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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 2195/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TRESS 1.12.0  (landing page)
Zhenxing Guo
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/TRESS
git_branch: RELEASE_3_20
git_last_commit: 947099a
git_last_commit_date: 2024-10-29 11:05:14 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for TRESS on kjohnson1

To the developers/maintainers of the TRESS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TRESS.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.

raw results


Summary

Package: TRESS
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TRESS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TRESS_1.12.0.tar.gz
StartedAt: 2024-12-21 12:34:08 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 12:39:28 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 320.1 seconds
RetCode: 0
Status:   OK  
CheckDir: TRESS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TRESS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TRESS_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TRESS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRESS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TRESS’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Vignette dependency required without any vignettes:: ‘knitr’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TRESS’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 ... NOTE
checkRd: (-1) CallCandidates.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) CallCandidates.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) CallPeaks.multiRep.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) CallPeaks.paramEsti.Rd:10: Escaped LaTeX specials: \&
checkRd: (-1) CallPeaks.paramEsti.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) findBumps.Rd:8: Escaped LaTeX specials: \&
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
CallDMRs.paramEsti 24.143  2.576  17.463
TRESS_DMRtest      25.094  1.522  14.128
CoefName           17.518  1.165  15.167
DMRInfer            8.270  0.954   0.269
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/TRESS.Rcheck/00check.log’
for details.


Installation output

TRESS.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TRESS
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘TRESS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TRESS)

Tests output


Example timings

TRESS.Rcheck/TRESS-Ex.timings

nameusersystemelapsed
CallCandidates1.8950.1162.019
CallDMRs.paramEsti24.143 2.57617.463
CallPeaks.multiRep1.7300.1411.885
CallPeaks.oneRep0.0790.0230.102
CallPeaks.paramEsti2.6260.1602.869
CoefName17.518 1.16515.167
DMRInfer8.2700.9540.269
DivideBins000
ShowOnePeak0.2290.0910.327
TRESS_DMRfit000
TRESS_DMRtest25.094 1.52214.128
TRESS_peak0.0000.0010.000
filterRegions0.0100.0120.022
findBumps0.0420.0290.071
meRatio0.0340.0270.061