BioC 2.13: CHECK report for mosaics on zin1

Package: mosaics

Version: 1.10.1

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings mosaics_1.10.1.tar.gz

StartedAt: 2014-04-05 02:34:08 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:35:47 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 98.6 seconds

RetCode: 0

Status:  OK

CheckDir: mosaics.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/mosaics.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mosaics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mosaics’ version ‘1.10.1’
* 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 ‘mosaics’ can be installed ... [13s/14s] 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
.mosaicsZ0: no visible global function definition for ‘mclapply’
mosaicsRunAll: no visible global function definition for ‘mclapply’
readBins: no visible global function definition for ‘mclapply’
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘mosaics-example.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [3s/6s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/mosaics.Rcheck/00check.log’
for details.

* installing *source* package ‘mosaics’ ...
** libs
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c convolution_1S.cpp -o convolution_1S.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c convolution_2S.cpp -o convolution_2S.o
g++ -shared -L/usr/local/lib -o mosaics.so convolution_1S.o convolution_2S.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/mosaics.Rcheck/mosaics/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘mosaics’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘mosaics’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mosaics)

name	user	system	elapsed
BinData-class	0.008	0.000	0.019
MosaicsFit-class	0.004	0.000	0.007
MosaicsPeak-class	0.004	0.004	0.007
constructBins	0.000	0.004	0.005
estimates	0.008	0.000	0.007
export	0.000	0.008	0.022
generateWig	0.008	0.000	0.017
mosaics-package	0.096	0.004	0.193
mosaicsFit	0.008	0.000	0.005
mosaicsPeak	0.000	0.004	0.005
mosaicsRunAll	0.000	0.008	0.023
readBins	0.008	0.000	0.018