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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:consensusDE.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings consensusDE_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/consensusDE.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘consensusDE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘consensusDE’ version ‘1.20.0’
* 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 ‘consensusDE’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'EnsDb.Hsapiens.v86' 'org.Hs.eg.db'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ‘consensusDE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: buildSummarized
> ### Title: Generate summarized Read File for DE analyses
> ### Aliases: buildSummarized
> 
> ### ** Examples
> 
> ## Extract summarized following example in the vignette
> ## The example below will return a summarized experiment
> ## tx_db is obtained from TxDb.Dmelanogaster.UCSC.dm3.ensGene library
> library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
Loading required package: GenomicFeatures
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> ## bam files are obtained from the GenomicAlignments package
> 
> ## 1. Build a sample table that lists files and groupings
> ## - obtain list of files
> file_list <- list.files(system.file("extdata", package="GenomicAlignments"),
+                         recursive = TRUE,
+                         pattern = "*bam$",
+                         full = TRUE)
> bam_dir <- as.character(gsub(basename(file_list)[1], "", file_list[1]))
> 
> ## - create a sample table to be used with buildSummarized() below
> ## must be comprised of a minimum of two columns, named "file" and "group",
> sample_table <- data.frame("file" = basename(file_list),
+                            "group" = c("treat", "untreat"))
> 
> summarized_dm3 <- buildSummarized(sample_table = sample_table,
+                                   bam_dir = bam_dir,
+                                   tx_db = TxDb.Dmelanogaster.UCSC.dm3.ensGene,
+                                   read_format = "paired",
+                                   force_build = TRUE)
strand_mode is defined as 0 (unstranded). This is appropriate for 
                unstranded protocols, or if you wish to ignore strandedness when
                counting reads. See ?strandMode in GenomicAlignments for more 
                information.
Warning in buildSummarized(sample_table = sample_table, bam_dir = bam_dir,  :
  No output directory provided. The se file and sample_table will not
          be saved
Warning in buildSummarized(sample_table = sample_table, bam_dir = bam_dir,  :
  The sample_table provided contains groups with less than two 
         replicates. You have selected to continue with force_build = TRUE
* 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: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/consensusDE.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL consensusDE
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘consensusDE’ ...
** using staged installation
** R
** 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 (consensusDE)