################################################################################################################################################################## Running command:###### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:blima.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings blima_1.44.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/blima.Rcheck’* using R version 4.5.2 Patched (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 ‘blima/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘blima’ version ‘1.44.0’* package encoding: UTF-8* 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 ‘blima’ can be installed ... OK* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’* 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 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 ... NOTEnonParametricEstimator: no visible global function definition for ‘var’performXieCorrection: no visible global function definition for ‘dnorm’performXieCorrection: no visible global function definition for ‘pnorm’vstFromLumi: no visible global function definition for ‘lm’vstFromLumi: no visible global function definition for ‘predict’Undefined global functions or variables: dnorm lm pnorm predict varConsider adding importFrom("stats", "dnorm", "lm", "pnorm", "predict", "var")to your NAMESPACE file.* checking Rd files ... NOTEcheckRd: (-1) createSummarizedMatrix.Rd:11: Lost braces; missing escapes or markup? 11 | \item{channelInclude}{This field allows user to set channel with weights which have to be from {0,1}. | ^checkRd: (-1) doProbeTTests.Rd:12: Lost braces; missing escapes or markup? 12 | \item{channelInclude}{This field allows user to set channel with weights which have to be {0,1}. | ^checkRd: (-1) doTTests.Rd:12: Lost braces; missing escapes or markup? 12 | \item{channelInclude}{This field allows user to set channel with weights which have to be {0,1}. | ^checkRd: (-1) meanDistribution.Rd:15: Lost braces; missing escapes or markup? 15 | \item{channelInclude}{This field allows user to set channel with weights which have to be in {0,1}. | ^checkRd: (-1) quantileNormalize.Rd:12: Lost braces; missing escapes or markup? 12 | \item{channelInclude}{This field allows user to set channel with weights which have to be in {0,1}. | ^checkRd: (-1) singleArrayNormalize.Rd:13: Lost braces; missing escapes or markup? 13 | \item{channelInclude}{This field allows user to set channel with weights which have to be in {0,1}. | ^checkRd: (-1) varianceBeadStabilise.Rd:11: Lost braces; missing escapes or markup? 11 | \item{channelInclude}{This field allows user to set channel with weights which have to be in {0,1}. | ^checkRd: (-1) varianceBeadStabiliseSingleArray.Rd:11: Lost braces; missing escapes or markup? 11 | \item{channelInclude}{This field allows user to set channel with weights which have to be in {0,1}. | ^checkRd: (-1) xieBacgroundCorrect.Rd:16: Lost braces; missing escapes or markup? 16 | \item{channelInclude}{This field allows user to set channel with weights which have to be from {0,1}. | ^checkRd: (-1) xieBacgroundCorrectSingleArray.Rd:18: Lost braces; missing escapes or markup? 18 | \item{channelInclude}{This field allows user to set channel with weights which have to be from {0,1}. | ^* 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 ... NOTERd files without \description: ‘interpolateSortedVectorRcpp_.Rd’Argument items with no description in Rd file 'interpolateSortedVectorRcpp_.Rd': ‘vector’ ‘newSize’Argument items with no description in Rd file 'nonParametricEstimator.Rd': ‘toCorrectAll’ ‘toCorrectNeg’Argument items with no description in Rd file 'numberOfDistributionElements.Rd': ‘channelInclude’Argument items with no description in Rd file 'performXieCorrection.Rd': ‘value’ ‘alpha’ ‘mu’ ‘sigma’Argument items with no description in Rd file 'singleNumberOfDistributionElements.Rd': ‘channelInclude’Argument items with no description in Rd file 'updateMeanDistribution.Rd': ‘meanDistribution’* checking for unstated dependencies in examples ... OK* checking line endings in C/C++/Fortran sources/headers ... OK* checking compiled code ... NOTENote: 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* DONEStatus: 4 NOTEsSee ‘/Users/biocbuild/bbs-3.22-bioc/meat/blima.Rcheck/00check.log’for details.################################################################################################################################################################## Running command:###### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL blima###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’* installing *source* package ‘blima’ ...** this is package ‘blima’ version ‘1.44.0’** using staged installation** libsusing C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’using SDK: ‘MacOSX11.3.1.sdk’clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c interpolateSortedVector.cpp -o interpolateSortedVector.oclang++ -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 blima.so RcppExports.o interpolateSortedVector.o -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-blima/00new/blima/libs** R** 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 (blima)
