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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:crlmm.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings crlmm_1.57.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/crlmm.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘crlmm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘crlmm’ version ‘1.57.0’
* 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: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   2.7Mb
* 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.
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) preprocessInf.Rd:55: Escaped LaTeX specials: \_ \_
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) snprma.Rd:38: Escaped LaTeX specials: \_ \_
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘crlmm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: crlmm
> ### Title: Genotype oligonucleotide arrays with CRLMM
> ### Aliases: crlmm crlmm2
> ### Keywords: classif
> 
> ### ** Examples
> 
> ## this can be slow
> library(oligoClasses)
> if (require(genomewidesnp6Crlmm) & require(hapmapsnp6)){
+   path <- system.file("celFiles", package="hapmapsnp6")
+ 
+   ## the filenames with full path...
+   ## very useful when genotyping samples not in the working directory
+   cels <- list.celfiles(path, full.names=TRUE)
+   (crlmmOutput <- crlmm(cels))
+   ## If gender is known, one should check that the assigned gender is
+   ## correct, or pass the integer coding of gender as an argument to the
+   ## crlmm function as done below
+ }
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.

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Loading annotations.
Determining gender.
Calling 906600 SNPs for recalibration... Done.
Estimating recalibration parameters.
Warning in crlmmGT(res[["A"]], res[["B"]], res[["SNR"]], res[["mixtureParams"]],  :
  Recalibration not possible. Possible cause: small sample size.
Calling 906600 SNPs... Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘crlmm_unit_tests.R’
 ERROR
Running the tests in ‘tests/crlmm_unit_tests.R’ failed.
Last 13 lines of output:
  Processing 3 files.
  
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    |======================================================================| 100%
  Loading annotations.
  Determining gender.
  Calling 906600 SNPs for recalibration... Done.
  Estimating recalibration parameters.
  Calling 906600 SNPs... Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘AffyGW.Rnw’... OK
  ‘CopyNumberOverview.Rnw’... OK
  ‘IlluminaPreprocessCN.Rnw’... OK
  ‘Infrastructure.Rnw’... OK
  ‘genotyping.Rnw’... failed to complete the test
  ‘gtypeDownstream.Rnw’... OK
 ERROR
Errors in running code in vignettes:
when running code in ‘genotyping.Rnw’
  ...

> path <- system.file("celFiles", package = "hapmapsnp6")

> celFiles <- list.celfiles(path, full.names = TRUE)

> system.time(crlmmResult <- crlmm(celFiles, verbose = FALSE))
Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19.
Killed

... incomplete output.  Crash?

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/crlmm.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL crlmm
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘crlmm’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c gtypeCaller.c -o gtypeCaller.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c trimmed.c -o trimmed.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c utils.c -o utils.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 1.61.0
Loading required package: preprocessCore
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to crlmm version 1.57.0
[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... Killed