Klara Kaleb
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/OmaDB |
| Branch: RELEASE_3_12 |
| Last Commit: f70bed3 |
| Last Changed Date: 2020-11-10 17:30:16 -0400 (Tue, 10 Nov 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:32:36 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the OmaDB package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1250/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmaDB 2.6.1 (landing page) Klara Kaleb
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: OmaDB |
| Version: 2.6.1 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmaDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings OmaDB_2.6.1.tar.gz |
| StartedAt: 2021-05-06 05:10:52 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:25:26 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 874.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: OmaDB.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmaDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings OmaDB_2.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/OmaDB.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OmaDB/DESCRIPTION' ... OK
* this is package 'OmaDB' version '2.6.1'
* 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 whether package 'OmaDB' 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 ... WARNING
install.R
These files are defunct. See manual 'Writing R Extensions'.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getGenome 66.64 0.61 102.61
getGenomePairs 20.79 0.25 31.24
getOMAGroup 1.50 0.02 7.05
searchProtein 0.05 0.00 187.66
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getGenome 71.58 0.50 103.43
getGenomePairs 18.20 0.14 27.17
getOMAGroup 1.60 0.03 7.17
searchProtein 0.00 0.00 187.74
* 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: 1 WARNING
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/OmaDB.Rcheck/00check.log'
for details.
OmaDB.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/OmaDB_2.6.1.tar.gz && rm -rf OmaDB.buildbin-libdir && mkdir OmaDB.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OmaDB.buildbin-libdir OmaDB_2.6.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL OmaDB_2.6.1.zip && rm OmaDB_2.6.1.tar.gz OmaDB_2.6.1.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
23 200k 23 47937 0 0 777k 0 --:--:-- --:--:-- --:--:-- 780k
100 200k 100 200k 0 0 3244k 0 --:--:-- --:--:-- --:--:-- 3231k
install for i386
* installing *source* package 'OmaDB' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'OmaDB'
finding HTML links ... done
OmaDB-deprecated html
OmaDB-package html
annotateSequence html
cash-.omadb_obj html
formatTopGO html
getAnnotation-deprecated html
getAttribute html
getData-deprecated html
getGenome html
getGenomeAlignment-deprecated html
getGenomePairs html
getHOG html
getLocus html
getOMAGroup html
getObjectAttributes html
getProtein html
getTaxonomy html
getTopGO html
getTree html
getVersion html
getXref-deprecated html
group html
hog html
mapSequence html
orthologs html
pairs html
protein html
resolveURL html
searchProtein html
sequence_annotation html
sequence_map html
setAPI html
taxonomy html
xref 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 'OmaDB' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmaDB' as OmaDB_2.6.1.zip
* DONE (OmaDB)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'OmaDB' successfully unpacked and MD5 sums checked
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OmaDB.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.
> library(testthat)
>
> test_that("Testing the URL validity", {
+ expect_equal(httr::status_code(httr::GET("https://omabrowser.org/api")), 200 ) #checking that the server is live and accesible
+
+ })
Test passed
>
>
>
>
> proc.time()
user system elapsed
1.21 0.10 3.68
|
OmaDB.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.
> library(testthat)
>
> test_that("Testing the URL validity", {
+ expect_equal(httr::status_code(httr::GET("https://omabrowser.org/api")), 200 ) #checking that the server is live and accesible
+
+ })
Test passed
>
>
>
>
> proc.time()
user system elapsed
1.29 0.09 3.26
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OmaDB.Rcheck/examples_i386/OmaDB-Ex.timings
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OmaDB.Rcheck/examples_x64/OmaDB-Ex.timings
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