| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:54 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the MinimumDistance package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MinimumDistance.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1157/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MinimumDistance 1.38.0 (landing page) Robert Scharpf
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MinimumDistance |
| Version: 1.38.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MinimumDistance.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MinimumDistance_1.38.0.tar.gz |
| StartedAt: 2022-04-12 22:55:47 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 23:02:42 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 414.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MinimumDistance.Rcheck |
| Warnings: 5 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MinimumDistance.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MinimumDistance_1.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MinimumDistance.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MinimumDistance/DESCRIPTION' ... OK
* this is package 'MinimumDistance' version '1.38.0'
* 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 whether package 'MinimumDistance' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'ff::pattern' by 'grid::pattern' when loading 'MinimumDistance'
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MinimumDistance.Rcheck/00install.out' for details.
* 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 ... NOTE
Namespace in Imports field not imported from: 'MatrixGenerics'
All declared Imports should be used.
Unexported object imported by a ':::' call: 'VanillaICE:::plotIdiogram'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
callDenovoSegments: no visible global function definition for
'read.bsfiles'
combineRanges: no visible global function definition for 'RangedData'
getRefGene: no visible global function definition for 'RangedData'
overlapsCentromere: no visible global function definition for
'RangedData'
pruneMD: no visible global function definition for 'RangedDataCBS'
pruneTrioSet: no visible global function definition for
'RangedDataList'
read.bsfiles2: no visible binding for global variable 'read.bsfiles'
GenomeAnnotatedDataFrameFrom,character: no visible global function
definition for 'read.bsfiles'
calculateMindist,list: no visible binding for global variable 'elt'
Undefined global functions or variables:
RangedData RangedDataCBS RangedDataList elt read.bsfiles
* checking Rd files ... WARNING
checkRd: (5) MinimumDistance.Rd:0-7: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'coerce' but not in code:
'as'
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'coerce':
'as'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... WARNING
Output for data("trioSetListExample", package = "MinimumDistance"):
Warning message:
replacing previous import 'ff::pattern' by 'grid::pattern' when loading 'MinimumDistance'
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'doRUnit.R'
OK
** running tests for arch 'x64' ...
Running 'doRUnit.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: 5 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/MinimumDistance.Rcheck/00check.log'
for details.
MinimumDistance.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MinimumDistance_1.38.0.tar.gz && rm -rf MinimumDistance.buildbin-libdir && mkdir MinimumDistance.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MinimumDistance.buildbin-libdir MinimumDistance_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MinimumDistance_1.38.0.zip && rm MinimumDistance_1.38.0.tar.gz MinimumDistance_1.38.0.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
44 938k 44 416k 0 0 584k 0 0:00:01 --:--:-- 0:00:01 584k
100 938k 100 938k 0 0 787k 0 0:00:01 0:00:01 --:--:-- 788k
install for i386
* installing *source* package 'MinimumDistance' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Warning: replacing previous import 'ff::pattern' by 'grid::pattern' when loading 'MinimumDistance'
Creating a new generic function for 'allNames' in package 'MinimumDistance'
in method for 'coerce' with signature '"RangedDataCNV","GRanges"': no definition for class "RangedDataCNV"
in method for 'todf' with signature 'object="TrioSet",rangeData="RangedData"': no definition for class "RangedData"
in method for 'prune' with signature 'object="TrioSet",ranges="RangedDataCNV"': no definition for class "RangedDataCNV"
in method for 'prune' with signature 'object="TrioSetList",ranges="RangedDataCNV"': no definition for class "RangedDataCNV"
** help
*** installing help indices
converting help for package 'MinimumDistance'
finding HTML links ... done
DNAcopyParam html
Defunct html
Deprecated html
FilterParamMD-class html
FilterParamMD html
MAP html
MAP2 html
MDRanges-class html
MinDistExperiment-class html
MinDistExperiment html
MinDistGRanges-class html
MinDistGRanges html
MinDistParam-class html
MinDistParam html
MinDistPosterior-class html
MinimumDistance html
ParentOffspring-class html
ParentOffspringList-class html
Pedigree-class html
Pedigree html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/MinimumDistance.buildbin-libdir/00LOCK-MinimumDistance/00new/MinimumDistance/help/Pedigree.html
PennParam html
TrioSet-class html
TrioSet html
TrioSetList-class html
TrioSetList html
TrioSetListLD html
acf2 html
calculateMindist html
coercion-methods html
denovo html
exampleTrioSetList html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/MinimumDistance.buildbin-libdir/00LOCK-MinimumDistance/00new/MinimumDistance/help/trioSetList.html
filterExperiment html
mad2 html
mdLegend html
md_exp html
md_gr html
mindist html
nMAD html
pedigreeGrid html
pedigreeName html
pedigreeViewports html
plotDenovo html
range-ILimit-method html
segment2 html
finding level-2 HTML links ... done
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Warning: replacing previous import 'ff::pattern' by 'grid::pattern' when loading 'MinimumDistance'
** testing if installed package can be loaded from final location
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Warning: replacing previous import 'ff::pattern' by 'grid::pattern' when loading 'MinimumDistance'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'MinimumDistance' ...
