BioC 2.13: CHECK report for chipseq on perceval

Package: chipseq

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch chipseq_1.12.0.tar.gz

StartedAt: 2014-04-05 00:12:33 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:17:50 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 317.2 seconds

RetCode: 0

Status:  OK

CheckDir: chipseq.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/chipseq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chipseq/DESCRIPTION’ ... OK
* this is package ‘chipseq’ version ‘1.12.0’
* 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 ‘chipseq’ can be installed ... [26s/26s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘BiocGenerics’ ‘IRanges’ ‘BSgenome’ ‘GenomicRanges’ ‘ShortRead’
A package should be listed in only one of these fields.
* 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 ... NOTE
‘:::’ call which should be ‘::’: ‘IRanges:::isTRUEorFALSE’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
correlation.estimate: no visible binding for global variable ‘mu’
correlation.estimate: no visible binding for global variable ‘corr’
coverage.estimate: no visible binding for global variable ‘mu’
coverage.estimate: no visible binding for global variable ‘covered’
islandDepthPlot: no visible binding for global variable ‘depth’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Workflow.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [60s/60s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
diffPeakSummary 22.879  1.258  24.155
subsetSummary    4.287  1.014   5.309
* 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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/chipseq.Rcheck/00check.log’
for details.

* installing *source* package ‘chipseq’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c rlesumprod.c -o rlesumprod.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o chipseq.so rlesumprod.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/chipseq.Rcheck/chipseq/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chipseq)

name	user	system	elapsed
chipseqFilter	0.637	0.022	0.718
coverageplot	0.187	0.004	0.192
cstest	2.199	0.078	2.277
diffPeakSummary	22.879	1.258	24.155
estimate.mean.fraglen	2.334	0.820	3.156
islandDepthPlot	3.735	0.868	4.607
laneSubsample	2.033	0.532	2.565
peakCutoff	3.550	0.851	4.406
subsetSummary	4.287	1.014	5.309