| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:35 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1086/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MACSr 1.9.0 (landing page) Qiang Hu
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: MACSr |
| Version: 1.9.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:MACSr.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings MACSr_1.9.0.tar.gz |
| StartedAt: 2023-06-06 01:07:32 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 01:13:12 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 339.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MACSr.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:MACSr.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings MACSr_1.9.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MACSr.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘MACSr/DESCRIPTION’ ... OK
* this is package ‘MACSr’ version ‘1.9.0’
* 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-3.18-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 ... 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 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 9.768 1.483 16.105
bdgdiff 6.719 0.244 10.166
refinepeak 6.123 0.112 9.485
cmbreps 5.427 0.177 8.849
bdgcmp 4.913 0.140 9.355
bdgopt 4.309 0.180 8.231
callpeak 3.706 0.135 7.110
* 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 ...
‘MACSr.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/MACSr.Rcheck/00check.log’
for details.
MACSr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL MACSr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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(MACSr)
>
> test_check("MACSr")
INFO @ Tue, 06 Jun 2023 01:12:22:
# Command line:
# ARGUMENTS LIST:
# name = run_callpeak_narrow0
# format = BED
# ChIP-seq file = ['/home/biocbuild/.cache/R/ExperimentHub/3f239776874810_4601']
# control file = ['/home/biocbuild/.cache/R/ExperimentHub/3f239729973b1a_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 @ Tue, 06 Jun 2023 01:12:22: #1 read tag files...
INFO @ Tue, 06 Jun 2023 01:12:22: #1 read treatment tags...
INFO @ Tue, 06 Jun 2023 01:12:23: #1.2 read input tags...
INFO @ Tue, 06 Jun 2023 01:12:23: #1 tag size is determined as 101 bps
INFO @ Tue, 06 Jun 2023 01:12:23: #1 tag size = 101.0
INFO @ Tue, 06 Jun 2023 01:12:23: #1 total tags in treatment: 49622
INFO @ Tue, 06 Jun 2023 01:12:23: #1 user defined the maximum tags...
INFO @ Tue, 06 Jun 2023 01:12:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ Tue, 06 Jun 2023 01:12:23: #1 tags after filtering in treatment: 48047
INFO @ Tue, 06 Jun 2023 01:12:23: #1 Redundant rate of treatment: 0.03
INFO @ Tue, 06 Jun 2023 01:12:23: #1 total tags in control: 50837
INFO @ Tue, 06 Jun 2023 01:12:23: #1 user defined the maximum tags...
INFO @ Tue, 06 Jun 2023 01:12:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ Tue, 06 Jun 2023 01:12:23: #1 tags after filtering in control: 50783
INFO @ Tue, 06 Jun 2023 01:12:23: #1 Redundant rate of control: 0.00
INFO @ Tue, 06 Jun 2023 01:12:23: #1 finished!
INFO @ Tue, 06 Jun 2023 01:12:23: #2 Build Peak Model...
INFO @ Tue, 06 Jun 2023 01:12:23: #2 looking for paired plus/minus strand peaks...
INFO @ Tue, 06 Jun 2023 01:12:23: #2 Total number of paired peaks: 469
INFO @ Tue, 06 Jun 2023 01:12:23: #2 Model building with cross-correlation: Done
INFO @ Tue, 06 Jun 2023 01:12:23: #2 finished!
INFO @ Tue, 06 Jun 2023 01:12:23: #2 predicted fragment length is 228 bps
INFO @ Tue, 06 Jun 2023 01:12:23: #2 alternative fragment length(s) may be 228 bps
INFO @ Tue, 06 Jun 2023 01:12:23: #2.2 Generate R script for model : /tmp/Rtmpo410Cn/run_callpeak_narrow0_model.r
INFO @ Tue, 06 Jun 2023 01:12:23: #3 Call peaks...
INFO @ Tue, 06 Jun 2023 01:12:23: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 06 Jun 2023 01:12:23: #3 Cutoff vs peaks called will be analyzed!
INFO @ Tue, 06 Jun 2023 01:12:24: #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/tmp/Rtmpo410Cn/run_callpeak_narrow0_cutoff_analysis.txt'
INFO @ Tue, 06 Jun 2023 01:12:24: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Tue, 06 Jun 2023 01:12:24: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg
INFO @ Tue, 06 Jun 2023 01:12:24: #3 Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg
INFO @ Tue, 06 Jun 2023 01:12:24: #3 Pileup will be based on sequencing depth in treatment.
INFO @ Tue, 06 Jun 2023 01:12:24: #3 Call peaks for each chromosome...
INFO @ Tue, 06 Jun 2023 01:12:24: #4 Write output xls file... /tmp/Rtmpo410Cn/run_callpeak_narrow0_peaks.xls
INFO @ Tue, 06 Jun 2023 01:12:24: #4 Write peak in narrowPeak format file... /tmp/Rtmpo410Cn/run_callpeak_narrow0_peaks.narrowPeak
INFO @ Tue, 06 Jun 2023 01:12:24: #4 Write summits bed file... /tmp/Rtmpo410Cn/run_callpeak_narrow0_summits.bed
INFO @ Tue, 06 Jun 2023 01:12:24: Done!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
>
> proc.time()
user system elapsed
39.150 1.955 67.621
MACSr.Rcheck/MACSr-Ex.timings
| name | user | system | elapsed | |
| bdgbroadcall | 9.768 | 1.483 | 16.105 | |
| bdgcmp | 4.913 | 0.140 | 9.355 | |
| bdgdiff | 6.719 | 0.244 | 10.166 | |
| bdgopt | 4.309 | 0.180 | 8.231 | |
| bdgpeakcall | 0.002 | 0.000 | 0.002 | |
| callpeak | 3.706 | 0.135 | 7.110 | |
| callvar | 0.002 | 0.000 | 0.002 | |
| cmbreps | 5.427 | 0.177 | 8.849 | |
| filterdup | 1.620 | 0.103 | 4.490 | |
| pileup | 1.444 | 0.072 | 3.820 | |
| predictd | 1.647 | 0.038 | 3.979 | |
| randsample | 1.436 | 0.036 | 3.739 | |
| refinepeak | 6.123 | 0.112 | 9.485 | |