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This page was generated on 2021-10-15 15:05:44 -0400 (Fri, 15 Oct 2021).

CHECK results for megadepth on nebbiolo1

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? here 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 1066/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
megadepth 1.2.3  (landing page)
David Zhang
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/megadepth
git_branch: RELEASE_3_13
git_last_commit: 844d5f2
git_last_commit_date: 2021-08-23 17:23:15 -0400 (Mon, 23 Aug 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: megadepth
Version: 1.2.3
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:megadepth.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings megadepth_1.2.3.tar.gz
StartedAt: 2021-10-14 10:28:54 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:30:37 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 103.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: megadepth.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:megadepth.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings megadepth_1.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/megadepth.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘megadepth/DESCRIPTION’ ... OK
* this is package ‘megadepth’ version ‘1.2.3’
* 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 10.962  0.472  12.207
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
     `actual[[5]][3:5]`: 0 0 0               and 12 more...
  `expected[[5]][3:24]`: 0 0 0 0 0 0 0 0 0 0            ...
  
     `actual[[6]][3:5]`: 0 0 0               and 12 more...
  `expected[[6]][3:24]`: 0 0 0 0 0 0 0 0 0 0            ...
  
     `actual[[7]][2:5]`: 0 1 1 20             and 13 more...
  `expected[[7]][2:24]`: 0 1 1  1 1 1 1 1 1 1            ...
  
     `actual[[8]][3:5]`: 0 0 0               and 12 more...
  `expected[[8]][3:24]`: 0 0 0 0 0 0 0 0 0 0            ...
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 129 ]
  Error: Test failures
  Execution halted
* 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
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/megadepth.Rcheck/00check.log’
for details.


Installation output

megadepth.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL megadepth
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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.fail


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(megadepth)
> 
> ## Install the latest version if necessary
> install_megadepth(force = TRUE)
The latest megadepth version is 1.1.1
This is not an interactive session, therefore megadepth has been installed temporarily to 
/tmp/Rtmpz7JVfb/megadepth
> 
> test_check("megadepth")
Processing BAM: "/home/biocbuild/bbs-3.13-bioc/R/library/megadepth/tests/test.bam"
Read 96 records
# of overlapping pairs: 27
Processing BAM: "/home/biocbuild/bbs-3.13-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/home/biocbuild/bbs-3.13-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/home/biocbuild/bbs-3.13-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/home/biocbuild/bbs-3.13-bioc/R/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
Processing BAM: "/home/biocbuild/bbs-3.13-bioc/R/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
building whole annotation region map done
2 chromosomes for annotated regions read
Processing /home/biocbuild/bbs-3.13-bioc/R/library/megadepth/tests/test.bam.all.bw
building whole annotation region map done
2 chromosomes for annotated regions read
Processing /home/biocbuild/bbs-3.13-bioc/R/library/megadepth/tests/test.bam.all.bw
The latest megadepth version is 1.1.1
building whole annotation region map done
2 chromosomes for annotated regions read
Processing BAM: "/home/biocbuild/bbs-3.13-bioc/R/library/megadepth/tests/test.bam"
Read 92 records
# of overlapping pairs: 27
Processing /tmp/Rtmpz7JVfb/test.bam.all.bw
Processing BAM: "/home/biocbuild/bbs-3.13-bioc/R/library/megadepth/tests/test3.bam"
Read 12 records
# of overlapping pairs: 3
building whole annotation region map done
2 chromosomes for annotated regions read
Processing http://stingray.cs.jhu.edu/data/temp/megadepth.test.bam.all.bw
building whole annotation region map done
2 chromosomes for annotated regions read
Processing /tmp/Rtmpz7JVfb/test.bam.all.bw
Processing BAM: "/home/biocbuild/bbs-3.13-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/home/biocbuild/bbs-3.13-bioc/R/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 2404 bytes
==================================================
downloaded 2404 bytes

