ OK: 2767 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
76.23 1.18 268.60
|
rols.Rcheck/tests_x64/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-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 2.12.2
>
> 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 bud, 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:0001833
Testing term SO:0001971
Testing term SO:0000254
Testing term SO:1001281
Testing term SO:0001137
Testing term SO:0001989
Testing term SO:0001964
Testing term SO:0001818
Testing term SO:0001285
Testing term SO:0000091
== testthat results ===========================================================
[ OK: 2767 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
84.56 0.92 279.31
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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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