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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NxtIRFcore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NxtIRFcore_1.5.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/NxtIRFcore.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NxtIRFcore/DESCRIPTION’ ... OK
* this is package ‘NxtIRFcore’ version ‘1.5.1’
* 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 ‘NxtIRFcore’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'NxtIRFcore' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.17-bioc/meat/NxtIRFcore.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
* used SDK: ‘’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 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 27.928  0.373  37.976
CollateData    25.799  0.748  35.003
Plot_Coverage   9.309  0.113  12.991
NxtSE-class     7.537  0.500  11.061
IRFinder        5.517  1.008   5.440
MakeSE          5.260  0.669   8.168
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/NxtIRFcore.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NxtIRFcore
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘NxtIRFcore’ ...
** using staged installation
Configuring without OpenMP for MacOS
** libs
using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using C++11
using SDK: ‘’
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppProgress/include' -I/usr/local/include    -DRNXTIRF -fPIC  -Wall -g -O2  -c BAM2blocks.cpp -o BAM2blocks.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppProgress/include' -I/usr/local/include    -DRNXTIRF -fPIC  -Wall -g -O2  -c FastaReader.cpp -o FastaReader.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppProgress/include' -I/usr/local/include    -DRNXTIRF -fPIC  -Wall -g -O2  -c FragmentBlocks.cpp -o FragmentBlocks.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppProgress/include' -I/usr/local/include    -DRNXTIRF -fPIC  -Wall -g -O2  -c GZTools.cpp -o GZTools.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppProgress/include' -I/usr/local/include    -DRNXTIRF -fPIC  -Wall -g -O2  -c IRFinder.cpp -o IRFinder.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppProgress/include' -I/usr/local/include    -DRNXTIRF -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppProgress/include' -I/usr/local/include    -DRNXTIRF -fPIC  -Wall -g -O2  -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppProgress/include' -I/usr/local/include    -DRNXTIRF -fPIC  -Wall -g -O2  -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppProgress/include' -I/usr/local/include    -DRNXTIRF -fPIC  -Wall -g -O2  -c covTools.cpp -o covTools.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -DRNXTIRF -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3/Resources/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 Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
Mar 28 04:40:12 Reference generated without non-polyA reference
Mar 28 04:40:12 Reference generated without Mappability reference
Mar 28 04:40:12 Reference generated without Blacklist exclusion
Mar 28 04:40:12 Converting FASTA to local TwoBitFile...done
Mar 28 04:40:14 Connecting to genome TwoBitFile...done
Mar 28 04:40:14 Making local copy of GTF file...done
Mar 28 04:40:15 Reading source GTF file...done
Mar 28 04:40:15 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Mar 28 04:40:21 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon islands
done
Mar 28 04:40:29 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
Mar 28 04:40:42 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

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done
Mar 28 04:40:46 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
Mar 28 04:40:49 Splice Annotations Filtered
Mar 28 04:40:49 Translating Alternate Splice Peptides...done
Mar 28 04:40:53 Splice Annotations finished

Reference build finished
Mar 28 04:40:53 Running IRFinder
Mar 28 04:40:54 Using MulticoreParam 1 threads
Mar 28 04:40:55 IRFinder processed Rtmpw9jvHK/02H003.bam
Mar 28 04:40:56 IRFinder processed Rtmpw9jvHK/02H025.bam
Mar 28 04:40:58 IRFinder processed Rtmpw9jvHK/02H026.bam
Mar 28 04:40:59 IRFinder processed Rtmpw9jvHK/02H033.bam
Mar 28 04:41:00 IRFinder processed Rtmpw9jvHK/02H043.bam
Mar 28 04:41:01 IRFinder processed Rtmpw9jvHK/02H046.bam
Mar 28 04:41:01 Validating Experiment; checking COV files...
Mar 28 04:41:03 Using MulticoreParam 1 threads
Mar 28 04:41:03 Compiling Sample Stats
Mar 28 04:41:03 Compiling Junction List...merging...done
Mar 28 04:41:05 Compiling Intron Retention List...done
Mar 28 04:41:06 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...saving annotations
...compiling rowEvents
done

Mar 28 04:41:12 Generating NxtIRF assays
Mar 28 04:41:14 Using MulticoreParam 1 threads

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Building Final SummarizedExperiment Object

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NxtIRF Collation Finished
Mar 28 04:41:24 Loading NxtSE object from file...done

Mar 28 04:41:25 Removing overlapping introns...
Mar 28 04:41:25 Iterating through IR events to determine introns of main isoforms
Mar 28 04:41:25 Iteration 1
Mar 28 04:41:26 Iteration 2
NxtIRF was compiled without OpenMP
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 16 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 16 ]
> 
> # bump to trigger r cmd check
> 
> proc.time()
   user  system elapsed 
 88.288   2.629 126.726