##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:exomePeak2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings exomePeak2_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/exomePeak2.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘exomePeak2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘exomePeak2’ version ‘1.15.1’
* package encoding: UTF-8
* 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 ‘exomePeak2’ 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 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotGCbias: no visible binding for global variable ‘glmFit’
plotGCbias: no visible binding for global variable ‘IP_input’
plotGCbias: no visible binding for global variable ‘Perturbation’
Undefined global functions or variables:
  IP_input Perturbation glmFit
* 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 ‘exomePeak2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: exomePeak2
> ### Title: Peak Calling and Differential Analysis of MeRIP-seq.
> ### Aliases: exomePeak2
> 
> ### ** Examples
> 
> 
> ## Specify File Directories
> GENE_ANNO_GTF = system.file("extdata", "example.gtf", package="exomePeak2")
> 
> f1 = system.file("extdata", "IP1.bam", package="exomePeak2")
> f2 = system.file("extdata", "IP2.bam", package="exomePeak2")
> f3 = system.file("extdata", "IP3.bam", package="exomePeak2")
> f4 = system.file("extdata", "IP4.bam", package="exomePeak2")
> IP_BAM = c(f1,f2,f3,f4)
> f1 = system.file("extdata", "Input1.bam", package="exomePeak2")
> f2 = system.file("extdata", "Input2.bam", package="exomePeak2")
> f3 = system.file("extdata", "Input3.bam", package="exomePeak2")
> INPUT_BAM = c(f1,f2,f3)
> 
> ## Peak Calling
> res <- exomePeak2(bam_ip = IP_BAM,
+                   bam_input = INPUT_BAM,
+                   gff = GENE_ANNO_GTF,
+                   genome = "hg19")
Error in load_package_gracefully("txdbmaker", "Starting with BioC 3.19, ",  : 
  Could not load package txdbmaker. Is it installed?

  Note that Starting with BioC 3.19, calling makeTxDbFromGFF() requires
  the txdbmaker package. Please install it with:

    BiocManager::install("txdbmaker")
Calls: exomePeak2 ... makeTxDbFromGFF -> call_fun_in_txdbmaker -> load_package_gracefully
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette_V_2.00.Rmd’ using rmarkdown

Quitting from lines 50-71 [unnamed-chunk-2] (Vignette_V_2.00.Rmd)
Error: processing vignette 'Vignette_V_2.00.Rmd' failed with diagnostics:
Could not load package txdbmaker. Is it installed?

  Note that Starting with BioC 3.19, calling makeTxDbFromGFF() requires
  the txdbmaker package. Please install it with:

    BiocManager::install("txdbmaker")
--- failed re-building ‘Vignette_V_2.00.Rmd’

SUMMARY: processing the following file failed:
  ‘Vignette_V_2.00.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/exomePeak2.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL exomePeak2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘exomePeak2’ ...
** 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
Warning in fun(libname, pkgname) :
  Package 'exomePeak2' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'exomePeak2' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (exomePeak2)