Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-18 18:01 -0400 (Tue, 18 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4758 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 1142/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MACSr 1.12.0 (landing page) Qiang Hu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the MACSr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MACSr.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: MACSr |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MACSr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MACSr_1.12.0.tar.gz |
StartedAt: 2024-06-18 01:03:14 -0400 (Tue, 18 Jun 2024) |
EndedAt: 2024-06-18 01:07:18 -0400 (Tue, 18 Jun 2024) |
EllapsedTime: 243.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MACSr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MACSr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MACSr_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MACSr.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MACSr/DESCRIPTION’ ... OK * this is package ‘MACSr’ 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 ... NOTE Found the following hidden files and directories: .BBSoptions 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 ‘MACSr’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/Users/biocbuild/bbs-3.19-bioc/meat/MACSr.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 line endings in shell scripts ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed bdgbroadcall 9.928 2.013 13.741 bdgdiff 5.930 0.375 7.903 refinepeak 5.177 0.278 6.679 cmbreps 4.662 0.316 6.267 bdgcmp 4.112 0.262 5.814 bdgopt 3.895 0.299 5.664 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/MACSr.Rcheck/00check.log’ for details.
MACSr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MACSr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘MACSr’ ... ** using non-staged installation via StagedInstall field ** 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 * DONE (MACSr)
MACSr.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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(MACSr) > > test_check("MACSr") INFO @ 18 Jun 2024 01:06:48: [735 MB] # Command line: # ARGUMENTS LIST: # name = run_callpeak_narrow0 # format = BED # ChIP-seq file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/571854168a5_4601'] # control file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/571893d2b55_4606'] # effective genome size = 5.20e+07 # band width = 300 # model fold = [5.0, 50.0] # qvalue cutoff = 5.00e-02 # The maximum gap between significant sites is assigned as the read length/tag size. # The minimum length of peaks is assigned as the predicted fragment length "d". # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 1000 bps and 10000 bps # Broad region calling is off # Additional cutoff on fold-enrichment is: 0.10 # Paired-End mode is off INFO @ 18 Jun 2024 01:06:48: [735 MB] #1 read tag files... INFO @ 18 Jun 2024 01:06:48: [735 MB] #1 read treatment tags... INFO @ 18 Jun 2024 01:06:48: [742 MB] #1.2 read input tags... INFO @ 18 Jun 2024 01:06:48: [743 MB] #1 tag size is determined as 101 bps INFO @ 18 Jun 2024 01:06:48: [743 MB] #1 tag size = 101.0 INFO @ 18 Jun 2024 01:06:48: [743 MB] #1 total tags in treatment: 49622 INFO @ 18 Jun 2024 01:06:48: [743 MB] #1 user defined the maximum tags... INFO @ 18 Jun 2024 01:06:48: [743 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ 18 Jun 2024 01:06:48: [743 MB] #1 tags after filtering in treatment: 48047 INFO @ 18 Jun 2024 01:06:48: [743 MB] #1 Redundant rate of treatment: 0.03 INFO @ 18 Jun 2024 01:06:48: [743 MB] #1 total tags in control: 50837 INFO @ 18 Jun 2024 01:06:48: [743 MB] #1 user defined the maximum tags... INFO @ 18 Jun 2024 01:06:48: [743 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ 18 Jun 2024 01:06:48: [743 MB] #1 tags after filtering in control: 50783 INFO @ 18 Jun 2024 01:06:48: [743 MB] #1 Redundant rate of control: 0.00 INFO @ 18 Jun 2024 01:06:48: [743 MB] #1 finished! INFO @ 18 Jun 2024 01:06:48: [743 MB] #2 Build Peak Model... INFO @ 18 Jun 2024 01:06:48: [743 MB] #2 looking for paired plus/minus strand peaks... INFO @ 18 Jun 2024 01:06:48: [743 MB] #2 Total number of paired peaks: 469 INFO @ 18 Jun 2024 01:06:48: [743 MB] #2 Model building with cross-correlation: Done INFO @ 18 Jun 2024 01:06:48: [743 MB] #2 finished! INFO @ 18 Jun 2024 01:06:48: [743 MB] #2 predicted fragment length is 228 bps INFO @ 18 Jun 2024 01:06:48: [743 MB] #2 alternative fragment length(s) may be 228 bps INFO @ 18 Jun 2024 01:06:48: [743 MB] #2.2 Generate R script for model : /tmp/RtmpR7kNSv/run_callpeak_narrow0_model.r INFO @ 18 Jun 2024 01:06:48: [743 MB] #3 Call peaks... INFO @ 18 Jun 2024 01:06:48: [743 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 18 Jun 2024 01:06:48: [743 MB] #3 Cutoff vs peaks called will be analyzed! INFO @ 18 Jun 2024 01:06:49: [767 MB] #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/tmp/RtmpR7kNSv/run_callpeak_narrow0_cutoff_analysis.txt' INFO @ 18 Jun 2024 01:06:49: [767 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 18 Jun 2024 01:06:49: [767 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg INFO @ 18 Jun 2024 01:06:49: [767 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg INFO @ 18 Jun 2024 01:06:49: [767 MB] #3 Pileup will be based on sequencing depth in treatment. INFO @ 18 Jun 2024 01:06:49: [767 MB] #3 Call peaks for each chromosome... INFO @ 18 Jun 2024 01:06:49: [769 MB] #4 Write output xls file... /tmp/RtmpR7kNSv/run_callpeak_narrow0_peaks.xls INFO @ 18 Jun 2024 01:06:49: [769 MB] #4 Write peak in narrowPeak format file... /tmp/RtmpR7kNSv/run_callpeak_narrow0_peaks.narrowPeak INFO @ 18 Jun 2024 01:06:49: [769 MB] #4 Write summits bed file... /tmp/RtmpR7kNSv/run_callpeak_narrow0_summits.bed INFO @ 18 Jun 2024 01:06:49: [769 MB] Done! [ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ] > > proc.time() user system elapsed 38.375 3.572 44.562
MACSr.Rcheck/MACSr-Ex.timings
name | user | system | elapsed | |
bdgbroadcall | 9.928 | 2.013 | 13.741 | |
bdgcmp | 4.112 | 0.262 | 5.814 | |
bdgdiff | 5.930 | 0.375 | 7.903 | |
bdgopt | 3.895 | 0.299 | 5.664 | |
bdgpeakcall | 0 | 0 | 0 | |
callpeak | 2.900 | 0.243 | 4.653 | |
callvar | 0.001 | 0.000 | 0.001 | |
cmbreps | 4.662 | 0.316 | 6.267 | |
filterdup | 1.370 | 0.142 | 2.645 | |
pileup | 1.439 | 0.150 | 2.433 | |
predictd | 1.487 | 0.139 | 2.485 | |
randsample | 1.353 | 0.130 | 2.343 | |
refinepeak | 5.177 | 0.278 | 6.679 | |