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This page was generated on 2024-10-18 20:40 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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 2020/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SOMNiBUS 1.12.0  (landing page)
Kathleen Klein
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/SOMNiBUS
git_branch: RELEASE_3_19
git_last_commit: a22c11b
git_last_commit_date: 2024-04-30 11:30:49 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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    NA  


CHECK results for SOMNiBUS on palomino7

To the developers/maintainers of the SOMNiBUS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SOMNiBUS.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: SOMNiBUS
Version: 1.12.0
Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SOMNiBUS.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SOMNiBUS_1.12.0.tar.gz
StartedAt: 2024-10-17 05:57:51 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 06:14:45 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 1013.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SOMNiBUS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SOMNiBUS.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SOMNiBUS_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/SOMNiBUS.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SOMNiBUS/DESCRIPTION' ... OK
* this is package 'SOMNiBUS' 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 ... OK
* checking for portable file names ... OK
* checking whether package 'SOMNiBUS' can be installed ... OK
* 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 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 whether startup messages can be suppressed ... 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 ... NOTE
testStat: no visible global function definition for 'pf'
Undefined global functions or variables:
  pf
Consider adding
  importFrom("stats", "pf")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
binomRegMethModel     234.61   5.49  240.11
runSOMNiBUS           190.48   3.72  194.26
binomRegMethModelPred  36.51   1.97   38.50
binomRegMethModelPlot  35.89   2.14   38.04
binomRegMethPredPlot   34.65   1.99   36.66
splitDataByGene        16.69   2.94   63.30
splitDataByChromatin   12.70   0.60   14.38
formatFromBismark       3.54   0.15   19.58
* 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: 1 NOTE
See
  'E:/biocbuild/bbs-3.19-bioc/meat/SOMNiBUS.Rcheck/00check.log'
for details.


Installation output

SOMNiBUS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL SOMNiBUS
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'SOMNiBUS' ...
** using staged installation
** R
** data
** 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 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 (SOMNiBUS)

Tests output


Example timings

SOMNiBUS.Rcheck/SOMNiBUS-Ex.timings

nameusersystemelapsed
binomRegMethModel234.61 5.49240.11
binomRegMethModelPlot35.89 2.1438.04
binomRegMethModelPred36.51 1.9738.50
binomRegMethModelSim1.740.282.01
binomRegMethPredPlot34.65 1.9936.66
formatFromBSmooth0.240.000.23
formatFromBSseq0.040.000.05
formatFromBismark 3.54 0.1519.58
runSOMNiBUS190.48 3.72194.26
splitDataByChromatin12.70 0.6014.38
splitDataByDensity2.740.042.80
splitDataByGRanges0.250.000.25
splitDataByGene16.69 2.9463.30
splitDataByRegion0.010.000.04