Package: cn.farms

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cn.farms.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cn.farms_1.32.0.tar.gz

StartedAt: 2019-10-16 01:34:41 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:39:55 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 314.0 seconds

RetCode: 0

Status:  OK

CheckDir: cn.farms.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cn.farms.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cn.farms_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cn.farms.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.32.0’
* 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 ... 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 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
calcDistance: no visible global function definition for ‘density’
callSummarizeH01: no visible binding for global variable ‘var’
callSummarizeH01: no visible global function definition for ‘rnorm’
createAnnotation: no visible global function definition for
  ‘installed.packages’
determineBaselineArray: no visible binding for global variable ‘median’
flcSnp6Std: no visible global function definition for ‘lowess’
flcSnp6Std: no visible global function definition for ‘approx’
flcSnp6StdH01: no visible global function definition for ‘lowess’
flcSnp6StdH01: no visible global function definition for ‘approx’
flcStd: no visible global function definition for ‘lowess’
flcStd: no visible global function definition for ‘approx’
flcStdH01: no visible global function definition for ‘lowess’
flcStdH01: no visible global function definition for ‘approx’
getProbePositionEffectDesignMatrix: no visible global function
  definition for ‘head’
getVar: no visible global function definition for ‘getFromNamespace’
initializeBigMatrix: no visible global function definition for
  ‘isPackageLoaded’
normalizeAverage: no visible binding for global variable ‘median’
normalizeAverage: no visible global function definition for ‘median’
normalizeSorH01: no visible binding for global variable ‘pairs’
normalizeSorH01: no visible global function definition for ‘median’
plotDendrogram : colLab: no visible global function definition for
  ‘is.leaf’
plotDendrogram: no visible global function definition for
  ‘as.dendrogram’
plotDendrogram: no visible global function definition for ‘hclust’
plotDendrogram: no visible global function definition for
  ‘order.dendrogram’
plotDendrogram: no visible global function definition for ‘dendrapply’
plotDendrogram: no visible global function definition for ‘plot’
plotDensity: no visible global function definition for ‘density’
plotDensity: no visible global function definition for ‘plot’
plotDensity: no visible global function definition for ‘lines’
plotEvalIc: no visible global function definition for ‘rgb’
plotEvalIc: no visible global function definition for ‘plot’
plotEvalIc: no visible global function definition for ‘rect’
plotEvalIc: no visible global function definition for ‘points’
plotEvalIc: no visible global function definition for ‘densCols’
plotEvalIc: no visible global function definition for ‘mtext’
plotRegions: no visible global function definition for ‘pdf’
plotRegions: no visible global function definition for ‘plot’
plotRegions: no visible global function definition for ‘text’
plotRegions: no visible global function definition for ‘par’
plotRegions: no visible global function definition for ‘matplot’
plotRegions: no visible global function definition for ‘abline’
plotRegions: no visible global function definition for ‘matlines’
plotRegions: no visible global function definition for ‘legend’
plotRegions: no visible global function definition for ‘axis’
plotRegions: no visible global function definition for ‘nclass.Sturges’
plotRegions: no visible global function definition for ‘dev.off’
plotSmoothScatter: no visible global function definition for ‘pdf’
plotSmoothScatter: no visible global function definition for
  ‘smoothScatter’
plotSmoothScatter: no visible global function definition for ‘abline’
plotSmoothScatter: no visible global function definition for ‘loess’
plotSmoothScatter: no visible global function definition for ‘points’
plotSmoothScatter: no visible global function definition for ‘dev.off’
setVar: no visible global function definition for ‘assignInNamespace’
sfClusterSetupSPRNG: no visible global function definition for ‘runif’
sfExport: no visible global function definition for ‘getFromNamespace’
sfExportAll: no visible global function definition for ‘na.omit’
sfInit: no visible global function definition for ‘packageDescription’
sfTest : testCalc1: no visible global function definition for ‘runif’
sfTest : testCalc2: no visible global function definition for ‘runif’
summarizeFarmsExact: no visible global function definition for ‘median’
summarizeFarmsExact: no visible binding for global variable ‘median’
summarizeFarmsExact: no visible global function definition for ‘pchisq’
summarizeFarmsExact2: no visible global function definition for
  ‘median’
summarizeFarmsExact2: no visible binding for global variable ‘median’
summarizeFarmsExact2: no visible global function definition for
  ‘pchisq’
summarizeFarmsExact3: no visible global function definition for
  ‘median’
summarizeFarmsExact3: no visible binding for global variable ‘median’
summarizeFarmsExact3: no visible global function definition for
  ‘pchisq’
summarizeFarmsGaussian: no visible global function definition for
  ‘median’
summarizeFarmsGaussian: no visible binding for global variable ‘median’
summarizeFarmsGaussian: no visible global function definition for ‘var’
summarizeFarmsStatistics: no visible binding for global variable
  ‘median’
summarizeFarmsStatistics: no visible global function definition for
  ‘median’
summarizeFarmsVariational: no visible binding for global variable
  ‘median’
summarizeFarmsVariational: no visible global function definition for
  ‘sd’
summarizeFarmsVariational: no visible global function definition for
  ‘median’
summarizeFarmsVariational: no visible global function definition for
  ‘var’
Undefined global functions or variables:
  abline approx as.dendrogram assignInNamespace axis dendrapply
  densCols density dev.off getFromNamespace hclust head
  installed.packages is.leaf isPackageLoaded legend lines loess lowess
  matlines matplot median mtext na.omit nclass.Sturges order.dendrogram
  packageDescription pairs par pchisq pdf plot points rect rgb rnorm
  runif sd smoothScatter text var
Consider adding
  importFrom("grDevices", "densCols", "dev.off", "nclass.Sturges", "pdf",
             "rgb")
  importFrom("graphics", "abline", "axis", "legend", "lines", "matlines",
             "matplot", "mtext", "pairs", "par", "plot", "points",
             "rect", "smoothScatter", "text")
  importFrom("stats", "approx", "as.dendrogram", "dendrapply", "density",
             "hclust", "is.leaf", "loess", "lowess", "median", "na.omit",
             "order.dendrogram", "pchisq", "rnorm", "runif", "sd", "var")
  importFrom("utils", "assignInNamespace", "getFromNamespace", "head",
             "installed.packages", "packageDescription")
to your NAMESPACE file.
* 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mlSummarization 7.200  0.401   7.643
slSummarization 5.777  0.142   6.047
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/cn.farms.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cn.farms
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘cn.farms’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c R_init_cnfarms.c -o R_init_cnfarms.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c sparse_farms.c -o sparse_farms.o
clang++ -std=gnu++11 -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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-cn.farms/00new/cn.farms/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cn.farms)

