BioC 3.0: CHECK report for ADaCGH2 on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ADaCGH2_2.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ADaCGH2.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ADaCGH2/DESCRIPTION’ ... OK
* this is package ‘ADaCGH2’ version ‘2.6.0’
* 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 ‘ADaCGH2’ can be installed ... [17s/18s] 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 ... NOTE
'library' or 'require' call to ‘Cairo’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
cutFile: no visible global function definition for ‘detectCores’
distribute: no visible global function definition for ‘clusterApply’
imagemap3: no visible global function definition for ‘CairoPNG’
inputToADaCGH: no visible global function definition for ‘detectCores’
pChromPlot: no visible global function definition for ‘detectCores’
pSegmentBioHMM: no visible global function definition for ‘detectCores’
pSegmentCGHseg: no visible global function definition for ‘detectCores’
pSegmentDNAcopy: no visible global function definition for
  ‘detectCores’
pSegmentGLAD: no visible global function definition for ‘detectCores’
pSegmentHMM: no visible global function definition for ‘detectCores’
pSegmentHaarSeg: no visible global function definition for
  ‘detectCores’
pSegmentWavelets: no visible global function definition for
  ‘detectCores’
* 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [73s/60s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
pChromPlot         15.577  9.683   6.095
pSegment           13.800  4.390  25.848
outputToCGHregions 11.776  2.791  10.942
inputToADaCGH       2.391  0.289   9.559
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/ADaCGH2.Rcheck/00check.log’
for details.

* installing *source* package ‘ADaCGH2’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c r_haarseg.c -o r_haarseg.o
r_haarseg.c:65:12: warning: unused variable 'totalNorm' [-Wunused-variable]
    double totalNorm;
           ^
r_haarseg.c:152:8: warning: '/*' within block comment [-Wcomment]
                                         }/* for j */
                                          ^
r_haarseg.c:176:8: warning: '/*' within block comment [-Wcomment]
                                         }/* for j */
                                          ^
r_haarseg.c:128:9: warning: unused variable 'j' [-Wunused-variable]
         int k,j;
               ^
4 warnings generated.
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 ADaCGH2.so init.o r_haarseg.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/ADaCGH2.Rcheck/ADaCGH2/libs
** R
** data
** inst
** preparing package for lazy loading
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
* DONE (ADaCGH2)

BioC 3.0: CHECK report for ADaCGH2 on oaxaca

Summary

Command output

name	user	system	elapsed
cutFile	0.005	0.001	0.005
inputToADaCGH	2.391	0.289	9.559
outputToCGHregions	11.776	2.791	10.942
pChromPlot	15.577	9.683	6.095
pSegment	13.800	4.390	25.848