Processing BAM: "/home/biocbuild/bbs-3.13-bioc/R/library/megadepth/tests/test.bam"
Read 96 records
# of overlapping pairs: 0
+ jx_file=/tmp/Rtmpz7JVfb/test.bam.all_jxs.tsv
+ export LC_ALL=C
+ LC_ALL=C
+ sort -k2,2 -k3,3n -k4,4n -k1,1 -u /tmp/Rtmpz7JVfb/test.bam.all_jxs.tsv
+ perl -ne 'chomp; ($qname,$c,$s,$e,$orient,$cigar,$is_unique)=split(/\t/,$_); if($pc) { if($s == $ps && $e == $pe && $o eq $po) { if($is_unique == 1) { $ucnt++; } else { $cnt++; } next; } else { print "$pc\t$ps\t$pe\t$po\t0\t0\t$ucnt\t$cnt\t\n"; }} $ucnt=0; $cnt=0; if($is_unique == 1) { $ucnt=1; } else { $cnt=1; } $pc=$c; $ps=$s; $pe=$e; $po=0; if($orient ne "0" && $orient ne "1") { $po=$orient eq "+"?1:2; } END { if($pc) { print "$pc\t$ps\t$pe\t$po\t0\t0\t$ucnt\t$cnt\t\n"; }}'
Rows: 24 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/Rtmpz7JVfb/test2.bam.all_jxs.tsv
+ export LC_ALL=C
+ LC_ALL=C
+ sort -k2,2 -k3,3n -k4,4n -k1,1 -u /tmp/Rtmpz7JVfb/test2.bam.all_jxs.tsv
+ perl -ne 'chomp; ($qname,$c,$s,$e,$orient,$cigar,$is_unique)=split(/\t/,$_); if($pc) { if($s == $ps && $e == $pe && $o eq $po) { if($is_unique == 1) { $ucnt++; } else { $cnt++; } next; } else { print "$pc\t$ps\t$pe\t$po\t0\t0\t$ucnt\t$cnt\t\n"; }} $ucnt=0; $cnt=0; if($is_unique == 1) { $ucnt=1; } else { $cnt=1; } $pc=$c; $ps=$s; $pe=$e; $po=0; if($orient ne "0" && $orient ne "1") { $po=$orient eq "+"?1:2; } END { if($pc) { print "$pc\t$ps\t$pe\t$po\t0\t0\t$ucnt\t$cnt\t\n"; }}'
Rows: 7 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.
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-read_junction.R:115:9): process_junction_table has correct output ──
process_junction_table(all_jxs) (`actual`) not equal to `processed_jxs_shell` (`expected`).

actual vs expected
                  chr   start     end strand intron_motif annotated uniquely_mapping_reads multimapping_reads
  actual[1, ]    chr1   18310  188572      0            0         0                      1                  0
  actual[2, ]    chr1  188585  188790      0            0         0                      1                  0
- actual[3, ]   chr10 4195113 4519182      0            0         0                      0                  3
- actual[4, ]   chr10 4246673 4519182      0            0         0                      0                  2
+ expected[3, ] chr10 4195113 4519182      0            0         0                      0                  1
+ expected[4, ] chr10 4195113 4519182      0            0         0                      0                  1
+ expected[5, ] chr10 4195113 4519182      0            0         0                      0                  1
+ expected[6, ] chr10 4246673 4519182      0            0         0                      0                  1
+ expected[7, ] chr10 4246673 4519182      0            0         0                      0                  1

`actual[[1]][2:4]`:   "chr1" "chr10" "chr10"                        
`expected[[1]][2:7]`: "chr1" "chr10" "chr10" "chr10" "chr10" "chr10"

  `actual[[2]]`: 18310 188585 4195113 4246673                        
`expected[[2]]`: 18310 188585 4195113 4195113 4195113 4246673 4246673

  `actual[[3]][2:4]`: 188790 4519182 4519182                        
`expected[[3]][2:7]`: 188790 4519182 4519182 4519182 4519182 4519182

  `actual[[4]][2:4]`: 0 0 0      
`expected[[4]][2:7]`: 0 0 0 0 0 0

  `actual[[5]][2:4]`: 0 0 0      
`expected[[5]][2:7]`: 0 0 0 0 0 0

  `actual[[6]][2:4]`: 0 0 0      
`expected[[6]][2:7]`: 0 0 0 0 0 0

  `actual[[7]][2:4]`: 1 0 0      
`expected[[7]][2:7]`: 1 0 0 0 0 0

  `actual[[8]]`: 0 0 3 2      
`expected[[8]]`: 0 0 1 1 1 1 1
── Failure (test-read_junction.R:120:9): process_junction_table has correct output ──
example_jxs2[["all_jxs.tsv"]] %>% read_junction_table() %>% process_junction_table() (`actual`) not equal to `processed_jxs2_shell` (`expected`).

