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CHECK report for bacon on merida1

This page was generated on 2020-12-01 12:00:59 -0500 (Tue, 01 Dec 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE bacon PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 107/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bacon 1.18.0
Maarten van Iterson
Snapshot Date: 2020-11-30 14:42:56 -0500 (Mon, 30 Nov 2020)
URL: https://git.bioconductor.org/packages/bacon
Branch: RELEASE_3_12
Last Commit: 8eb9db7
Last Changed Date: 2020-10-27 11:12:21 -0500 (Tue, 27 Oct 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: bacon
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bacon.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bacon_1.18.0.tar.gz
StartedAt: 2020-11-30 23:20:23 -0500 (Mon, 30 Nov 2020)
EndedAt: 2020-11-30 23:21:35 -0500 (Mon, 30 Nov 2020)
EllapsedTime: 72.9 seconds
RetCode: 0
Status:  OK 
CheckDir: bacon.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bacon.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bacon_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/bacon.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bacon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bacon’ version ‘1.18.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘bacon’ 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 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
.hist: no visible binding for global variable ‘..density..’
Undefined global functions or variables:
  ..density..
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
bacon            12.954  0.257   5.139
es-methods        7.426  0.251   2.651
meta-methods      6.666  0.142   2.273
topTable-methods  6.556  0.182   2.253
se-methods        6.453  0.171   2.285
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/bacon.Rcheck/00check.log’
for details.



Installation output

bacon.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bacon
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘bacon’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rinit.c -o Rinit.o
Rinit.c:11:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
  NULL
  ^~~~
  {   }
/Library/Developer/CommandLineTools/usr/lib/clang/11.0.0/include/stddef.h:105:16: note: expanded from macro 'NULL'
#  define NULL ((void*)0)
               ^~~~~~~~~~
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c bacon.c -o bacon.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o bacon.so Rinit.o bacon.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-bacon/00new/bacon/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bacon)

Tests output

bacon.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(bacon)
Loading required package: ggplot2
Loading required package: BiocParallel
Loading required package: ellipse

Attaching package: 'ellipse'

The following object is masked from 'package:graphics':

    pairs

> test_check("bacon")
[1]  0.914158192 -0.009646065  0.997805988
> 
> proc.time()
   user  system elapsed 
 11.526   0.441   6.831 

Example timings

bacon.Rcheck/bacon-Ex.timings

nameusersystemelapsed
bacon12.954 0.257 5.139
bias-methods0.1730.0050.179
dnormmix0.0040.0010.006
es-methods7.4260.2512.651
estimates-methods0.1600.0040.165
fit-methods0.1590.0030.162
inflation-methods0.1520.0060.157
meta-methods6.6660.1422.273
plotnormmix0.0040.0020.005
posteriors-methods0.1620.0060.168
pval-methods0.1210.0020.123
rnormmix0.0010.0000.001
se-methods6.4530.1712.285
topTable-methods6.5560.1822.253
traces-methods0.2670.0130.281
tstat-methods0.1460.0020.148