Qiang Hu
| Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/MACSr |
| git_branch: RELEASE_3_19 |
| git_last_commit: 1a4cf27 |
| git_last_commit_date: 2024-04-30 11:31:05 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-07 20:24 -0400 (Fri, 07 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" | 4755 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 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 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 ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 2024-06-06 00:28:03 -0400 (Thu, 06 Jun 2024) |
| EndedAt: 2024-06-06 00:31:36 -0400 (Thu, 06 Jun 2024) |
| EllapsedTime: 212.5 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 4.4.0 (2024-04-24)
* 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 22.04.4 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 6.703 1.165 8.945
bdgdiff 4.849 0.280 5.498
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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 @ 06 Jun 2024 00:31:01: [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 @ 06 Jun 2024 00:31:01: [627 MB] #1 read tag files...
INFO @ 06 Jun 2024 00:31:01: [627 MB] #1 read treatment tags...
INFO @ 06 Jun 2024 00:31:01: [633 MB] #1.2 read input tags...
INFO @ 06 Jun 2024 00:31:01: [635 MB] #1 tag size is determined as 101 bps
INFO @ 06 Jun 2024 00:31:01: [635 MB] #1 tag size = 101.0
INFO @ 06 Jun 2024 00:31:01: [635 MB] #1 total tags in treatment: 49622
INFO @ 06 Jun 2024 00:31:01: [635 MB] #1 user defined the maximum tags...
INFO @ 06 Jun 2024 00:31:01: [635 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ 06 Jun 2024 00:31:01: [635 MB] #1 tags after filtering in treatment: 48047
INFO @ 06 Jun 2024 00:31:01: [635 MB] #1 Redundant rate of treatment: 0.03
INFO @ 06 Jun 2024 00:31:01: [635 MB] #1 total tags in control: 50837
INFO @ 06 Jun 2024 00:31:01: [635 MB] #1 user defined the maximum tags...
INFO @ 06 Jun 2024 00:31:01: [635 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ 06 Jun 2024 00:31:01: [635 MB] #1 tags after filtering in control: 50783
INFO @ 06 Jun 2024 00:31:01: [635 MB] #1 Redundant rate of control: 0.00
INFO @ 06 Jun 2024 00:31:01: [635 MB] #1 finished!
INFO @ 06 Jun 2024 00:31:01: [635 MB] #2 Build Peak Model...
INFO @ 06 Jun 2024 00:31:01: [635 MB] #2 looking for paired plus/minus strand peaks...
INFO @ 06 Jun 2024 00:31:01: [635 MB] #2 Total number of paired peaks: 469
INFO @ 06 Jun 2024 00:31:01: [635 MB] #2 Model building with cross-correlation: Done
INFO @ 06 Jun 2024 00:31:01: [635 MB] #2 finished!
INFO @ 06 Jun 2024 00:31:01: [635 MB] #2 predicted fragment length is 228 bps
INFO @ 06 Jun 2024 00:31:01: [635 MB] #2 alternative fragment length(s) may be 228 bps
INFO @ 06 Jun 2024 00:31:01: [635 MB] #2.2 Generate R script for model : /tmp/RtmpvdAfEo/run_callpeak_narrow0_model.r
INFO @ 06 Jun 2024 00:31:01: [635 MB] #3 Call peaks...
INFO @ 06 Jun 2024 00:31:01: [635 MB] #3 Pre-compute pvalue-qvalue table...
INFO @ 06 Jun 2024 00:31:01: [635 MB] #3 Cutoff vs peaks called will be analyzed!
INFO @ 06 Jun 2024 00:31:01: [657 MB] #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/tmp/RtmpvdAfEo/run_callpeak_narrow0_cutoff_analysis.txt'
INFO @ 06 Jun 2024 00:31:01: [657 MB] #3 In the peak calling step, the following will be performed simultaneously:
INFO @ 06 Jun 2024 00:31:01: [657 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg
INFO @ 06 Jun 2024 00:31:01: [657 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg
INFO @ 06 Jun 2024 00:31:01: [657 MB] #3 Pileup will be based on sequencing depth in treatment.
INFO @ 06 Jun 2024 00:31:01: [657 MB] #3 Call peaks for each chromosome...
INFO @ 06 Jun 2024 00:31:02: [657 MB] #4 Write output xls file... /tmp/RtmpvdAfEo/run_callpeak_narrow0_peaks.xls
INFO @ 06 Jun 2024 00:31:02: [657 MB] #4 Write peak in narrowPeak format file... /tmp/RtmpvdAfEo/run_callpeak_narrow0_peaks.narrowPeak
INFO @ 06 Jun 2024 00:31:02: [657 MB] #4 Write summits bed file... /tmp/RtmpvdAfEo/run_callpeak_narrow0_summits.bed
INFO @ 06 Jun 2024 00:31:02: [657 MB] Done!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
>
> proc.time()
user system elapsed
27.209 2.137 29.808
MACSr.Rcheck/MACSr-Ex.timings
| name | user | system | elapsed | |
| bdgbroadcall | 6.703 | 1.165 | 8.945 | |
| bdgcmp | 3.662 | 0.312 | 4.357 | |
| bdgdiff | 4.849 | 0.280 | 5.498 | |
| bdgopt | 3.233 | 0.284 | 3.904 | |
| bdgpeakcall | 0 | 0 | 0 | |
| callpeak | 2.909 | 0.231 | 3.483 | |
| callvar | 0 | 0 | 0 | |
| cmbreps | 3.816 | 0.224 | 4.402 | |
| filterdup | 1.291 | 0.124 | 1.728 | |
| pileup | 1.296 | 0.116 | 1.685 | |
| predictd | 1.325 | 0.117 | 1.709 | |
| randsample | 1.224 | 0.091 | 1.599 | |
| refinepeak | 4.035 | 0.188 | 4.573 | |