Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:57 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 | |||||||||
merida1 | 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: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:megadepth.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings megadepth_1.12.0.tar.gz |
StartedAt: 2024-04-16 02:22:38 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 02:24:32 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 114.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: megadepth.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:megadepth.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings megadepth_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/megadepth.Rcheck' * using R version 4.3.3 (2024-02-29 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * 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 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 8.7 0.32 9.38 * 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: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL megadepth ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-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)
megadepth.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpAh9uoh/megadepth.exe > > test_check("megadepth") Processing BAM: "F:/biocbuild/bbs-3.18-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "F:/biocbuild/bbs-3.18-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "F:/biocbuild/bbs-3.18-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "F:/biocbuild/bbs-3.18-bioc/R/library/megadepth/tests/long_reads.bam" Read 3 records # of overlapping pairs: 0 Processing BAM: "F:/biocbuild/bbs-3.18-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 1 chromosomes for annotated regions read, collapsed 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. total number of annotations in collapsed: 1 Processing F:/biocbuild/bbs-3.18-bioc/R/library/megadepth/tests/test.bam.all.bw building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed 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. total number of annotations in collapsed: 1 Processing F:/biocbuild/bbs-3.18-bioc/R/library/megadepth/tests/test.bam.all.bw The latest megadepth version is 1.2.0 Processing F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpAh9uoh/test.bam.all.bw Processing BAM: "F:/biocbuild/bbs-3.18-bioc/R/library/megadepth/tests/test3.bam" WARNING: writing BigWigs (--bigwig) is not supported on Windows at this time, no BigWig file(s) will be written, but any other options will still be processed. Read 12 records # of overlapping pairs: 3 building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed 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. total number of annotations in collapsed: 1 Processing https://snaptron.cs.jhu.edu/data/temp/megadepth.test.bam.all.bw building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed 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. total number of annotations in collapsed: 1 Processing F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpAh9uoh/test.bam.all.bw Processing BAM: "F:/biocbuild/bbs-3.18-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "F:/biocbuild/bbs-3.18-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 108 ] > > proc.time() user system elapsed 5.03 0.75 11.60
megadepth.Rcheck/megadepth-Ex.timings
name | user | system | elapsed | |
bam_to_bigwig | 0.06 | 0.00 | 0.86 | |
bam_to_junctions | 0.77 | 0.11 | 1.34 | |
get_coverage | 8.70 | 0.32 | 9.38 | |
install_megadepth | 0.02 | 0.03 | 0.61 | |
megadepth_cmd | 0.20 | 0.12 | 1.43 | |
process_junction_table | 0.36 | 0.21 | 0.93 | |
read_coverage | 0.36 | 0.17 | 0.84 | |
read_junction_table | 0.25 | 0.08 | 0.69 | |