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) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:41 -0400 (Fri, 15 Oct 2021).
|
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. |
| Package 1066/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| megadepth 1.2.3 (landing page) David Zhang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: megadepth |
| Version: 1.2.3 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:megadepth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings megadepth_1.2.3.tar.gz |
| StartedAt: 2021-10-14 20:47:03 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 20:49:30 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 147.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: megadepth.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:megadepth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings megadepth_1.2.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/megadepth.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.2.3’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 15.005 0.564 15.586
* 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 2 | 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, 1 NOTE
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/megadepth.Rcheck/00check.log’
for details.
megadepth.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL megadepth ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)
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-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 1.1.1
This is not an interactive session, therefore megadepth has been installed temporarily to
/tmp/RtmphgroDE/megadepth
>
> test_check("megadepth")
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/megadepth/tests/test.bam"
Read 96 records
# of overlapping pairs: 27
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.1/Resources/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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/megadepth/tests/test.bam.all.bw
building whole annotation region map done
2 chromosomes for annotated regions read
Processing /Library/Frameworks/R.framework/Versions/4.1/Resources/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: "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/megadepth/tests/test.bam"
Read 92 records
# of overlapping pairs: 27
Processing /tmp/RtmphgroDE/test.bam.all.bw
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.1/Resources/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/RtmphgroDE/test.bam.all.bw
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.1/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 2404 bytes
==================================================
downloaded 2404 bytes
Processing BAM: "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/megadepth/tests/test.bam"
Read 96 records
# of overlapping pairs: 0
+ jx_file=/tmp/RtmphgroDE/test.bam.all_jxs.tsv
+ export LC_ALL=C
+ LC_ALL=C
+ sort -k2,2 -k3,3n -k4,4n -k1,1 -u /tmp/RtmphgroDE/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$cnt\t\n"; }}'
Rows: 24 Columns: 9
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): chr
dbl (7): start, end, strand, intron_motif, annotated, uniquely_mapping_reads...
lgl (1): X9
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
+ jx_file=/tmp/RtmphgroDE/test2.bam.all_jxs.tsv
+ export LC_ALL=C
+ LC_ALL=C
+ sort -k2,2 -k3,3n -k4,4n -k1,1 -u /tmp/RtmphgroDE/test2.bam.all_jxs.tsv
+ perl -ne 'chomp; ($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 2 | SKIP 0 | PASS 129 ]
Error: Test failures
Execution halted
megadepth.Rcheck/megadepth-Ex.timings
| name | user | system | elapsed | |
| bam_to_bigwig | 1.442 | 0.379 | 3.622 | |
| bam_to_junctions | 0.057 | 0.017 | 0.077 | |
| get_coverage | 15.005 | 0.564 | 15.586 | |
| install_megadepth | 0.003 | 0.005 | 0.010 | |
| megadepth_cmd | 0.087 | 0.043 | 0.140 | |
| process_junction_table | 0.254 | 0.025 | 0.279 | |
| read_coverage | 0.290 | 0.031 | 0.318 | |
| read_junction_table | 0.092 | 0.023 | 0.113 | |