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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cn.farms.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cn.farms_1.59.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/cn.farms.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* 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 ‘1.59.0’
* 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
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 code 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 whether startup messages can be suppressed ... 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’
plotDensity: no visible global function definition for ‘density’
plotDensity: no visible global function definition for ‘lines’
plotEvalIc: no visible global function definition for ‘rgb’
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 ‘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 ‘makeNWScluster’
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
  makeNWScluster matlines matplot median mtext na.omit nclass.Sturges
  order.dendrogram packageDescription pairs par pchisq pdf 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", "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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'cn.farms.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'combineData.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'dnaCopySf.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'fragLengCorr.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'mlSummarization.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'normalizeNone.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'normalizeNpData.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'normalizeSequenceEffect.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'normalizeSor.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'plotEvalIc.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'plotRegions.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'plotSmoothScatter.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'plotViolines.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'slSummarization.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... INFO
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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.23-bioc/meat/cn.farms.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cn.farms
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘cn.farms’ ...
** this is package ‘cn.farms’ version ‘1.59.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_cnfarms.c -o R_init_cnfarms.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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 -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sparse_farms.c -o sparse_farms.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/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)