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CHECK report for BEAT on tokay1

This page was generated on 2020-08-09 12:03:24 -0400 (Sun, 09 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BEAT PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 130/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEAT 1.27.0
Kemal Akman
Snapshot Date: 2020-08-08 14:51:01 -0400 (Sat, 08 Aug 2020)
URL: https://git.bioconductor.org/packages/BEAT
Branch: master
Last Commit: c69043d
Last Changed Date: 2020-04-27 14:37:58 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BEAT
Version: 1.27.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BEAT_1.27.0.tar.gz
StartedAt: 2020-08-09 01:07:45 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 01:16:43 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 537.9 seconds
RetCode: 0
Status:  OK  
CheckDir: BEAT.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BEAT_1.27.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BEAT.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.27.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
epimutation_calls 60.94   1.54   62.72
generate_results  52.67   0.13   52.79
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
epimutation_calls 56.59   0.39   57.12
generate_results  43.46   0.12   43.60
* 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BEAT.Rcheck/00check.log'
for details.



Installation output

BEAT.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BEAT_1.27.0.tar.gz && rm -rf BEAT.buildbin-libdir && mkdir BEAT.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BEAT.buildbin-libdir BEAT_1.27.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BEAT_1.27.0.zip && rm BEAT_1.27.0.tar.gz BEAT_1.27.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3000k  100 3000k    0     0  38.8M      0 --:--:-- --:--:-- --:--:-- 41.2M

install for i386

* 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

install for x64

* installing *source* package 'BEAT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BEAT' as BEAT_1.27.0.zip
* DONE (BEAT)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BEAT' successfully unpacked and MD5 sums checked

Tests output


Example timings

BEAT.Rcheck/examples_i386/BEAT-Ex.timings

nameusersystemelapsed
epimutation_calls60.94 1.5462.72
generate_results52.67 0.1352.79
makeParams3.850.143.99
positions_to_regions4.440.014.46

BEAT.Rcheck/examples_x64/BEAT-Ex.timings

nameusersystemelapsed
epimutation_calls56.59 0.3957.12
generate_results43.46 0.1243.60
makeParams2.570.072.63
positions_to_regions2.590.002.59