This page was generated on 2018-10-17 08:50:32 -0400 (Wed, 17 Oct 2018).
annmap 1.22.0 Chris Wirth
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
URL: https://git.bioconductor.org/packages/annmap |
Branch: RELEASE_3_7 |
Last Commit: e62e90a |
Last Changed Date: 2018-04-30 10:35:25 -0400 (Mon, 30 Apr 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED... |
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.
> if( require( "RUnit", quietly=TRUE ) ) {
+ pkg <- "annmap"
+
+ if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
+ path <- file.path( getwd(), "..", "inst", "unitTests" )
+ }
+ else {
+ path <- system.file( package=pkg, "unitTests" )
+ }
+
+ cat( "\nRunning unit tests\n" )
+ print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+ library( package=pkg, character.only=TRUE )
+
+ annmapClearCache()
+
+ # Run the old style RangedData for tim...
+ #annmapSetParam( oldstylekey='P0fSpS' )
+ annmapSetParam( spacefn=if( annmap:::.usegranges() ) seqnames else space )
+ annmapSetParam( defaultclass=if( annmap:::.usegranges() ) 'GRanges' else 'RangedData' )
+
+ #Fail on warnings
+ options( warn=2 )
+
+ # Get the pattern (if there is one?)
+ patt = Sys.getenv( "RUNITFILEPATTERN" )
+ func = Sys.getenv( 'RUNITFUNCPATTERN' )
+ if( is.null( patt ) || nchar( patt ) == 0 ) {
+ patt = "^runit.+\\.[rR]$"
+ }
+ else {
+ patt = paste( "^runit\\.", patt, "\\.[rR]$", sep="" )
+ }
+ if( is.null( func ) || nchar( func ) == 0 ) {
+ func = "^test.+"
+ }
+ else {
+ func = paste( "^test\\.", func, ".+", sep="" )
+ }
+ testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=patt, testFuncRegexp=func, dirs=path )
+ tests <- runTestSuite( testSuite )
+
+ pathReport <- file.path( path, "report" )
+
+ cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+ printTextProtocol( tests, showDetails=FALSE )
+ printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+ printTextProtocol( tests, showDetails=TRUE, fileName=paste( pathReport, ".txt", sep="" ) )
+
+ printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+
+ tmp <- getErrors( tests )
+ if( tmp$nFail > 0 | tmp$nErr > 0 ) {
+ stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ", tmp$nErr, ")\n\n", sep="" ) )
+ }
+ } else {
+ warning( "cannot run unit tests -- package RUnit is not available" )
+ }
Running unit tests
$pkg
[1] "annmap"
$getwd
[1] "/Users/biocbuild/bbs-3.7-bioc/meat/annmap.Rcheck/tests"
$pathToUnitTests
[1] "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/annmap/unitTests"
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Using /Users/biocbuild/.annmap as our configuration directory.
Executing test function test.template ... done successfully.
Executing test function test.all.queries ... [1] "\nSkipping allXXX tests, as not on a PICR machine"
done successfully.
Executing test function test.gotsomefunctions ... done successfully.
Executing test function test.cache ... done successfully.
Executing test function test.ANNMAP112 ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.huisun.ANNMAP48 ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.chaining ... [1] "Cannot find datasource 'hs-test' so skipping this test."
done successfully.
Executing test function test.addConnection ... Using /Users/biocbuild/.annmap as our configuration directory.
[1] "Got conf.dir /Users/biocbuild/.annmap"
Connection a added.
Connection b added.
Connection a updated.
[1] "Resetting conf.dir to /Users/biocbuild/.annmap"
done successfully.
Executing test function test.buildsql ... Using /Users/biocbuild/.annmap as our configuration directory.
[1] "Got conf.dir /Users/biocbuild/.annmap"
[1] "Resetting conf.dir to /Users/biocbuild/.annmap"
done successfully.
Executing test function test.connection ... Using /Users/biocbuild/.annmap as our configuration directory.
[1] "Got conf.dir /Users/biocbuild/.annmap"
[1] "Cannot find datasource 'hs-test', so skipping these tests."
[1] "Resetting conf.dir to /Users/biocbuild/.annmap"
done successfully.
Executing test function test.databases.txt ... Using /Users/biocbuild/.annmap as our configuration directory.
[1] "Got conf.dir /Users/biocbuild/.annmap"
[1] "Mocking annmapConnect()"
[1] "setting conf.dir to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/annmap/unitTests/tabConfig"
[1] "setting conf.dir to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/annmap/unitTests/commaConfig"
[1] "restoring connect method"
[1] "Resetting conf.dir to /Users/biocbuild/.annmap"
done successfully.
Executing test function test.details.queries ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
[1] "Cannot find datasource 'mm-test', so skipping these tests."
[1] "Cannot find datasource 'rn-test', so skipping these tests."
[1] "Cannot find datasource 'pb-test', so skipping these tests."
done successfully.
Executing test function test.gotsomefunctions ... done successfully.
Executing test function test.filters ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.bug.ACBBUTIL33 ... [1] "Cannot find datasource 'mm-test', so skipping this test."
done successfully.
Executing test function test.bug.ANNMAP40 ... [1] "Cannot find datasource 'hs-test', so skipping this test."
done successfully.
Executing test function test.bug.ANNMAP44 ... [1] "Cannot find datasource 'hs-test', so skipping this test."
done successfully.
Executing test function test.gotsomefunctions ... done successfully.
Executing test function test.multi.queries ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.range.queries ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
[1] "Cannot find datasource 'mm-test', so skipping these tests."
[1] "Cannot find datasource 'rn-test', so skipping these tests."
[1] "Cannot find datasource 'pb-test', so skipping these tests."
done successfully.
Executing test function test.expr.query ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.gotsomefunctions ... done successfully.
Executing test function test.to.queries ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
[1] "Cannot find datasource 'mm-test', so skipping these tests."
[1] "Cannot find datasource 'rn-test', so skipping these tests."
[1] "Cannot find datasource 'pb-test', so skipping these tests."
done successfully.
Executing test function test.transcript.to.translatedprobes ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.ANNMAP.109 ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.ANNMAP.97 ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.ANNMAP.98 ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.array.type ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.make.params ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.needs.array ... done successfully.
Executing test function test.rangeapply ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.reality ... done successfully.
Executing test function test.seqnames ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.set.get.params ... done successfully.
Executing test function test.ANNMAP118 ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.michal.utr.bug ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.michal.utr.bug.three ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.michal.utr.bug.two ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.utr ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.yaoyong.utr.bug ... [1] "Cannot find datasource 'hs-test', so skipping these tests."
done successfully.
Executing test function test.ANNMAP33 ... [1] "\nSkipping webservice tests, no route to annmap website"
done successfully.
Executing test function test.connection ... [1] "\nSkipping webservice tests, no route to annmap website"
done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Tue Oct 16 19:56:32 2018
***********************************************
Number of test functions: 42
Number of errors: 0
Number of failures: 0
1 Test Suite :
annmap unit testing - 42 test functions, 0 errors, 0 failures
>
> proc.time()
user system elapsed
7.692 0.504 161.711