Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-27 13:52:22 -0400 (Wed, 27 Oct 2021).

CHECK results for biodb on nebbiolo2

To the developers/maintainers of the biodb package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodb.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 175/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodb 1.2.0  (landing page)
Pierrick Roger
Snapshot Date: 2021-10-26 14:50:08 -0400 (Tue, 26 Oct 2021)
git_url: https://git.bioconductor.org/packages/biodb
git_branch: RELEASE_3_14
git_last_commit: 51fdbaf
git_last_commit_date: 2021-10-26 13:09:33 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  YES
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  YES
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: biodb
Version: 1.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:biodb.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings biodb_1.2.0.tar.gz
StartedAt: 2021-10-26 19:25:03 -0400 (Tue, 26 Oct 2021)
EndedAt: 2021-10-26 19:28:36 -0400 (Tue, 26 Oct 2021)
EllapsedTime: 213.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:biodb.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings biodb_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/biodb.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodb/DESCRIPTION’ ... OK
* this is package ‘biodb’ version ‘1.2.0’
* 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 ‘biodb’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   9.1Mb
* checking package 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/biodb.Rcheck/00check.log’
for details.



Installation output

biodb.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL biodb
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘biodb’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c closeMatchPpm.cpp -o closeMatchPpm.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c test-100-ms_matching.cpp -o test-100-ms_matching.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c test-runner.cpp -o test-runner.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o biodb.so RcppExports.o closeMatchPpm.o test-100-ms_matching.o test-runner.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-biodb/00new/biodb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodb)

Tests output

biodb.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> test_check("biodb")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1493 ]
> 
> proc.time()
   user  system elapsed 
109.241   2.868 129.701 

Example timings

biodb.Rcheck/biodb-Ex.timings

nameusersystemelapsed
BiodbConfig1.4460.0781.527
BiodbConn0.3300.0000.331
BiodbConnBase0.2090.0020.211
BiodbCsvEntry0.0020.0000.002
BiodbDbInfo0.2160.0000.216
BiodbDbsInfo0.2440.0050.250
BiodbEntry0.5020.0030.506
BiodbEntryField0.2270.0040.232
BiodbEntryFields0.2270.0000.226
BiodbFactory0.2920.0000.291
BiodbHtmlEntry0.0010.0000.000
BiodbJsonEntry000
BiodbListEntry0.0010.0000.000
BiodbMain0.2130.0000.213
BiodbPersistentCache0.9000.0020.902
BiodbRequest0.4680.0031.443
BiodbRequestScheduler0.3470.0011.286
BiodbSdfEntry0.0010.0000.000
BiodbTestMsgAck0.1960.0020.197
BiodbTxtEntry000
BiodbUrl0.0010.0000.001
BiodbXmlEntry000
CompCsvFileConn0.3320.0000.333
CompCsvFileEntry0.3560.0030.360
CompSqliteConn0.2940.0000.294
CompSqliteEntry0.2930.0020.295
CsvFileConn0.3210.0000.321
ExtConnClass0.1560.0040.160
ExtCpp0.2870.0040.291
ExtDefinitions0.0870.0000.087
ExtDescriptionFile0.0550.0040.059
ExtEntryClass0.0630.0040.068
ExtFileGenerator0.0670.0000.067
ExtGenerator1.5690.0081.580
ExtGitignore0.0620.0000.063
ExtLicense0.080.000.08
ExtMakefile0.1390.0000.139
ExtPackage1.6790.1441.823
ExtPackageFile0.0540.0000.053
ExtRbuildignore0.0480.0030.051
ExtReadme0.0410.0040.044
ExtTests0.5860.0040.590
ExtTravisFile0.2200.0640.284
ExtVignette0.0510.0000.050
MassCsvFileConn0.3840.0420.426
MassCsvFileEntry0.3950.0000.396
MassSqliteConn0.2430.0000.243
MassSqliteEntry0.2260.0020.228
Progress0.0040.0000.004
Range0.0480.0000.048
SqliteConn0.2290.0020.230
TestRefEntries0.0160.0000.016
checkDeprecatedCacheFolders0.0010.0000.001
createBiodbTestInstance0.0920.0010.093
df2str0.0010.0000.001
error0.0010.0000.002
error00.0010.0000.001
genNewExtPkg1.2600.0081.268
getConnClassName000
getConnTypes000
getDefaultCacheDir0.0010.0000.000
getEntryClassName000
getEntryTypes000
getLicenses0.0000.0000.001
getLogger0.0040.0000.004
getPkgName000
getReposName0.0000.0000.001
getTestOutputDir000
listTestRefEntries0.0120.0000.012
logDebug000
logDebug0000
logInfo0.0010.0000.001
logInfo00.0010.0000.001
logTrace000
logTrace00.0010.0000.000
lst2str000
newInst0.1960.0040.200
runGenericTests0.0890.0000.088
testContext0.3820.0020.384
testThat0.1590.0060.166
upgradeExtPkg1.5820.0081.590
warn0.0020.0000.001
warn00.0010.0000.002