Benilton S Carvalho
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/crlmm |
| Branch: RELEASE_3_9 |
| Last Commit: 7054c21 |
| Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:47:28 -0400 (Wed, 16 Oct 2019).
| Package 366/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| crlmm 1.42.0 Benilton S Carvalho
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: crlmm |
| Version: 1.42.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:crlmm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings crlmm_1.42.0.tar.gz |
| StartedAt: 2019-10-16 01:53:27 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:07:50 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 863.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: crlmm.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:crlmm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings crlmm_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/crlmm.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crlmm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘crlmm’ version ‘1.42.0’
* 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 ‘crlmm’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘preprocessCore’ is only usable in R >= 3.0.2
* 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
'library' or 'require' call to ‘RUnit’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
‘SNPchip’ ‘splines’
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
.test: no visible global function definition for ‘defineTestSuite’
.test: no visible global function definition for ‘runTestSuite’
.test: no visible global function definition for ‘printTextProtocol’
calculateRBafCNSet : processByChromosome: no visible global function
definition for ‘position’
genotypeInf: no visible binding for global variable ‘anno’
krlmm: no visible binding for global variable ‘VGLMparameters’
Undefined global functions or variables:
VGLMparameters anno defineTestSuite position printTextProtocol
runTestSuite
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
genotype 113.075 12.519 128.266
crlmm 110.250 5.185 115.633
snprma 24.088 2.495 26.921
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘crlmm_unit_tests.R’
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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/crlmm.Rcheck/00check.log’
for details.
crlmm.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL crlmm ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘crlmm’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c gtypeCaller.c -o gtypeCaller.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c trimmed.c -o trimmed.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils.c -o utils.o clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-crlmm/00new/crlmm/libs ** R ** data ** 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 (crlmm)
crlmm.Rcheck/tests/crlmm_unit_tests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.
> require("crlmm") || stop("unable to load crlmm package")
Loading required package: crlmm
Loading required package: oligoClasses
Welcome to oligoClasses version 1.46.0
Loading required package: preprocessCore
Welcome to crlmm version 1.42.0
[1] TRUE
> crlmm:::.test()
Loading required package: genomewidesnp6Crlmm
Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19.
Loading required package: hapmapsnp6
/-------------------------------------------\
| SAMPLE HAPMAP SNP 6.0 |
|-------------------------------------------|
| Data obtained from http://www.hapmap.org |
| This package is meant to be used only for |
| demonstration of BioConductor packages. |
| Access http://www.hapmap.org for details. |
|-------------------------------------------|
| The contents of this package are provided |
| in good faith and the maintainer does not |
| warrant their accuracy. |
\-------------------------------------------/
Loading annotations and mixture model parameters.
Processing 3 files.
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
Loading annotations.
Determining gender.
Calling 906600 SNPs for recalibration... Done.
Estimating recalibration parameters.
Calling 906600 SNPs... Done.
Error in crlmm(cels[c(1, 1, 2)]) : sample identifiers are not unique
In addition: Warning message:
In crlmmGT(res[["A"]], res[["B"]], res[["SNR"]], res[["mixtureParams"]], :
Recalibration not possible. Possible cause: small sample size.
RUNIT TEST PROTOCOL -- Wed Oct 16 02:05:33 2019
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
crlmm RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
123.791 6.244 130.180
crlmm.Rcheck/tests/doRUnit.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.
> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+ pkg <- "crlmm"
+
+ 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()
+
+ ## do not fail on warnings (needed for crlmm() test)
+ 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" )
+ }
Running unit tests
$pkg
[1] "crlmm"
$getwd
[1] "/Users/biocbuild/bbs-3.9-bioc/meat/crlmm.Rcheck/tests"
$pathToUnitTests
[1] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/crlmm/unitTests"
Loading required package: oligoClasses
Welcome to oligoClasses version 1.46.0
Loading required package: preprocessCore
Welcome to crlmm version 1.42.0
Executing test function test_crlmm ... Loading required package: genomewidesnp6Crlmm
Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19.
Loading required package: hapmapsnp6
/-------------------------------------------\
| SAMPLE HAPMAP SNP 6.0 |
|-------------------------------------------|
| Data obtained from http://www.hapmap.org |
| This package is meant to be used only for |
| demonstration of BioConductor packages. |
| Access http://www.hapmap.org for details. |
|-------------------------------------------|
| The contents of this package are provided |
| in good faith and the maintainer does not |
| warrant their accuracy. |
\-------------------------------------------/
Loading annotations and mixture model parameters.
Processing 3 files.
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
Loading annotations.
Determining gender.
Calling 906600 SNPs for recalibration... Done.
Estimating recalibration parameters.
Calling 906600 SNPs... Done.
done successfully.
Executing test function test_duplicates ... Error in crlmm(cels[c(1, 1, 2)]) : sample identifiers are not unique
In addition: Warning message:
In crlmmGT(res[["A"]], res[["B"]], res[["SNR"]], res[["mixtureParams"]], :
Recalibration not possible. Possible cause: small sample size.
done successfully.
Executing test function test_dataExamples ... done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Wed Oct 16 02:07:41 2019
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
crlmm unit testing - 3 test functions, 0 errors, 0 failures
>
> proc.time()
user system elapsed
122.310 6.252 128.574
crlmm.Rcheck/crlmm-Ex.timings
| name | user | system | elapsed | |
| ListClassConstructors | 1.937 | 0.081 | 2.020 | |
| PredictionRegion-class | 0.002 | 0.001 | 0.003 | |
| batchStatisticAccessors | 0.373 | 0.049 | 0.423 | |
| calculateRBaf | 1.160 | 0.053 | 1.213 | |
| celfile-utils | 3.615 | 0.667 | 4.311 | |
| cnSetExample | 0.648 | 0.095 | 0.742 | |
| constructInf | 0.000 | 0.000 | 0.001 | |
| copynumberAccessors | 0.000 | 0.001 | 0.002 | |
| crlmm | 110.250 | 5.185 | 115.633 | |
| genotype.Illumina | 0.001 | 0.001 | 0.002 | |
| genotype | 113.075 | 12.519 | 128.266 | |
| genotypeInf | 0.001 | 0.000 | 0.001 | |
| genotypes | 0.015 | 0.000 | 0.015 | |
| plotSNPs | 0 | 0 | 0 | |
| posteriorProbability | 1.834 | 0.415 | 2.248 | |
| predictionRegion | 0.501 | 0.047 | 0.549 | |
| preprocessInf | 0 | 0 | 0 | |
| readGenCallOutput | 0.001 | 0.000 | 0.000 | |
| readIdatFiles | 0.001 | 0.000 | 0.001 | |
| snprma | 24.088 | 2.495 | 26.921 | |
| validCdfNames | 0.001 | 0.001 | 0.001 | |
| xyplot | 0.731 | 0.099 | 0.832 | |