BioC 2.14: CHECK report for cn.mops on zin2

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.10.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/cn.mops.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cn.mops/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.mops’ 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 ‘cn.mops’ can be installed ... [12s/12s] 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:
  ‘BiocGenerics’ ‘IRanges’
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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘BiocGenerics’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.cn.mopsC’ ‘.convertToFastSegRes’ ‘.makeLogRatios’
  ‘.referencecn.mops’ ‘segment’
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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [57s/57s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
calcFractionalCopyNumbers 13.253  0.024  13.390
cn.mops                   11.780  0.036  11.844
referencecn.mops          10.221  0.008  10.297
exomecn.mops               5.129  0.016   5.173
* 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-2.14-bioc/meat/cn.mops.Rcheck/00check.log’
for details.

* installing *source* package ‘cn.mops’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_cnmops.c -o R_init_cnmops.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c cnmops.cpp -o cnmops.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c segment.cpp -o segment.o
segment.cpp: In function ‘SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
segment.cpp:59:20: warning: variable ‘globalSd’ set but not used [-Wunused-but-set-variable]
segment.cpp:60:9: warning: variable ‘oldStatistic’ set but not used [-Wunused-but-set-variable]
segment.cpp:61:31: warning: variable ‘maxStatistic’ set but not used [-Wunused-but-set-variable]
segment.cpp:62:40: warning: variable ‘maxIdx’ set but not used [-Wunused-but-set-variable]
segment.cpp:64:9: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
g++ -shared -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/cn.mops.Rcheck/cn.mops/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘cn.mops’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.mops)

name	user	system	elapsed
CNVDetectionResult	0.000	0.000	0.002
calcFractionalCopyNumbers	13.253	0.024	13.390
calcIntegerCopyNumbers	0.728	0.004	0.731
cn.mops	11.780	0.036	11.844
cnvr	0.328	0.000	0.328
cnvs	0.332	0.000	0.333
exomecn.mops	5.129	0.016	5.173
getReadCountsFromBAM	0.232	0.000	0.232
getSegmentReadCountsFromBAM	0.060	0.004	0.065
gr	0.396	0.004	0.400
haplocn.mops	1.66	0.00	1.66
individualCall	0.548	0.000	0.551
iniCall	0.368	0.000	0.368
integerCopyNumber	0.368	0.000	0.369
localAssessments	0.364	0.000	0.365
makeRobustCNVR	0.568	0.000	0.568
normalizeChromosomes	0.412	0.004	0.418
normalizeGenome	0.408	0.004	0.413
normalizedData	0.524	0.004	0.568
params	0.332	0.008	0.340
posteriorProbs	0.324	0.000	0.326
referencecn.mops	10.221	0.008	10.297
sampleNames	0.328	0.000	0.327
segment	0.028	0.004	0.035
segmentation	0.364	0.004	0.370
segplot	1.608	0.008	1.616
singlecn.mops	1.284	0.000	1.286

BioC 2.14: CHECK report for cn.mops on zin2

Summary

Command output