Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:31 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
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 |
Package 1184/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
megadepth 1.12.0 (landing page) David Zhang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the megadepth package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: megadepth |
Version: 1.12.0 |
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_1.12.0.tar.gz |
StartedAt: 2024-03-03 21:37:38 -0500 (Sun, 03 Mar 2024) |
EndedAt: 2024-03-03 21:39:59 -0500 (Sun, 03 Mar 2024) |
EllapsedTime: 141.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: megadepth.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/megadepth.Rcheck’ * using R version 4.3.2 Patched (2023-11-01 r85457) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘megadepth/DESCRIPTION’ ... OK * this is package ‘megadepth’ version ‘1.12.0’ * 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 14.895 0.716 17.098 bam_to_bigwig 1.540 0.477 6.184 * 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
megadepth.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL megadepth ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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
R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (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/RtmpbpjMPb/megadepth > > test_check("megadepth") Processing BAM: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/megadepth/tests/test.bam" Read 96 records # of overlapping pairs: 27 Processing BAM: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/megadepth/tests/long_reads.bam" Read 3 records # of overlapping pairs: 0 Processing BAM: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/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/4.3-x86_64/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/4.3-x86_64/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/4.3-x86_64/Resources/library/megadepth/tests/test.bam" Read 92 records # of overlapping pairs: 27 Processing /tmp/RtmpbpjMPb/test.bam.all.bw Processing BAM: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/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 /tmp/RtmpbpjMPb/test.bam.all.bw Processing BAM: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/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/4.3-x86_64/Resources/library/megadepth/tests/test.bam" Read 96 records # of overlapping pairs: 0 + jx_file=/tmp/RtmpbpjMPb/test.bam.all_jxs.tsv + export LC_ALL=C + LC_ALL=C + sort -k2,2 -k3,3n -k4,4n -k1,1 -u /tmp/RtmpbpjMPb/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/RtmpbpjMPb/test2.bam.all_jxs.tsv + export LC_ALL=C + LC_ALL=C + sort -k2,2 -k3,3n -k4,4n -k1,1 -u /tmp/RtmpbpjMPb/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 0 | SKIP 0 | PASS 131 ] > > proc.time() user system elapsed 9.582 3.490 18.493
megadepth.Rcheck/megadepth-Ex.timings
name | user | system | elapsed | |
bam_to_bigwig | 1.540 | 0.477 | 6.184 | |
bam_to_junctions | 0.192 | 0.062 | 1.085 | |
get_coverage | 14.895 | 0.716 | 17.098 | |
install_megadepth | 0.058 | 0.042 | 0.856 | |
megadepth_cmd | 0.245 | 0.095 | 1.103 | |
process_junction_table | 0.290 | 0.076 | 1.391 | |
read_coverage | 0.314 | 0.087 | 1.225 | |
read_junction_table | 0.256 | 0.077 | 1.129 | |