Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘protGear/DESCRIPTION’ ... OK
* preparing ‘protGear’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘protGear_0.99.542.tar.gz’

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 BiocCheckGitClone('protGear')

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This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2460/79c00667252888c06194e3363e6490620151f99a/protGear.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘protGear/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘protGear’ version ‘0.99.542’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'limma', 'magrittr', 'ggplot2', 'tidyr', 'data.table', 'ggpubr',
  'gtools', 'gridExtra', 'tibble', 'rlang', 'rmarkdown', 'knitr',
  'vsn', 'genefilter', 'readr', 'Biobase', 'plyr', 'Kendall', 'dplyr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [46s/47s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘magrittr::set_names’ by ‘rlang::set_names’ when loading ‘protGear’
  Warning: replacing previous import ‘gtools::chr’ by ‘rlang::chr’ when loading ‘protGear’
  Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘protGear’
  Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘protGear’
  Warning: replacing previous import ‘magrittr::extract’ by ‘tidyr::extract’ when loading ‘protGear’
  Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘protGear’
  Warning: replacing previous import ‘stats::lag’ by ‘dplyr::lag’ when loading ‘protGear’
  Warning: replacing previous import ‘shinydashboard::renderValueBox’ by ‘flexdashboard::renderValueBox’ when loading ‘protGear’
  Warning: replacing previous import ‘shinydashboard::valueBox’ by ‘flexdashboard::valueBox’ when loading ‘protGear’
  Warning: replacing previous import ‘shinydashboard::valueBoxOutput’ by ‘flexdashboard::valueBoxOutput’ when loading ‘protGear’
See ‘/Users/pkgbuild/packagebuilder/workers/jobs/2460/79c00667252888c06194e3363e6490620151f99a/protGear.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       4.5Mb
    extdata   1.3Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘rlang’ ‘factoextra’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘gridExtra’ ‘knitr’ ‘vsn’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘dplyr:::select’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [51s/54s] 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’
remove_batch_effect: no visible binding for global variable ‘bts’
remove_batch_effect: no visible binding for global variable ‘site’
remove_batch_effect: no visible binding for global variable
  ‘exprs_antigen_vsn’
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 bts buffers
  day_batches exprs_antigen_vsn 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 site slide stdev_all_anti temp v1 v2 val
  value variable x xbar
* checking Rd files ... [1s/1s] NOTE
prepare_Rd: error_replicates.Rd:18-20: Dropping empty section \examples
prepare_Rd: launch_select.Rd:18-20: Dropping empty section \examples
prepare_Rd: remove_batch_effect.Rd:15-17: Dropping empty section \examples
prepare_Rd: rlm_normalise.Rd:18-20: Dropping empty section \examples
prepare_Rd: rlm_normalise_matrix.Rd:22-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [44s/45s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘scales’
* 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 WARNING, 7 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2460/79c00667252888c06194e3363e6490620151f99a/protGear.Rcheck/00check.log’
for details.






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 BiocCheck('protGear_0.99.542.tar.gz')

