##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:crlmm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings crlmm_1.66.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/crlmm.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crlmm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘crlmm’ version ‘1.66.0’
* 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
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 whether startup messages can be suppressed ... NOTE
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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.
Namespace in Imports field not imported from: ‘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 ... WARNING
checkRd: (5) CNSet-methods.Rd:39-41: \item in \describe must have non-empty label
checkRd: (5) CNSet-methods.Rd:65-67: \item in \describe must have non-empty label
checkRd: (5) CNSet-methods.Rd:69-71: \item in \describe must have non-empty label
checkRd: (-1) constructInf.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) genotype.Illumina.Rd:48: Escaped LaTeX specials: \_ \_
checkRd: (-1) genotype.Illumina.Rd:127: Lost braces
   127 |   Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA.
       |                                               ^
checkRd: (-1) preprocessInf.Rd:55: Escaped LaTeX specials: \_ \_
checkRd: (-1) readGenCallOutput.Rd:39: Lost braces
    39 |   Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA.
       |                                               ^
checkRd: (-1) readIdatFiles.Rd:39: Escaped LaTeX specials: \_ \_
checkRd: (-1) readIdatFiles.Rd:55: Escaped LaTeX specials: \_ \_
checkRd: (-1) readIdatFiles.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) readIdatFiles.Rd:68: Lost braces
    68 |   Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA.
       |                                               ^
checkRd: (-1) snprma.Rd:38: Escaped LaTeX specials: \_ \_
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'genotype.Illumina.Rd':
  ‘[oligoClasses]{ldOpts}’

Non-topic package-anchored link(s) in Rd file 'genotype.Rd':
  ‘[oligoClasses]{ldOpts}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AssayData-methods.Rd: CNSet-class
  CNSet-methods.Rd: CNSet-class
  ListClassConstructors.Rd: BeadStudioSetList-class
  PredictionRegion-class.Rd: AssayData-class, list_or_ffdf-class
  batchStatisticAccessors.Rd: batchStatistics
  celfile-utils.Rd: read.celfile
  constructInf.Rd: ldPath, ocSamples, ocProbesets, CNSet-class
  copynumberAccessors.Rd: CNSet-class
  crlmm.Rd: i2p, snpCall, snpCallProbability
  genotype.Rd: batch
  genotypeAffy.Rd: calls, confs
  genotypeInf.Rd: snpCall, snpCallProbability, annotationPackages
  preprocessInf.Rd: CNSet-class, A, B, annotationPackages
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 (user + system) or elapsed time > 5s
           user system elapsed
crlmm    39.359  0.625  40.114
genotype 32.160  1.658  34.945
snprma    7.706  0.351   8.078
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/crlmm.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL crlmm
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘crlmm’ ...
** this is package ‘crlmm’ version ‘1.66.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c gtypeCaller.c -o gtypeCaller.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c trimmed.c -o trimmed.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.c -o utils.o
utils.c:81:13: warning: variable 'n1' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
            ^
utils.c:81:17: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
                ^
utils.c:81:21: warning: variable 'n3' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
                    ^
utils.c:207:13: warning: variable 'n1' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
            ^
utils.c:207:17: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
                ^
utils.c:207:21: warning: variable 'n3' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
                    ^
6 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-crlmm/00new/crlmm/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** help
*** installing help indices
** 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’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** testing if installed package keeps a record of temporary installation path
* DONE (crlmm)

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 1.70.0
Loading required package: preprocessCore
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to crlmm version 1.66.0
[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 -- Mon Apr 21 18:54:51 2025 
*********************************************** 
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 
 44.300   0.812  45.345 

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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-3.21-bioc/meat/crlmm.Rcheck/tests"

$pathToUnitTests
[1] "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpplMu67/RLIBS_1174d591624b1/crlmm/unitTests"

Loading required package: oligoClasses
Welcome to oligoClasses version 1.70.0
Loading required package: preprocessCore
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to crlmm version 1.66.0


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 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 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 -- Mon Apr 21 18:55:36 2025 
*********************************************** 
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
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
> 
> proc.time()
   user  system elapsed 
 43.791   0.754  44.933