BioC 3.2: CHECK report for cn.farms on linux1.bioconductor.org

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cn.farms_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/cn.farms.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cn.farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.farms’ version ‘1.18.0’
* 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 ‘cn.farms’ can be installed ... [13s/13s] 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
initializeBigMatrix: no visible global function definition for
  ‘isPackageLoaded’
* 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 R/sysdata.rda ... 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 ... [20s/20s] 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-3.2-bioc/meat/cn.farms.Rcheck/00check.log’
for details.

* installing *source* package ‘cn.farms’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c laplace.cpp -o laplace.o
laplace.cpp: In function ‘SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
laplace.cpp:442:6: warning: unused variable ‘method’ [-Wunused-variable]
  int method=0;
      ^
laplace.cpp: In function ‘void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)’:
laplace.cpp:368:56: warning: ‘I1right’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  double rightMoment1=1.0*rightMy*I0right+1.0*rightSigma*I1right;
                                                        ^
laplace.cpp:367:52: warning: ‘I1left’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  double leftMoment1=1.0*leftMy*I0left+1.0*leftSigma*I1left;
                                                    ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sparse_farms.c -o sparse_farms.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/cn.farms.Rcheck/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.farms)

name	user	system	elapsed
cn.farms	0.001	0.001	0.001
combineData	1.032	0.020	1.051
createAnnotation	0.001	0.000	0.000
distributionDistance	0.413	0.004	0.417
dnaCopySf	0.116	0.004	0.120
fragLengCorr	2.592	0.023	2.616
mlSummarization	3.420	0.088	3.508
normalizeAverage	0.001	0.000	0.001
normalizeCels	0	0	0
normalizeNpData	0	0	0
plotDendrogram	0.395	0.000	0.395
plotDensity	0.636	0.007	0.644
plotEvalIc	0.404	0.008	0.411
plotRegions	0.177	0.000	0.178
plotSmoothScatter	0.663	0.007	0.672
plotViolines	0.156	0.000	0.156
slSummarization	3.284	0.017	3.303
sparseFarmsC	0.001	0.000	0.001
summarizeFarmsExact	0.004	0.000	0.004
summarizeFarmsExact2	0.004	0.000	0.004
summarizeFarmsExact3	0.004	0.000	0.004
summarizeFarmsGaussian	0.001	0.000	0.001
summarizeFarmsMethods	0.002	0.000	0.002
summarizeFarmsVariational	0.002	0.000	0.002
summarizeWindowBps	0.005	0.000	0.005
summarizeWindowMethods	0.002	0.000	0.002
summarizeWindowStd	0.003	0.000	0.002

BioC 3.2: CHECK report for cn.farms on linux1.bioconductor.org

Summary

Command output