Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-20 11:06:48 -0500 (Thu, 20 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4162
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4057
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3999
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4116
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 riesling1


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? here 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 134/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEAT 1.33.0  (landing page)
Kemal Akman
Snapshot Date: 2022-01-19 13:55:26 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/BEAT
git_branch: master
git_last_commit: 11aa516
git_last_commit_date: 2021-10-26 12:11:32 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BEAT
Version: 1.33.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BEAT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BEAT_1.33.0.tar.gz
StartedAt: 2022-01-19 18:18:09 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 18:22:09 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 239.5 seconds
RetCode: 0
Status:   OK  
CheckDir: BEAT.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BEAT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BEAT_1.33.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BEAT.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BEAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BEAT' version '1.33.0'
* 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 11.5Mb
  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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
generate_results  31.03   0.40   31.56
epimutation_calls 30.53   0.81   31.36
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/BEAT.Rcheck/00check.log'
for details.



Installation output

BEAT.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BEAT
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'BEAT'
    finding HTML links ... done
    BEAT                                    html  
    epimutation_calls                       html  
    generate_results                        html  
    makeParams                              html  
    positions                               html  
    positions.reference                     html  
    positions_to_regions                    html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'hiAnnotator' is missing or broken
 done

Tests output


Example timings

BEAT.Rcheck/BEAT-Ex.timings

nameusersystemelapsed
epimutation_calls30.53 0.8131.36
generate_results31.03 0.4031.56
makeParams1.890.102.00
positions_to_regions2.230.162.39