Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-02-03 11:05:58 -0500 (Fri, 03 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4511
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4289
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4318
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

CHECK results for BEAT on palomino4


To the developers/maintainers of the BEAT package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BEAT.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 138/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEAT 1.36.0  (landing page)
Kemal Akman
Snapshot Date: 2023-02-02 14:00:04 -0500 (Thu, 02 Feb 2023)
git_url: https://git.bioconductor.org/packages/BEAT
git_branch: RELEASE_3_16
git_last_commit: 4ad65bd
git_last_commit_date: 2022-11-01 11:09:07 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BEAT
Version: 1.36.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BEAT.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings BEAT_1.36.0.tar.gz
StartedAt: 2023-02-02 23:09:48 -0500 (Thu, 02 Feb 2023)
EndedAt: 2023-02-02 23:14:40 -0500 (Thu, 02 Feb 2023)
EllapsedTime: 291.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BEAT.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BEAT.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings BEAT_1.36.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/BEAT.Rcheck'
* using R version 4.2.2 (2022-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BEAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BEAT' version '1.36.0'
* 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 'BEAT' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.4Mb
  sub-directories of 1Mb or more:
    extdata  10.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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
koeff: no visible global function definition for 'dbinom'
positionsReadCSV: no visible global function definition for 'read.csv'
printEpimutStats: no visible global function definition for 'median'
priorr: no visible global function definition for 'dbeta'
Undefined global functions or variables:
  dbeta dbinom median read.csv
Consider adding
  importFrom("stats", "dbeta", "dbinom", "median")
  importFrom("utils", "read.csv")
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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
epimutation_calls 36.92   0.59   37.88
generate_results  34.72   0.25   34.97
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/BEAT.Rcheck/00check.log'
for details.



Installation output

BEAT.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL BEAT
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'BEAT' ...
** 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 (BEAT)

Tests output


Example timings

BEAT.Rcheck/BEAT-Ex.timings

nameusersystemelapsed
epimutation_calls36.92 0.5937.88
generate_results34.72 0.2534.97
makeParams2.320.102.42
positions_to_regions2.470.012.49