BioC 3.1: CHECK report for cn.farms on morelia

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cn.farms_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/cn.farms.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.16.0’
* 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/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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] 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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/cn.farms.Rcheck/00check.log’
for details.

* installing *source* package ‘cn.farms’ ...
** 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 R_init_cnfarms.c -o R_init_cnfarms.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 laplace.cpp -o laplace.o
laplace.cpp:275:10: warning: variable 'I1left' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if(argLeft >= 0.0 && argRight >= 0.0) {
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:364:36: note: uninitialized use occurs here
        double I2left=(-leftMy/leftSigma)*I1left+I0left;
                                          ^˜˜˜˜˜
laplace.cpp:275:7: note: remove the 'if' if its condition is always true
        else if(argLeft >= 0.0 && argRight >= 0.0) {
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:275:10: warning: variable 'I1left' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
        else if(argLeft >= 0.0 && argRight >= 0.0) {
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:364:36: note: uninitialized use occurs here
        double I2left=(-leftMy/leftSigma)*I1left+I0left;
                                          ^˜˜˜˜˜
laplace.cpp:275:10: note: remove the '&&' if its condition is always true
        else if(argLeft >= 0.0 && argRight >= 0.0) {
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:198:15: note: initialize the variable 'I1left' to silence this warning
        double I1left;
                     ^
                      = 0.0
laplace.cpp:275:10: warning: variable 'I1right' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if(argLeft >= 0.0 && argRight >= 0.0) {
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:365:39: note: uninitialized use occurs here
        double I2right=(-rightMy/rightSigma)*I1right+I0right;
                                             ^˜˜˜˜˜˜
laplace.cpp:275:7: note: remove the 'if' if its condition is always true
        else if(argLeft >= 0.0 && argRight >= 0.0) {
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:275:10: warning: variable 'I1right' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
        else if(argLeft >= 0.0 && argRight >= 0.0) {
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:365:39: note: uninitialized use occurs here
        double I2right=(-rightMy/rightSigma)*I1right+I0right;
                                             ^˜˜˜˜˜˜
laplace.cpp:275:10: note: remove the '&&' if its condition is always true
        else if(argLeft >= 0.0 && argRight >= 0.0) {
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:199:16: note: initialize the variable 'I1right' to silence this warning
        double I1right;
                      ^
                       = 0.0
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
        int method=0;
            ^
laplace.cpp:23:11: warning: unused variable 'steps' [-Wunused-const-variable]
const int steps=30;
          ^
laplace.cpp:26:14: warning: unused variable 'integrationFailureFactor' [-Wunused-const-variable]
const double integrationFailureFactor=5.0;
             ^
laplace.cpp:27:14: warning: unused variable 'sigmaFactor' [-Wunused-const-variable]
const double sigmaFactor=0.1;
             ^
laplace.cpp:30:14: warning: unused variable 'Pi' [-Wunused-const-variable]
const double Pi=M_PI;
             ^
laplace.cpp:31:14: warning: unused variable 'E' [-Wunused-const-variable]
const double E=M_E;
             ^
laplace.cpp:34:14: warning: unused variable 'sqrt3' [-Wunused-const-variable]
const double sqrt3=1.7320508075688772935274463415058723669428052538104;
             ^
laplace.cpp:35:14: warning: unused variable 'sqrt2Pi' [-Wunused-const-variable]
const double sqrt2Pi=2.5066282746310005024157652848110452530069867406099;
             ^
12 warnings generated.
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 sparse_farms.c -o sparse_farms.o
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 cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/cn.farms.Rcheck/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (cn.farms)

name	user	system	elapsed
cn.farms	0.001	0.000	0.001
combineData	1.168	0.045	1.303
createAnnotation	0	0	0
distributionDistance	0.105	0.011	0.116
dnaCopySf	0.107	0.002	0.108
fragLengCorr	2.305	0.268	2.606
mlSummarization	2.700	0.343	3.102
normalizeAverage	0.001	0.001	0.003
normalizeCels	0.001	0.000	0.001
normalizeNpData	0.001	0.000	0.001
plotDendrogram	0.090	0.003	0.093
plotDensity	0.456	0.015	0.471
plotEvalIc	0.342	0.079	0.524
plotRegions	0.117	0.028	0.165
plotSmoothScatter	0.252	0.031	0.292
plotViolines	0.124	0.005	0.144
slSummarization	2.871	0.314	3.293
sparseFarmsC	0.001	0.001	0.001
summarizeFarmsExact	0.004	0.001	0.005
summarizeFarmsExact2	0.003	0.001	0.004
summarizeFarmsExact3	0.004	0.001	0.005
summarizeFarmsGaussian	0.003	0.000	0.004
summarizeFarmsMethods	0.002	0.000	0.003
summarizeFarmsVariational	0.004	0.001	0.005
summarizeWindowBps	0.007	0.000	0.008
summarizeWindowMethods	0.003	0.000	0.002
summarizeWindowStd	0.003	0.000	0.003

BioC 3.1: CHECK report for cn.farms on morelia

Summary

Command output