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### 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_1.41.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/blima.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘blima/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘blima’ version ‘1.41.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.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 ... NOTE
nonParametricEstimator: 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 var
Consider adding
  importFrom("stats", "dnorm", "lm", "pnorm", "predict", "var")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-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 ... NOTE
Rd 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 ... 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
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/blima.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL blima
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘blima’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.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  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
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  -DR_NO_REMAP -c interpolateSortedVector.cpp -o interpolateSortedVector.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 blima.so RcppExports.o interpolateSortedVector.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing 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)