##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:prebs.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings prebs_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/prebs.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 ‘prebs/DESCRIPTION’ ... OK
* this is package ‘prebs’ version ‘1.39.0’
* 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 ‘prebs’ can be installed ... OK
* 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("rma_c_complete_copy", ..., PACKAGE = "affy")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
granges_from_cdf: no visible global function definition for
  ‘read.table’
is.installed: no visible global function definition for
  ‘installed.packages’
Undefined global functions or variables:
  installed.packages read.table
Consider adding
  importFrom("utils", "installed.packages", "read.table")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘prebs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calc_prebs
> ### Title: Calculate PREBS values
> ### Aliases: calc_prebs
> 
> ### ** Examples
> 
> if (require(prebsdata)) {
+   # Get full paths to data files in \code{prebsdata} package
+   bam_file1 <- system.file(file.path("sample_bam_files", "input1.bam"), package="prebsdata")
+   bam_file2 <- system.file(file.path("sample_bam_files", "input2.bam"), package="prebsdata")
+   bam_files <- c(bam_file1, bam_file2)
+   custom_cdf_mapping1 <- system.file(file.path("custom-cdf", "HGU133Plus2_Hs_ENSG_mapping.txt"),
+                                      package="prebsdata")
+   custom_cdf_mapping2 <- system.file(file.path("custom-cdf", "HGU133A2_Hs_ENSG_mapping.txt"),
+                                      package="prebsdata")
+   manufacturer_cdf_mapping <- system.file(file.path("manufacturer-cdf", "HGU133Plus2_mapping.txt"),
+                                           package="prebsdata")
+   if (interactive()) {
+     # Run PREBS using custom CDF without parallelization ("rpa" mode)
+     prebs_values <- calc_prebs(bam_files, custom_cdf_mapping1)
+     head(exprs(prebs_values))
+ 
+     # Run PREBS using custom CDF without parallelization ("rma" mode)
+     prebs_values <- calc_prebs(bam_files, custom_cdf_mapping1, sum.method="rma")
+     head(exprs(prebs_values))
+ 
+     # Run PREBS using custom CDF with parallelization
+     library(parallel)
+     N_CORES = 2
+     CLUSTER <- makeCluster(N_CORES)
+     prebs_values <- calc_prebs(bam_files, custom_cdf_mapping1, cluster=CLUSTER)
+     stopCluster(CLUSTER)
+ 
+     # Run PREBS using another custom CDF
+     prebs_values <- calc_prebs(bam_files, custom_cdf_mapping2)
+ 
+     # Run PREBS and return data frame instead of ExpressionSet object
+     prebs_values <- calc_prebs(bam_files, custom_cdf_mapping1, output_eset=FALSE)
+     head(prebs_values)
+   }
+ 
+   # Run PREBS using Manufacturer's CDF (outputs probe set expressions)
+   prebs_values <- calc_prebs(bam_files, manufacturer_cdf_mapping)
+   head(exprs(prebs_values))
+ 
+   # Same as above, but state CDF package name explicitly
+   prebs_values <- calc_prebs(bam_files, manufacturer_cdf_mapping, cdf_name="hgu133plus2cdf")
+ }
Loading required package: prebsdata
Inferred name for CDF package: HGU133Plus2_mapping.txt -> hgu133plus2cdf

Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu133plus2cdf’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu133plus2cdf’

[1] "Finished: input1.bam"
[1] "Finished: input2.bam"
Note: Some probe IDs contain duplicates. If you are using manufacturer's CDF then you can ignore this message.

Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘prebs.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/prebs.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL prebs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘prebs’ ...
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (prebs)