Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-15 21:53 -0400 (Tue, 15 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
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 | |||||||||
merida1 | macOS 12.7.5 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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MACSr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MACSr_1.12.0.tar.gz |
StartedAt: 2024-10-14 01:26:54 -0400 (Mon, 14 Oct 2024) |
EndedAt: 2024-10-14 01:30:25 -0400 (Mon, 14 Oct 2024) |
EllapsedTime: 210.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MACSr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MACSr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MACSr_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MACSr.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.5 LTS * using session charset: UTF-8 * 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 ‘/home/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 loading without being on the library search path ... 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 6.462 1.115 8.187 bdgdiff 4.849 0.479 6.378 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/MACSr.Rcheck/00check.log’ for details.
MACSr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MACSr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 @ 14 Oct 2024 01:29:50: [627 MB] # Command line: # ARGUMENTS LIST: # name = run_callpeak_narrow0 # format = BED # ChIP-seq file = ['/home/biocbuild/.cache/R/ExperimentHub/1e5a96bd5911c_4601'] # control file = ['/home/biocbuild/.cache/R/ExperimentHub/1e5a963d85fa01_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 @ 14 Oct 2024 01:29:50: [627 MB] #1 read tag files... INFO @ 14 Oct 2024 01:29:50: [627 MB] #1 read treatment tags... INFO @ 14 Oct 2024 01:29:50: [634 MB] #1.2 read input tags... INFO @ 14 Oct 2024 01:29:50: [635 MB] #1 tag size is determined as 101 bps INFO @ 14 Oct 2024 01:29:50: [635 MB] #1 tag size = 101.0 INFO @ 14 Oct 2024 01:29:50: [635 MB] #1 total tags in treatment: 49622 INFO @ 14 Oct 2024 01:29:50: [635 MB] #1 user defined the maximum tags... INFO @ 14 Oct 2024 01:29:50: [635 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ 14 Oct 2024 01:29:50: [635 MB] #1 tags after filtering in treatment: 48047 INFO @ 14 Oct 2024 01:29:50: [635 MB] #1 Redundant rate of treatment: 0.03 INFO @ 14 Oct 2024 01:29:50: [635 MB] #1 total tags in control: 50837 INFO @ 14 Oct 2024 01:29:50: [635 MB] #1 user defined the maximum tags... INFO @ 14 Oct 2024 01:29:50: [635 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ 14 Oct 2024 01:29:50: [635 MB] #1 tags after filtering in control: 50783 INFO @ 14 Oct 2024 01:29:50: [635 MB] #1 Redundant rate of control: 0.00 INFO @ 14 Oct 2024 01:29:50: [635 MB] #1 finished! INFO @ 14 Oct 2024 01:29:50: [635 MB] #2 Build Peak Model... INFO @ 14 Oct 2024 01:29:50: [635 MB] #2 looking for paired plus/minus strand peaks... INFO @ 14 Oct 2024 01:29:50: [635 MB] #2 Total number of paired peaks: 469 INFO @ 14 Oct 2024 01:29:50: [635 MB] #2 Model building with cross-correlation: Done INFO @ 14 Oct 2024 01:29:50: [635 MB] #2 finished! INFO @ 14 Oct 2024 01:29:50: [635 MB] #2 predicted fragment length is 228 bps INFO @ 14 Oct 2024 01:29:50: [635 MB] #2 alternative fragment length(s) may be 228 bps INFO @ 14 Oct 2024 01:29:50: [635 MB] #2.2 Generate R script for model : /tmp/Rtmpz0qszy/run_callpeak_narrow0_model.r INFO @ 14 Oct 2024 01:29:50: [635 MB] #3 Call peaks... INFO @ 14 Oct 2024 01:29:50: [635 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 14 Oct 2024 01:29:50: [635 MB] #3 Cutoff vs peaks called will be analyzed! INFO @ 14 Oct 2024 01:29:51: [657 MB] #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/tmp/Rtmpz0qszy/run_callpeak_narrow0_cutoff_analysis.txt' INFO @ 14 Oct 2024 01:29:51: [657 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 14 Oct 2024 01:29:51: [657 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg INFO @ 14 Oct 2024 01:29:51: [657 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg INFO @ 14 Oct 2024 01:29:51: [657 MB] #3 Pileup will be based on sequencing depth in treatment. INFO @ 14 Oct 2024 01:29:51: [657 MB] #3 Call peaks for each chromosome... INFO @ 14 Oct 2024 01:29:51: [658 MB] #4 Write output xls file... /tmp/Rtmpz0qszy/run_callpeak_narrow0_peaks.xls INFO @ 14 Oct 2024 01:29:51: [658 MB] #4 Write peak in narrowPeak format file... /tmp/Rtmpz0qszy/run_callpeak_narrow0_peaks.narrowPeak INFO @ 14 Oct 2024 01:29:51: [658 MB] #4 Write summits bed file... /tmp/Rtmpz0qszy/run_callpeak_narrow0_summits.bed INFO @ 14 Oct 2024 01:29:51: [658 MB] Done! [ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ] > > proc.time() user system elapsed 27.226 2.399 30.531
MACSr.Rcheck/MACSr-Ex.timings
name | user | system | elapsed | |
bdgbroadcall | 6.462 | 1.115 | 8.187 | |
bdgcmp | 3.327 | 0.272 | 3.955 | |
bdgdiff | 4.849 | 0.479 | 6.378 | |
bdgopt | 3.275 | 0.385 | 4.006 | |
bdgpeakcall | 0.001 | 0.000 | 0.000 | |
callpeak | 2.693 | 0.353 | 3.425 | |
callvar | 0 | 0 | 0 | |
cmbreps | 3.642 | 0.228 | 4.485 | |
filterdup | 1.288 | 0.102 | 1.645 | |
pileup | 1.294 | 0.128 | 1.678 | |
predictd | 1.281 | 0.140 | 1.677 | |
randsample | 1.266 | 0.077 | 1.597 | |
refinepeak | 4.032 | 0.152 | 4.515 | |