name	user	system	elapsed
cn.farms	0	0	0
combineData	2.770	0.118	2.910
createAnnotation	0	0	0
distributionDistance	0.128	0.031	0.160
dnaCopySf	0.156	0.005	0.168
fragLengCorr	3.714	0.174	3.906
mlSummarization	7.200	0.401	7.643
normalizeAverage	0.003	0.001	0.004
normalizeCels	0	0	0
normalizeNpData	0.001	0.000	0.001
plotDendrogram	0.159	0.024	0.186
plotDensity	0.539	0.034	0.591
plotEvalIc	0.455	0.029	0.533
plotRegions	0.201	0.013	0.232
plotSmoothScatter	0.376	0.040	0.441
plotViolines	0.188	0.005	0.284
slSummarization	5.777	0.142	6.047
sparseFarmsC	0.002	0.001	0.002
summarizeFarmsExact	0.009	0.004	0.013
summarizeFarmsExact2	0.010	0.004	0.014
summarizeFarmsExact3	0.009	0.004	0.013
summarizeFarmsGaussian	0.004	0.001	0.004
summarizeFarmsMethods	0.003	0.001	0.004
summarizeFarmsVariational	0.008	0.003	0.011
summarizeWindowBps	0.005	0.001	0.006
summarizeWindowMethods	0.004	0.000	0.004
summarizeWindowStd	0.006	0.001	0.006