Package: bacon

Version: 1.11.1

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_1.11.1.tar.gz

StartedAt: 2019-04-08 23:59:10 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-09 00:00:21 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 70.7 seconds

RetCode: 0

Status:  OK

CheckDir: bacon.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.11.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/bacon.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.11.1’
* 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..’
.qq: no visible binding for global variable ‘column’
Undefined global functions or variables:
  ..density.. column
* 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 or elapsed time > 5s
                   user system elapsed
bacon            12.940  0.503   5.163
topTable-methods  7.139  0.320   2.609
meta-methods      6.926  0.406   2.515
se-methods        7.015  0.300   2.541
es-methods        6.913  0.296   2.524
* 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-3.9-bioc/meat/bacon.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bacon
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘bacon’ ...
** using staged installation
** libs
clang -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
  ^˜˜˜
  {   }
/usr/local/clang4/bin/../lib/clang/4.0.0/include/stddef.h:105:16: note: expanded from macro 'NULL'
#  define NULL ((void*)0)
               ^˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c bacon.c -o bacon.o
clang -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/3.6/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)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 3 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  2.660   0.280   2.894 

name	user	system	elapsed
bacon	12.940	0.503	5.163
bias-methods	0.126	0.004	0.130
dnormmix	0.006	0.003	0.009
es-methods	6.913	0.296	2.524
estimates-methods	0.177	0.006	0.183
fit-methods	0.181	0.006	0.187
inflation-methods	0.172	0.005	0.177
meta-methods	6.926	0.406	2.515
plotnormmix	0.007	0.003	0.010
posteriors-methods	0.132	0.005	0.137
pval-methods	0.126	0.002	0.129
rnormmix	0.001	0.000	0.000
se-methods	7.015	0.300	2.541
topTable-methods	7.139	0.320	2.609
traces-methods	0.225	0.017	0.242
tstat-methods	0.173	0.005	0.177