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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:blima.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings blima_1.40.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/blima.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘blima/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘blima’ version ‘1.40.0’
* 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: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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 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
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/blima.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL blima
###
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘blima’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c interpolateSortedVector.cpp -o interpolateSortedVector.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o blima.so RcppExports.o interpolateSortedVector.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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)