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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:megadepth.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings megadepth_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/megadepth.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘megadepth/DESCRIPTION’ ... OK
* this is package ‘megadepth’ version ‘1.18.0’
* 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 ‘megadepth’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
get_coverage 5.266  0.206   6.243
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL megadepth
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘megadepth’ ...
** this is package ‘megadepth’ version ‘1.18.0’
** 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 (megadepth)

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(megadepth)
> 
> ## Install the latest version if necessary
> install_megadepth(force = TRUE)
The latest megadepth version is 1.2.0
This is not an interactive session, therefore megadepth has been installed temporarily to 
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpR9wzV7/megadepth
> 
> test_check("megadepth")
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/megadepth/tests/test.bam"
Read 96 records
# of overlapping pairs: 27
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
unsorted interval: chr10	4359156	4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 1
Processing /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/megadepth/tests/test.bam.all.bw
unsorted interval: chr10	4359156	4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 1
Processing /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/megadepth/tests/test.bam.all.bw
The latest megadepth version is 1.2.0
building whole annotation region map done
2 chromosomes for annotated regions read
0 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/megadepth/tests/test.bam"
Read 92 records
# of overlapping pairs: 27
Processing /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpR9wzV7/test.bam.all.bw
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/megadepth/tests/test3.bam"
Read 12 records
# of overlapping pairs: 3
unsorted interval: chr10	4359156	4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 1
Processing https://snaptron.cs.jhu.edu/data/temp/megadepth.test.bam.all.bw
unsorted interval: chr10	4359156	4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 1
Processing /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpR9wzV7/test.bam.all.bw
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
trying URL 'https://raw.githubusercontent.com/ChristopherWilks/megadepth/master/junctions/process_jx_output.sh'
Content type 'text/plain; charset=utf-8' length 2472 bytes
==================================================
downloaded 2472 bytes

Processing BAM: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/megadepth/tests/test.bam"
Read 96 records
# of overlapping pairs: 0
+ jx_file=/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpR9wzV7/test.bam.all_jxs.tsv
+ export LC_ALL=C
+ LC_ALL=C
+ sort -k2,2 -k3,3n -k4,4n -k1,1 -u /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpR9wzV7/test.bam.all_jxs.tsv
+ cut -f 1,2-4,6,7
+ perl -ne 'chomp; ($qname,$c,$s,$e,$cigar,$is_unique)=split(/\t/,$_); if($pc) { if($s == $ps && $e == $pe) { if($is_unique == 1) { $ucnt++; } else { $cnt++; } next; } else { print "$pc\t$ps\t$pe\t0\t0\t0\t$ucnt\t$cnt\t\n"; }} $ucnt=0; $cnt=0; if($is_unique == 1) { $ucnt=1; } else { $cnt=1; } $pc=$c; $ps=$s; $pe=$e; END { if($pc) { print "$pc\t$ps\t$pe\t0\t0\t0\t$ucnt\t$cnt\t\n"; }}'
Rows: 5 Columns: 9
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): chr
dbl (7): start, end, strand, intron_motif, annotated, uniquely_mapping_reads...
lgl (1): X9

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
+ jx_file=/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpR9wzV7/test2.bam.all_jxs.tsv
+ export LC_ALL=C
+ LC_ALL=C
+ sort -k2,2 -k3,3n -k4,4n -k1,1 -u /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpR9wzV7/test2.bam.all_jxs.tsv
+ perl -ne 'chomp; ($qname,$c,$s,$e,$cigar,$is_unique)=split(/\t/,$_); if($pc) { if($s == $ps && $e == $pe) { if($is_unique == 1) { $ucnt++; } else { $cnt++; } next; } else { print "$pc\t$ps\t$pe\t0\t0\t0\t$ucnt\t$cnt\t\n"; }} $ucnt=0; $cnt=0; if($is_unique == 1) { $ucnt=1; } else { $cnt=1; } $pc=$c; $ps=$s; $pe=$e; END { if($pc) { print "$pc\t$ps\t$pe\t0\t0\t0\t$ucnt\t$cnt\t\n"; }}'
+ cut -f 1,2-4,6,7
Rows: 4 Columns: 9
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): chr
dbl (7): start, end, strand, intron_motif, annotated, uniquely_mapping_reads...
lgl (1): X9

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 131 ]
> 
> proc.time()
   user  system elapsed 
  3.227   1.333  10.269