** testing if installed package can be loaded
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Warning: replacing previous import 'ff::pattern' by 'grid::pattern' when loading 'MinimumDistance'
* MD5 sums
packaged installation of 'MinimumDistance' as MinimumDistance_1.38.0.zip
* DONE (MinimumDistance)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MinimumDistance' successfully unpacked and MD5 sums checked
|
MinimumDistance.Rcheck/tests_i386/doRUnit.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+ pkg <- "MinimumDistance"
+
+ 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 )
+
+ ##xmap.clear.cache()
+
+ ##Fail on warnings
+ options( warn=1 )
+
+ ## Get the pattern (if there is one?)
+ patt <- Sys.getenv( "RUNITFILEPATTERN" )
+ if( is.null( patt ) || nchar( patt ) == 0 ) {
+ testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ dirs=path,
+ testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ))
+ } else {
+ ##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path )
+ testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
+ dirs=path )
+ }
+ tests <- runTestSuite( testSuite )
+
+ pathReport <- file.path( path, "report" )
+
+ cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+ printTextProtocol( tests, showDetails=FALSE )
+ printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+ printTextProtocol( tests, showDetails=TRUE, fileName=paste( pathReport, ".txt", sep="" ) )
+
+ printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+
+ tmp <- getErrors( tests )
+ if( tmp$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] "MinimumDistance"
$getwd
[1] "C:/Users/biocbuild/bbs-3.14-bioc/meat/MinimumDistance.Rcheck/tests_i386"
$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.14-bioc/R/library/MinimumDistance/unitTests"
Loading required package: VanillaICE
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to VanillaICE version 1.56.3
Welcome to MinimumDistance version 1.38.0
Attaching package: 'MinimumDistance'
The following object is masked from 'package:VanillaICE':
acf2
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_MDE ... done successfully.
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_Pedigree_construction ... Welcome to oligoClasses version 1.56.0
done successfully.
Executing test function test_subsetPedigree ... Error in validObject(.Object) :
invalid class "Pedigree" object: fatherNames can not be the same as the offspringNames
In addition: Warning message:
replacing previous import 'ff::pattern' by 'grid::pattern' when loading 'MinimumDistance'
done successfully.
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_TrioSet ... done successfully.
Executing test function test_TrioSetList_construction ... done successfully.
Executing test function test_TrioSetListdataExamples ... done successfully.
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_calculateMindist ... Parallel computing support for 'oligo/crlmm': Disabled
- Load 'ff'
- Load and register a 'foreach' adaptor
Example - Using 'multicore' for 2 cores:
library(doMC)
registerDoMC(2)
================================================================================
done successfully.
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_callDenovoSegments ...
Attaching package: 'data.table'
The following object is masked from 'package:SummarizedExperiment':
shift
The following object is masked from 'package:GenomicRanges':
shift
The following object is masked from 'package:IRanges':
shift
The following objects are masked from 'package:S4Vectors':
first, second
Welcome to human610quadv1bCrlmm version 1.0.3
done successfully.
