Benilton Carvalho
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/oligoClasses |
| git_branch: master |
| git_last_commit: c385539 |
| git_last_commit_date: 2021-10-26 11:51:32 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:12 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 oligoClasses package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oligoClasses.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. |
| Package 1326/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| oligoClasses 1.57.0 (landing page) Benilton Carvalho
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: oligoClasses |
| Version: 1.57.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:oligoClasses.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings oligoClasses_1.57.0.tar.gz |
| StartedAt: 2022-03-17 19:46:00 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:48:48 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 167.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: oligoClasses.Rcheck |
| Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:oligoClasses.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings oligoClasses_1.57.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/oligoClasses.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'oligoClasses/DESCRIPTION' ... OK * this is package 'oligoClasses' version '1.57.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Packages which this enhances but not available for checking: 'doMC', 'doMPI', 'doRedis' * 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 'oligoClasses' can be installed ... OK * checking installed package size ... OK * 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 ... NOTE Namespace in Imports field not imported from: 'RSQLite' All declared Imports should be used. Unexported object imported by a ':::' call: 'Biobase:::assayDataEnvLock' 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 getSequenceLengths: no visible binding for global variable 'seqlengths' chromosome,gSetList: no visible global function definition for 'chromosomeList' coerce,CNSet-CopyNumberSet: no visible global function definition for 'totalCopynumber' geometry,FeatureSet: no visible global function definition for 'getPD' Undefined global functions or variables: chromosomeList getPD seqlengths totalCopynumber * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '[' and siglist 'CNSet,ANY,ANY,ANY' generic '[' and siglist 'gSetList,ANY,ANY,ANY' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in 'vignettes' ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': 'scriptsForExampleData/CreateExampleData.R' Package has no Sweave vignette sources and no VignetteBuilder field. * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'doRUnit.R' OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 3 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/oligoClasses.Rcheck/00check.log' for details.
oligoClasses.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL oligoClasses
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'oligoClasses' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'oligoClasses'
finding HTML links ... done
AlleleSet-class html
finding level-2 HTML links ... done
AlleleSet-methods html
AssayData-methods html
AssayDataList html
BeadStudioSet-class html
BeadStudioSetList-class html
CNSet-class html
ClassesNotExported html
CopyNumberSet-class html
CopyNumberSet-methods html
DBPDInfo-class html
FeatureSetExtensions-class html
GRanges-methods html
GenomeAnnotatedDataFrame-class html
GenomeAnnotatedDataFrameFrom-methods html
SnpSet-methods html
SnpSet2-class html
SnpSuperSet-class html
SummarizedExperiment-methods html
affyPlatforms html
annotationPackages html
assayDataList-methods html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-oligoClasses/00new/oligoClasses/help/assayDataList.html
batch html
batchStatistics html
celfileDate html
celfileName html
checkExists html
checkOrder html
chromosome-methods html
chromosome2integer html
clusterOpts html
clusterOptsDeprecated html
createFF html
data-efsExample html
data-scqsExample html
data-sfsExample html
data-sqsExample html
db html
defunct html
exprs-methods html
featureDataList-methods html
ff_matrix html
ff_or_matrix-class html
ffdf html
fileConnections html
flags html
gSet-class html
gSetList-class html
generics html
genomeBuild html
geometry-methods html
getBar html
getSequenceLengths html
i2p_p2i html
integerMatrix html
is.ffmatrix html
isPackageLoaded html
isSnp-methods html
kind html
largeObjects html
ldOpts html
length-methods html
library2 html
list.celfiles html
locusLevelData html
makeFeatureGRanges html
manufacturer-methods html
ocLapply html
oligoSetExample html
oligoSnpSet-methods html
parStatus html
pdPkgFromBioC html
platform-methods html
pmFragmentLength-methods html
position-methods html
requireAnnotation html
requireClusterPkgSetDeprecated html
sampleNames-methods html
splitVec 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
* DONE (oligoClasses)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'sRACIPE' is missing or broken
done
oligoClasses.Rcheck/tests/doRUnit.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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.
> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+ ## loading Biobase below b/c we're simply Import:ing it, rather than Depend:ing on it
+ ## then functions from there are not visible downstream
+ library(Biobase)
+ pkg <- "oligoClasses"
+
+ 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=2 )
+ options(warn=0)
+
+ ## 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" )
+ }
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Running unit tests
$pkg
[1] "oligoClasses"
$getwd
[1] "D:/biocbuild/bbs-3.15-bioc/meat/oligoClasses.Rcheck/tests"
$pathToUnitTests
[1] "D:/biocbuild/bbs-3.15-bioc/R/library/oligoClasses/unitTests"
Welcome to oligoClasses version 1.57.0
Executing test function test_annotation ... Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19.
Build requested, but only build hg18 is available.
done successfully.
Executing test function test_BafLrrSetList ... done successfully.
Executing test function test_BeadStudioSet ... done successfully.
Executing test function test_CNSet_construction ... done successfully.
Executing test function test_CopyNumberSet_construction ... Loading required package: pd.mapping50k.hind240
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
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: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligo
================================================================================
Welcome to oligo version 1.59.0
================================================================================
Loading required package: DBI
Loading required package: pd.mapping50k.xba240
done successfully.
