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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:protGear.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings protGear_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/protGear.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘protGear/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘protGear’ version ‘1.6.0’
* 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 ‘protGear’ 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
best_CV_estimation: no visible binding for global variable ‘x’
best_CV_estimation: no visible binding for global variable ‘prop’
best_CV_estimation: no visible binding for global variable ‘val’
best_CV_estimation: no visible binding for global variable ‘meanX1_X2’
best_CV_estimation: no visible binding for global variable ‘meanX2_X3’
best_CV_estimation: no visible binding for global variable ‘xbar’
best_CV_estimation: no visible binding for global variable ‘CVX’
best_CV_estimation: no visible binding for global variable ‘meanX’
best_CV_estimation: no visible binding for global variable ‘selected’
best_CV_estimation: no visible binding for global variable ‘CVX2_X3’
best_CV_estimation: no visible binding for global variable ‘CVX1_X3’
best_CV_estimation: no visible binding for global variable ‘CVX1_X2’
best_CV_estimation: no visible binding for global variable ‘best_CV’
best_CV_estimation: no visible binding for global variable
  ‘FMedianBG_correct’
bg_correct: no visible binding for global variable ‘sampleID’
bg_correct: no visible binding for global variable ‘Name’
bg_correct: no visible binding for global variable ‘antigen’
bg_correct: no visible binding for global variable ‘sample_array_ID’
bg_correct: no visible binding for global variable ‘Block’
bg_correct: no visible binding for global variable ‘Column’
bg_correct: no visible binding for global variable ‘Row’
bg_correct: no visible binding for global variable ‘FMedian’
bg_correct: no visible binding for global variable ‘FMedianBG_correct’
bg_correct: no visible binding for global variable ‘global_BGMedian’
bg_correct: no visible binding for global variable ‘minimum_BGMedian’
bg_correct: no visible binding for global variable ‘BGMedian’
buffer_spots: no visible binding for global variable ‘sampleID’
buffer_spots: no visible binding for global variable ‘antigen’
buffer_spots: no visible binding for global variable
  ‘FMedianBG_correct’
buffer_spots: no visible binding for global variable ‘Block’
buffer_spots: no visible binding for global variable ‘Column’
buffer_spots: no visible binding for global variable ‘Row’
cv_by_sample_estimation: no visible binding for global variable
  ‘variable’
cv_by_sample_estimation: no visible binding for global variable ‘value’
cv_by_sample_estimation: no visible binding for global variable ‘temp’
cv_estimation: no visible binding for global variable
  ‘FMedianBG_correct’
cv_estimation: no visible binding for global variable ‘sdX’
cv_estimation: no visible binding for global variable ‘meanX’
cv_estimation: no visible binding for global variable ‘sdX2_X3’
cv_estimation: no visible binding for global variable ‘meanX2_X3’
cv_estimation: no visible binding for global variable ‘sdX1_X3’
cv_estimation: no visible binding for global variable ‘meanX1_X3’
cv_estimation: no visible binding for global variable ‘sdX1_X2’
cv_estimation: no visible binding for global variable ‘meanX1_X2’
cv_estimation: no visible binding for global variable ‘CVX’
cv_estimation: no visible binding for global variable ‘CVX2_X3’
cv_estimation: no visible binding for global variable ‘CVX1_X3’
cv_estimation: no visible binding for global variable ‘CVX1_X2’
cv_estimation: no visible binding for global variable ‘antigen’
cv_estimation: no visible binding for global variable ‘sampleID’
cv_estimation: no visible binding for global variable ‘sample_array_ID’
extract_bg: no visible binding for global variable ‘v1’
extract_bg: no visible binding for global variable ‘v2’
extract_bg: no visible binding for global variable ‘index’
extract_bg: no visible binding for global variable ‘Name’
extract_bg: no visible binding for global variable ‘Block’
extract_bg: no visible binding for global variable ‘antigen’
matrix_normalise: no visible binding for global variable ‘day_batches’
matrix_normalise: no visible binding for global variable ‘machines’
matrix_normalise: no visible binding for global variable ‘variable’
matrix_normalise: no visible binding for global variable ‘value’
matrix_normalise: no visible binding for global variable ‘antigen’
matrix_normalise: no visible binding for global variable ‘sampleID2’