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_MAP2 ... Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:VanillaICE':
deletion
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Analyzing: NA12891
Analyzing: NA12892
Analyzing: NA12878
Analyzing: md_NA12878
done successfully.
Executing test function test_pennParam ... done successfully.
Executing test function test_posteriorCalls ... done successfully.
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_cbsSplits ... done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Tue Apr 12 23:01:50 2022
***********************************************
Number of test functions: 12
Number of errors: 0
Number of failures: 0
1 Test Suite :
MinimumDistance unit testing - 12 test functions, 0 errors, 0 failures
>
> proc.time()
user system elapsed
43.96 2.14 46.40
|
MinimumDistance.Rcheck/tests_x64/doRUnit.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+ pkg <- "MinimumDistance"
+
+ if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
+ path <- file.path( getwd(), "..", "inst", "unitTests" )
+ } else {
+ path <- system.file( package=pkg, "unitTests" )
+ }
+
+ cat( "\nRunning unit tests\n" )
+ print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+ library( package=pkg, character.only=TRUE )
+
+ ##xmap.clear.cache()
+
+ ##Fail on warnings
+ options( warn=1 )
+
+ ## Get the pattern (if there is one?)
+ patt <- Sys.getenv( "RUNITFILEPATTERN" )
+ if( is.null( patt ) || nchar( patt ) == 0 ) {
+ testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ dirs=path,
+ testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ))
+ } else {
+ ##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path )
+ testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
+ 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] "MinimumDistance"
$getwd
[1] "C:/Users/biocbuild/bbs-3.14-bioc/meat/MinimumDistance.Rcheck/tests_x64"
$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.14-bioc/R/library/MinimumDistance/unitTests"
Loading required package: VanillaICE
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to VanillaICE version 1.56.3
Welcome to MinimumDistance version 1.38.0
Attaching package: 'MinimumDistance'
The following object is masked from 'package:VanillaICE':
acf2
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_MDE ... done successfully.
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_Pedigree_construction ... Welcome to oligoClasses version 1.56.0
done successfully.
Executing test function test_subsetPedigree ... Error in validObject(.Object) :
invalid class "Pedigree" object: fatherNames can not be the same as the offspringNames
In addition: Warning message:
replacing previous import 'ff::pattern' by 'grid::pattern' when loading 'MinimumDistance'
done successfully.
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_TrioSet ... done successfully.
Executing test function test_TrioSetList_construction ... done successfully.
Executing test function test_TrioSetListdataExamples ... done successfully.
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_calculateMindist ... Parallel computing support for 'oligo/crlmm': Disabled
- Load 'ff'
- Load and register a 'foreach' adaptor
Example - Using 'multicore' for 2 cores:
library(doMC)
registerDoMC(2)
================================================================================
done successfully.
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_callDenovoSegments ...
Attaching package: 'data.table'
The following object is masked from 'package:SummarizedExperiment':
shift
The following object is masked from 'package:GenomicRanges':
shift
The following object is masked from 'package:IRanges':
shift
The following objects are masked from 'package:S4Vectors':
first, second
Welcome to human610quadv1bCrlmm version 1.0.3
done successfully.
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_MAP2 ... Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:VanillaICE':
deletion
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Analyzing: NA12891
Analyzing: NA12892
Analyzing: NA12878
Analyzing: md_NA12878
done successfully.
Executing test function test_pennParam ... done successfully.
Executing test function test_posteriorCalls ... done successfully.
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Executing test function test_cbsSplits ... done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Tue Apr 12 23:02:32 2022
***********************************************
Number of test functions: 12
Number of errors: 0
Number of failures: 0
1 Test Suite :
MinimumDistance unit testing - 12 test functions, 0 errors, 0 failures
>
> proc.time()
user system elapsed
41.14 0.95 42.07
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MinimumDistance.Rcheck/examples_i386/MinimumDistance-Ex.timings
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MinimumDistance.Rcheck/examples_x64/MinimumDistance-Ex.timings
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