Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-30 12:37:01 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 1106/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MACSr 1.13.0 (landing page) Qiang Hu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
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: 1.13.0 |
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_1.13.0.tar.gz |
StartedAt: 2024-05-30 03:06:34 -0400 (Thu, 30 May 2024) |
EndedAt: 2024-05-30 03:14:54 -0400 (Thu, 30 May 2024) |
EllapsedTime: 499.9 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_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MACSr.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-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 Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MACSr/DESCRIPTION’ ... OK * this is package ‘MACSr’ version ‘1.13.0’ * 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-3.20-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 18.323 3.616 24.828 bdgdiff 10.733 0.678 12.946 refinepeak 9.826 0.423 14.869 bdgcmp 8.775 0.490 10.350 cmbreps 8.348 0.543 19.994 bdgopt 6.662 0.479 8.344 callpeak 5.840 0.391 7.257 predictd 2.653 0.214 6.931 filterdup 2.612 0.235 7.752 randsample 2.530 0.221 6.844 * 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-3.20-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-x86_64/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 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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 @ 30 May 2024 03:14:01: [709 MB] # Command line: # ARGUMENTS LIST: # name = run_callpeak_narrow0 # format = BED # ChIP-seq file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/38f5a26b912_4601'] # control file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/38f5744051f2_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 @ 30 May 2024 03:14:01: [709 MB] #1 read tag files... INFO @ 30 May 2024 03:14:01: [709 MB] #1 read treatment tags... INFO @ 30 May 2024 03:14:01: [715 MB] #1.2 read input tags... INFO @ 30 May 2024 03:14:01: [717 MB] #1 tag size is determined as 101 bps INFO @ 30 May 2024 03:14:01: [717 MB] #1 tag size = 101.0 INFO @ 30 May 2024 03:14:01: [717 MB] #1 total tags in treatment: 49622 INFO @ 30 May 2024 03:14:01: [717 MB] #1 user defined the maximum tags... INFO @ 30 May 2024 03:14:01: [717 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ 30 May 2024 03:14:01: [717 MB] #1 tags after filtering in treatment: 48047 INFO @ 30 May 2024 03:14:01: [717 MB] #1 Redundant rate of treatment: 0.03 INFO @ 30 May 2024 03:14:01: [717 MB] #1 total tags in control: 50837 INFO @ 30 May 2024 03:14:01: [717 MB] #1 user defined the maximum tags... INFO @ 30 May 2024 03:14:01: [717 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ 30 May 2024 03:14:01: [717 MB] #1 tags after filtering in control: 50783 INFO @ 30 May 2024 03:14:01: [717 MB] #1 Redundant rate of control: 0.00 INFO @ 30 May 2024 03:14:01: [717 MB] #1 finished! INFO @ 30 May 2024 03:14:01: [717 MB] #2 Build Peak Model... INFO @ 30 May 2024 03:14:01: [717 MB] #2 looking for paired plus/minus strand peaks... INFO @ 30 May 2024 03:14:01: [717 MB] #2 Total number of paired peaks: 469 INFO @ 30 May 2024 03:14:01: [717 MB] #2 Model building with cross-correlation: Done INFO @ 30 May 2024 03:14:01: [717 MB] #2 finished! INFO @ 30 May 2024 03:14:01: [717 MB] #2 predicted fragment length is 228 bps INFO @ 30 May 2024 03:14:01: [717 MB] #2 alternative fragment length(s) may be 228 bps INFO @ 30 May 2024 03:14:01: [717 MB] #2.2 Generate R script for model : /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmpP2PcME/run_callpeak_narrow0_model.r INFO @ 30 May 2024 03:14:01: [717 MB] #3 Call peaks... INFO @ 30 May 2024 03:14:01: [717 MB] #3 Pre-compute pvalue-qvalue table... INFO @ 30 May 2024 03:14:01: [717 MB] #3 Cutoff vs peaks called will be analyzed! INFO @ 30 May 2024 03:14:03: [756 MB] #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmpP2PcME/run_callpeak_narrow0_cutoff_analysis.txt' INFO @ 30 May 2024 03:14:03: [756 MB] #3 In the peak calling step, the following will be performed simultaneously: INFO @ 30 May 2024 03:14:03: [756 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg INFO @ 30 May 2024 03:14:03: [756 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg INFO @ 30 May 2024 03:14:03: [756 MB] #3 Pileup will be based on sequencing depth in treatment. INFO @ 30 May 2024 03:14:03: [756 MB] #3 Call peaks for each chromosome... INFO @ 30 May 2024 03:14:03: [767 MB] #4 Write output xls file... /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmpP2PcME/run_callpeak_narrow0_peaks.xls INFO @ 30 May 2024 03:14:03: [767 MB] #4 Write peak in narrowPeak format file... /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmpP2PcME/run_callpeak_narrow0_peaks.narrowPeak INFO @ 30 May 2024 03:14:04: [767 MB] #4 Write summits bed file... /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmpP2PcME/run_callpeak_narrow0_summits.bed INFO @ 30 May 2024 03:14:04: [767 MB] Done! [ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ] > > proc.time() user system elapsed 63.756 6.754 79.853
MACSr.Rcheck/MACSr-Ex.timings
name | user | system | elapsed | |
bdgbroadcall | 18.323 | 3.616 | 24.828 | |
bdgcmp | 8.775 | 0.490 | 10.350 | |
bdgdiff | 10.733 | 0.678 | 12.946 | |
bdgopt | 6.662 | 0.479 | 8.344 | |
bdgpeakcall | 0.001 | 0.000 | 0.000 | |
callpeak | 5.840 | 0.391 | 7.257 | |
callvar | 0.000 | 0.001 | 0.000 | |
cmbreps | 8.348 | 0.543 | 19.994 | |
filterdup | 2.612 | 0.235 | 7.752 | |
pileup | 2.590 | 0.248 | 4.217 | |
predictd | 2.653 | 0.214 | 6.931 | |
randsample | 2.530 | 0.221 | 6.844 | |
refinepeak | 9.826 | 0.423 | 14.869 | |