matrix_normalise: no visible binding for global variable ‘temp’
merge_sampleID: no visible binding for global variable ‘v1’
merge_sampleID: no visible binding for global variable ‘v2’
merge_sampleID: no visible binding for global variable ‘index’
merge_sampleID: no visible binding for global variable ‘Name’
plot_FB: no visible binding for global variable ‘.id’
plot_FB: no visible binding for global variable ‘log_fb’
plot_FB: no visible binding for global variable ‘log_bg’
plot_FB: no visible binding for global variable ‘antigen’
plot_FB: no visible binding for global variable ‘FBG_Median’
plot_FB: no visible binding for global variable ‘BG_Median’
plot_bg: no visible binding for global variable ‘.id’
plot_buffer: no visible binding for global variable ‘buffers’
plot_normalised: no visible binding for global variable ‘mean_all_anti’
plot_normalised: no visible binding for global variable
  ‘rank_mean_all_anti’
plot_normalised: no visible binding for global variable
  ‘stdev_all_anti’
plot_normalised_antigen: no visible binding for global variable
  ‘antigen’
plot_normalised_antigen: no visible binding for global variable ‘MFI’
plot_normalised_antigen: no visible binding for global variable
  ‘mean_mfi’
plot_normalised_antigen: no visible binding for global variable
  ‘rank_mean_all_anti’
plot_normalised_antigen: no visible binding for global variable
  ‘sd_mfi’
read_array_files: no visible binding for global variable ‘Block’
read_array_files: no visible binding for global variable
  ‘global_BGMedian’
read_array_files: no visible binding for global variable
  ‘minimum_BGMedian’
rlm_normalise: no visible binding for global variable ‘Description’
rlm_normalise: no visible binding for global variable ‘Array’
rlm_normalise: no visible binding for global variable ‘Block’
rlm_normalise: no visible binding for global variable ‘antigen’
rlm_normalise: no visible binding for global variable ‘MFI_val’
rlm_normalise: no visible binding for global variable ‘antigen_name’
rlm_normalise: no visible binding for global variable ‘meanBest2_RLM’
rlm_normalise: no visible binding for global variable ‘sample_index’
rlm_normalise: no visible binding for global variable ‘slide’
rlm_normalise: no visible binding for global variable ‘sampleID2’
rlm_normalise_matrix: no visible binding for global variable ‘slide’
rlm_normalise_matrix: no visible binding for global variable
  ‘sample_index’
rlm_normalise_matrix: no visible binding for global variable ‘antigen’
rlm_normalise_matrix: no visible binding for global variable ‘MFI_val’
rlm_normalise_matrix: no visible binding for global variable
  ‘sample_array_ID’
rlm_normalise_matrix: no visible binding for global variable ‘Block’
tag_subtract: no visible binding for global variable ‘TAG’
tag_subtract: no visible binding for global variable ‘TAG_name’
tag_subtract: no visible binding for global variable ‘TAG_mfi’
visualize_slide: no visible binding for global variable ‘Block’
visualize_slide: no visible binding for global variable ‘X’
visualize_slide: no visible binding for global variable ‘Y’
visualize_slide: no visible binding for global variable ‘meanX’
visualize_slide: no visible binding for global variable ‘meanY’
visualize_slide_2d: no visible binding for global variable ‘Block’
visualize_slide_2d: no visible binding for global variable ‘X’
visualize_slide_2d: no visible binding for global variable ‘Y’
visualize_slide_2d: no visible binding for global variable ‘meanX’
visualize_slide_2d: no visible binding for global variable ‘meanY’
Undefined global functions or variables:
  .id Array BGMedian BG_Median Block CVX CVX1_X2 CVX1_X3 CVX2_X3 Column
  Description FBG_Median FMedian FMedianBG_correct MFI MFI_val Name Row
  TAG TAG_mfi TAG_name X Y antigen antigen_name best_CV buffers
  day_batches global_BGMedian index log_bg log_fb machines
  meanBest2_RLM meanX meanX1_X2 meanX1_X3 meanX2_X3 meanY mean_all_anti
  mean_mfi minimum_BGMedian prop rank_mean_all_anti sampleID sampleID2
  sample_array_ID sample_index sdX sdX1_X2 sdX1_X3 sdX2_X3 sd_mfi
  selected slide stdev_all_anti temp v1 v2 val value variable x xbar
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/protGear.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL protGear
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘protGear’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
** testing if installed package can be loaded from final location
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
** testing if installed package keeps a record of temporary installation path
* DONE (protGear)