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This page was generated on 2024-02-22 12:48:25 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
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 2155/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TRESS 1.9.0  (landing page)
Zhenxing Guo
Snapshot Date: 2024-02-21 14:10:10 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/TRESS
git_branch: devel
git_last_commit: 31094a4
git_last_commit_date: 2023-10-24 11:37:07 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for TRESS on nebbiolo1


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: 1.9.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:TRESS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings TRESS_1.9.0.tar.gz
StartedAt: 2024-02-22 03:48:57 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 03:54:00 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 303.1 seconds
RetCode: 0
Status:   OK  
CheckDir: TRESS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:TRESS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings TRESS_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/TRESS.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘TRESS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TRESS’ 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 ... 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 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 ... 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
CoefName           18.843  2.244  16.199
TRESS_DMRtest      19.695  1.375  13.920
CallDMRs.paramEsti 16.975  2.036  16.012
CallPeaks.multiRep 11.423  2.751   1.792
DMRInfer            9.039  1.224   0.178
findBumps           4.819  0.488   0.110
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/TRESS.Rcheck/00check.log’
for details.



Installation output

TRESS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL TRESS
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
CallCandidates0.8050.1450.950
CallDMRs.paramEsti16.975 2.03616.012
CallPeaks.multiRep11.423 2.751 1.792
CallPeaks.oneRep0.0760.0250.102
CallPeaks.paramEsti2.6790.8263.505
CoefName18.843 2.24416.199
DMRInfer9.0391.2240.178
DivideBins000
ShowOnePeak0.1690.0360.207
TRESS_DMRfit0.0010.0000.001
TRESS_DMRtest19.695 1.37513.920
TRESS_peak0.0000.0010.001
filterRegions0.0080.0020.010
findBumps4.8190.4880.110
meRatio0.0240.0000.024