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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NxtIRFcore.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings NxtIRFcore_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/NxtIRFcore.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘NxtIRFcore/DESCRIPTION’ ... OK
* this is package ‘NxtIRFcore’ version ‘1.6.0’
* 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 ‘NxtIRFcore’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'NxtIRFcore' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.17-bioc/meat/NxtIRFcore.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   4.2Mb
* 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 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 ... 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
BuildReference 17.917  0.438  18.327
CollateData    15.699  1.221  16.964
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘NxtIRF.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL NxtIRFcore
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘NxtIRFcore’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c BAM2blocks.cpp -o BAM2blocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c FastaReader.cpp -o FastaReader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c FragmentBlocks.cpp -o FragmentBlocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c GZTools.cpp -o GZTools.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c IRFinder.cpp -o IRFinder.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c covTools.cpp -o covTools.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o NxtIRFcore.so BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o IRFinder.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o covTools.o -fopenmp -DRNXTIRF -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-NxtIRFcore/00new/NxtIRFcore/libs
** 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: Package 'NxtIRFcore' is deprecated and will be removed from
  Bioconductor version 3.18
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'NxtIRFcore' is deprecated and will be removed from
  Bioconductor version 3.18
** testing if installed package keeps a record of temporary installation path
* DONE (NxtIRFcore)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> library(testthat)
> library(NxtIRFcore)
Loading required package: NxtIRFdata
Warning message:
Package 'NxtIRFcore' is deprecated and will be removed from
  Bioconductor version 3.18 
> 
> test_check("NxtIRFcore")
Oct 15 23:29:47 Reference generated without non-polyA reference
Oct 15 23:29:47 Reference generated without Mappability reference
Oct 15 23:29:47 Reference generated without Blacklist exclusion
Oct 15 23:29:47 Converting FASTA to local TwoBitFile...done
Oct 15 23:29:48 Connecting to genome TwoBitFile...done
Oct 15 23:29:49 Making local copy of GTF file...done
Oct 15 23:29:49 Reading source GTF file...done
Oct 15 23:29:49 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Oct 15 23:29:53 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon islands
done
Oct 15 23:30:02 Generating IRFinder reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
IRFinder reference generation completed
Oct 15 23:30:12 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

  |                                                                            
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  |======================================================================| 100%
done
Oct 15 23:30:16 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Oct 15 23:30:18 Splice Annotations Filtered
Oct 15 23:30:18 Translating Alternate Splice Peptides...done
Oct 15 23:30:21 Splice Annotations finished

Reference build finished
Oct 15 23:30:21 Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 1 threads
/tmp/RtmpEwxwl9/02H003.bam processed
/tmp/RtmpEwxwl9/02H025.bam processed
/tmp/RtmpEwxwl9/02H026.bam processed
/tmp/RtmpEwxwl9/02H033.bam processed
/tmp/RtmpEwxwl9/02H043.bam processed
/tmp/RtmpEwxwl9/02H046.bam processed
Oct 15 23:30:25 Validating Experiment; checking COV files...
Oct 15 23:30:29 Using MulticoreParam 1 threads
Oct 15 23:30:29 Compiling Sample Stats
Oct 15 23:30:29 Compiling Junction List...merging...done
Oct 15 23:30:31 Compiling Intron Retention List...done
Oct 15 23:30:32 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...saving annotations
...compiling rowEvents
done

Oct 15 23:30:34 Generating NxtIRF assays
Oct 15 23:30:36 Using MulticoreParam 1 threads

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Building Final SummarizedExperiment Object

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NxtIRF Collation Finished
Oct 15 23:30:41 Loading NxtSE object from file...done

Oct 15 23:30:42 Removing overlapping introns...
Oct 15 23:30:42 Iterating through IR events to determine introns of main isoforms
Oct 15 23:30:42 Iteration 1
Oct 15 23:30:42 Iteration 2
Oct 15 23:30:45 Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 1 threads
Processing BAM file /tmp/RtmpEwxwl9/02H003.bam
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing COV file
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/tmp/RtmpEwxwl9/02H003.bam processed
Oct 15 23:30:45 Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 2 threads
Processing BAM file /tmp/RtmpEwxwl9/02H003.bam
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Compiling data from threads
Performing final sort of fragment maps
Writing COV file
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/tmp/RtmpEwxwl9/02H003.bam processed
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
> 
> # bump to trigger r cmd check
> 
> proc.time()
   user  system elapsed 
 77.721   5.153  83.979