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This page was generated on 2022-05-23 12:08:06 -0400 (Mon, 23 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for megadepth on merida1


To the developers/maintainers of the megadepth package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/megadepth.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1108/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
megadepth 1.6.0  (landing page)
David Zhang
Snapshot Date: 2022-05-22 13:55:15 -0400 (Sun, 22 May 2022)
git_url: https://git.bioconductor.org/packages/megadepth
git_branch: RELEASE_3_15
git_last_commit: 8168273
git_last_commit_date: 2022-04-26 12:10:00 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: megadepth
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2022-05-23 04:11:25 -0400 (Mon, 23 May 2022)
EndedAt: 2022-05-23 04:14:40 -0400 (Mon, 23 May 2022)
EllapsedTime: 194.9 seconds
RetCode: 0
Status:   OK  
CheckDir: megadepth.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/megadepth.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘megadepth/DESCRIPTION’ ... OK
* this is package ‘megadepth’ 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 ‘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 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 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  20.379  0.751  21.164
bam_to_bigwig  1.896  0.437  10.894
* 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: OK


Installation output

megadepth.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL megadepth
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘megadepth’ ...
** 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)

Tests output

megadepth.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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(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 
/tmp/RtmpjQjyMX/megadepth
> 
> test_check("megadepth")
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/megadepth/tests/test.bam"
Read 96 records
# of overlapping pairs: 27
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.2/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/4.2/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/4.2/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/4.2/Resources/library/megadepth/tests/test.bam"
Read 92 records
# of overlapping pairs: 27
Processing /tmp/RtmpjQjyMX/test.bam.all.bw
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.2/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 http://stingray.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 /tmp/RtmpjQjyMX/test.bam.all.bw
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/megadepth/tests/test.bam"
Read 96 records
# of overlapping pairs: 0
+ jx_file=/tmp/RtmpjQjyMX/test.bam.all_jxs.tsv
+ export LC_ALL=C
+ LC_ALL=C
+ sort -k2,2 -k3,3n -k4,4n -k1,1 -u /tmp/RtmpjQjyMX/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=/tmp/RtmpjQjyMX/test2.bam.all_jxs.tsv
+ export LC_ALL=C
+ LC_ALL=C
+ sort -k2,2 -k3,3n -k4,4n -k1,1 -u /tmp/RtmpjQjyMX/test2.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: 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 2 | SKIP 0 | PASS 131 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 131 ]
> 
> proc.time()
   user  system elapsed 
 13.431   3.593  21.965 

Example timings

megadepth.Rcheck/megadepth-Ex.timings

nameusersystemelapsed
bam_to_bigwig 1.896 0.43710.894
bam_to_junctions0.0910.0170.111
get_coverage20.379 0.75121.164
install_megadepth0.0050.0040.010
megadepth_cmd0.1160.0450.173
process_junction_table0.2750.0510.323
read_coverage0.3490.0540.400
read_junction_table0.1340.0210.154