Executing test function test_GenomeAnnotatedDataFrameWithFF ... Loading required package: ff
Loading required package: bit
Attaching package: 'bit'
The following object is masked from 'package:base':
xor
Attaching package ff
- getOption("fftempdir")=="D:/biocbuild/bbs-3.15-bioc/tmpdir/Rtmpike0aT/ff"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
- Probesets: 20,000
- Samples..: 100
- Path.....: D:/biocbuild/bbs-3.15-bioc/meat/oligoClasses.Rcheck/tests
================================================================================
Attaching package: 'ff'
The following objects are masked from 'package:Biostrings':
mismatch, pattern
The following objects are masked from 'package:utils':
write.csv, write.csv2
The following objects are masked from 'package:base':
is.factor, is.ordered
done successfully.
Executing test function test_GenomeAnnotatedDataFrame_construction ... done successfully.
Executing test function test_dataExamples ... done successfully.
Executing test function test_oligoSnpSet_construction ... done successfully.
Executing test function test_conversions ... done successfully.
Executing test function test_makeFeatureRanges ... done successfully.
Executing test function test_oligoSnpSet ... done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Thu Mar 17 19:48:37 2022
***********************************************
Number of test functions: 12
Number of errors: 0
Number of failures: 0
1 Test Suite :
oligoClasses unit testing - 12 test functions, 0 errors, 0 failures
Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
5: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
6: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
7: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
8: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
>
> proc.time()
user system elapsed
13.43 0.98 15.50
oligoClasses.Rcheck/oligoClasses-Ex.timings
| name | user | system | elapsed | |
| AlleleSet-class | 0.10 | 0.00 | 0.09 | |
| AssayData-methods | 0.79 | 0.09 | 0.89 | |
| AssayDataList | 0.02 | 0.00 | 0.02 | |
| BeadStudioSet-class | 0.03 | 0.00 | 0.03 | |
| CNSet-class | 0.02 | 0.00 | 0.02 | |
| CopyNumberSet-class | 0.01 | 0.00 | 0.01 | |
| CopyNumberSet-methods | 0.59 | 0.02 | 0.61 | |
| FeatureSetExtensions-class | 0.08 | 0.00 | 0.08 | |
| GRanges-methods | 0.27 | 0.00 | 0.26 | |
| GenomeAnnotatedDataFrameFrom-methods | 0.45 | 0.03 | 0.63 | |
| SnpSet-methods | 0.02 | 0.00 | 0.02 | |
| SnpSet2-class | 0.03 | 0.00 | 0.03 | |
| SnpSuperSet-class | 0.03 | 0.00 | 0.03 | |
| affyPlatforms | 0 | 0 | 0 | |
| batch | 0.03 | 0.00 | 0.03 | |
| celfileDate | 0.02 | 0.00 | 0.01 | |
| celfileName | 0 | 0 | 0 | |
| checkExists | 0.01 | 0.00 | 0.02 | |
| checkOrder | 0.19 | 0.01 | 0.20 | |
| chromosome-methods | 0 | 0 | 0 | |
| chromosome2integer | 0 | 0 | 0 | |
| clusterOpts | 0 | 0 | 0 | |
| data-efsExample | 0 | 0 | 0 | |
| data-scqsExample | 0 | 0 | 0 | |
| data-sfsExample | 0 | 0 | 0 | |
| data-sqsExample | 0.00 | 0.02 | 0.01 | |
| db | 0 | 0 | 0 | |
| ff_matrix | 0 | 0 | 0 | |
| ff_or_matrix-class | 0 | 0 | 0 | |
| fileConnections | 0 | 0 | 0 | |
| flags | 0.03 | 0.00 | 0.04 | |
| gSet-class | 0 | 0 | 0 | |
| gSetList-class | 0 | 0 | 0 | |
| genomeBuild | 0.02 | 0.00 | 0.01 | |
| geometry-methods | 1.29 | 0.00 | 1.30 | |
| getBar | 0 | 0 | 0 | |
| getSequenceLengths | 0.11 | 0.01 | 0.12 | |
| i2p_p2i | 0 | 0 | 0 | |
| integerMatrix | 0 | 0 | 0 | |
| is.ffmatrix | 0 | 0 | 0 | |
| isPackageLoaded | 0 | 0 | 0 | |
| kind | 0.14 | 0.04 | 0.17 | |
| largeObjects | 0 | 0 | 0 | |
| ldOpts | 0 | 0 | 0 | |
| library2 | 0.03 | 0.00 | 0.03 | |
| list.celfiles | 0.02 | 0.00 | 0.03 | |
| locusLevelData | 0.04 | 0.00 | 0.05 | |
| makeFeatureGRanges | 0.21 | 0.01 | 0.22 | |
| oligoSetExample | 0.15 | 0.02 | 0.17 | |
| pdPkgFromBioC | 0 | 0 | 0 | |
| requireAnnotation | 0 | 0 | 0 | |
| splitVec | 0.00 | 0.01 | 0.02 | |