actual vs expected
                   chr   start     end strand intron_motif annotated uniquely_mapping_reads multimapping_reads
  actual[2, ]    chr10 8458623 8778558      0            0         0                      0                  1
  actual[3, ]    chr10 8722315 8848720      0            0         0                      1                  0
  actual[4, ]    chr10 8722508 8870679      0            0         0                      1                  0
- actual[5, ]    chr10 8756762 8780518      0            0         0                     20                  0
+ expected[5, ]  chr10 8756762 8780518      0            0         0                      1                  0
+ expected[6, ]  chr10 8756762 8780518      0            0         0                      1                  0
+ expected[7, ]  chr10 8756762 8780518      0            0         0                      1                  0
+ expected[8, ]  chr10 8756762 8780518      0            0         0                      1                  0
+ expected[9, ]  chr10 8756762 8780518      0            0         0                      1                  0
+ expected[10, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[11, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[12, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[13, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[14, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[15, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[16, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[17, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[18, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[19, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[20, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[21, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[22, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[23, ] chr10 8756762 8780518      0            0         0                      1                  0
+ expected[24, ] chr10 8756762 8780518      0            0         0                      1                  0

    actual[[1]] | expected[[1]]                
[3] "chr10"     | "chr10"       [3]            
[4] "chr10"     | "chr10"       [4]            
[5] "chr10"     | "chr10"       [5]            
                - "chr10"       [6]            
                - "chr10"       [7]            
                - "chr10"       [8]            
                - "chr10"       [9]            
                - "chr10"       [10]           
                - "chr10"       [11]           
                - "chr10"       [12]           
... ...           ...           and 12 more ...

    actual[[2]] | expected[[2]]                
[3] 8722315     | 8722315       [3]            
[4] 8722508     | 8722508       [4]            
[5] 8756762     | 8756762       [5]            
                - 8756762       [6]            
                - 8756762       [7]            
                - 8756762       [8]            
                - 8756762       [9]            
                - 8756762       [10]           
                - 8756762       [11]           
                - 8756762       [12]           
... ...           ...           and 12 more ...

    actual[[3]] | expected[[3]]                
[3] 8848720     | 8848720       [3]            
[4] 8870679     | 8870679       [4]            
[5] 8780518     | 8780518       [5]            
                - 8780518       [6]            
                - 8780518       [7]            
                - 8780518       [8]            
                - 8780518       [9]            
                - 8780518       [10]           
                - 8780518       [11]           
                - 8780518       [12]           
... ...           ...           and 12 more ...

   `actual[[4]][3:5]`: 0 0 0               and 12 more...
`expected[[4]][3:24]`: 0 0 0 0 0 0 0 0 0 0            ...

   `actual[[5]][3:5]`: 0 0 0               and 12 more...
`expected[[5]][3:24]`: 0 0 0 0 0 0 0 0 0 0            ...

   `actual[[6]][3:5]`: 0 0 0               and 12 more...
`expected[[6]][3:24]`: 0 0 0 0 0 0 0 0 0 0            ...

   `actual[[7]][2:5]`: 0 1 1 20             and 13 more...
`expected[[7]][2:24]`: 0 1 1  1 1 1 1 1 1 1            ...

   `actual[[8]][3:5]`: 0 0 0               and 12 more...
`expected[[8]][3:24]`: 0 0 0 0 0 0 0 0 0 0            ...

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 129 ]
Error: Test failures
Execution halted

Example timings

megadepth.Rcheck/megadepth-Ex.timings

nameusersystemelapsed
bam_to_bigwig0.8460.3432.618
bam_to_junctions0.1170.0270.815
get_coverage10.962 0.47212.207
install_megadepth0.0740.0331.662
megadepth_cmd0.1190.0370.893
process_junction_table0.2780.0431.057
read_coverage0.2810.0971.087
read_junction_table0.1650.0490.943