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BioC 3.4: CHECK report for bacon on zin1

This page was generated on 2016-09-21 03:40:39 -0700 (Wed, 21 Sep 2016).

Package 74/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bacon 1.1.6
Maarten van Iterson
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bacon
Last Changed Rev: 120384 / Revision: 121152
Last Changed Date: 2016-08-24 05:51:46 -0700 (Wed, 24 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bacon
Version: 1.1.6
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings bacon_1.1.6.tar.gz
StartedAt: 2016-09-20 03:24:02 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 03:25:04 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 62.1 seconds
RetCode: 0
Status:  OK 
CheckDir: bacon.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings bacon_1.1.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/bacon.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.1.6’
* 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 loading without being on the library search path ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
bacon            2.780  0.016  11.615
topTable-methods 0.072  0.012   5.986
es-methods       0.020  0.016   5.487
se-methods       0.024  0.012   5.759
meta-methods     0.020  0.012   5.816
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/bacon.Rcheck/00check.log’
for details.


bacon.Rcheck/00install.out:

* installing *source* package ‘bacon’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
Rinit.c:9:40: warning: missing braces around initializer [-Wmissing-braces]
 static const R_CMethodDef cMethods[] = {
                                        ^
Rinit.c:9:40: note: (near initialization for ‘cMethods’)
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c bacon.c -o bacon.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o bacon.so Rinit.o bacon.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/bacon.Rcheck/bacon/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘bacon’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bacon)

bacon.Rcheck/bacon-Ex.timings:

nameusersystemelapsed
bacon 2.780 0.01611.615
bias-methods0.2960.0000.295
dnormmix0.0040.0000.003
es-methods0.0200.0165.487
estimates-methods0.2840.0000.291
fit-methods0.3320.0000.332
inflation-methods0.2840.0000.287
meta-methods0.0200.0125.816
plotnormmix0.0040.0000.003
posteriors-methods0.2960.0000.296
pval-methods0.2880.0000.287
rnormmix0.0040.0000.001
se-methods0.0240.0125.759
topTable-methods0.0720.0125.986
traces-methods0.3480.0040.352
tstat-methods0.2840.0000.287