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This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
  running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2460/79c00667252888c06194e3363e6490620151f99a/protGear_0.99.542.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp2fPRUQ/file2d0d178c7fc/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
    * NOTE: Update R version dependency from 4.1 to 4.2.0.
* Checking package size...
    * ERROR: Package Source tarball exceeds Bioconductor size
      requirement.
        Package Size: 5.4984 MB
        Size Requirement: 5.0000 MB
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
    * NOTE: Consider adding these automatically suggested biocViews:
      Transcription, Sequencing, ChipOnChip, Metabolomics, Epigenetics,
      Cheminformatics, Transcriptomics, Bayesian, Clustering,
      Regression, ExonArray, GeneExpression, RNASeq, TwoChannel,
      MicroRNAArray, mRNAMicroarray, ProprietaryPlatforms, CellBiology,
      FunctionalGenomics, SystemsBiology, ImmunoOncology,
      AlternativeSplicing, DifferentialExpression,
      DifferentialSplicing, GeneSetEnrichment, MultipleComparison,
      QualityControl, TimeCourse, DataImport
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2
Warning: replacing previous import ‘magrittr::set_names’ by ‘rlang::set_names’ when loading ‘protGear’
Warning: replacing previous import ‘gtools::chr’ by ‘rlang::chr’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘protGear’
Warning: replacing previous import ‘magrittr::extract’ by ‘tidyr::extract’ when loading ‘protGear’
Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘protGear’
Warning: replacing previous import ‘stats::lag’ by ‘dplyr::lag’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::renderValueBox’ by ‘flexdashboard::renderValueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBox’ by ‘flexdashboard::valueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBoxOutput’ by ‘flexdashboard::valueBoxOutput’ when loading ‘protGear’
* Checking .Rbuildignore...
* Checking vignette directory...
    * NOTE: 'sessionInfo' not found in vignette(s)
      Missing from file(s):
        vignettes/vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of protGear...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        buffer_spot_functions.R (line 19, column 24)
        cv_estimation_tag_functions.R (line 152, column 18)
        normalisation_functions.R (line 256, column 25)
        normalisation_functions.R (line 275, column 24)
        normalisation_functions.R (line 280, column 24)
        normalisation_functions.R (line 287, column 24)
        normalisation_functions.R (line 306, column 13)
        normalisation_functions.R (line 309, column 15)
        normalisation_functions.R (line 365, column 10)
        read_files_functions.R (line 113, column 34)
        read_files_functions.R (line 114, column 50)
        read_files_functions.R (line 132, column 20)
        read_files_functions.R (line 150, column 25)
        read_files_functions.R (line 173, column 24)
        read_files_functions.R (line 389, column 24)
        read_files_functions.R (line 407, column 26)
        read_files_functions.R (line 419, column 33)
        read_files_functions.R (line 432, column 26)
        read_files_functions.R (line 445, column 26)
        read_files_functions.R (line 462, column 26)
        read_files_functions.R (line 476, column 26)
        read_files_functions.R (line 503, column 35)
        read_files_functions.R (line 529, column 33)
        read_files_functions.R (line 590, column 34)
        read_files_functions.R (line 590, column 83)
        read_files_functions.R (line 606, column 20)
        read_files_functions.R (line 624, column 25)
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
      Found in files:
        print() in R/cv_estimation_tag_functions.R (line 67, column 11)
        print() in R/global_functions.R (line 165, column 3)
        print() in R/normalisation_functions.R (line 152, column 5)
        print() in R/read_files_functions.R (line 128, column 5)
        print() in R/read_files_functions.R (line 602, column 5)
    * NOTE: Avoid the use of 'paste' in condition signals
      Found in files:
        R/cv_estimation_tag_functions.R (line 40, column 17)
        R/cv_estimation_tag_functions.R (line 65, column 17)
        R/global_functions.R (line 128, column 17)
        R/read_files_functions.R (line 57, column 16)
        R/read_files_functions.R (line 112, column 13)
        R/read_files_functions.R (line 589, column 13)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 8 functions > 50 lines.
      The longest 5 functions are:
        rlm_normalise() (R/normalisation_functions.R, line 212): 197
      lines
        bg_correct() (R/read_files_functions.R, line 373): 162 lines
        matrix_normalise() (R/normalisation_functions.R, line 36): 100
      lines
        cv_estimation() (R/cv_estimation_tag_functions.R, line 22): 84
      lines
        extract_bg() (R/read_files_functions.R, line 103): 76 lines
* Checking man page documentation...
Warning: replacing previous import ‘magrittr::set_names’ by ‘rlang::set_names’ when loading ‘protGear’
Warning: replacing previous import ‘gtools::chr’ by ‘rlang::chr’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘protGear’
Warning: replacing previous import ‘magrittr::extract’ by ‘tidyr::extract’ when loading ‘protGear’
Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘protGear’
Warning: replacing previous import ‘stats::lag’ by ‘dplyr::lag’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::renderValueBox’ by ‘flexdashboard::renderValueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBox’ by ‘flexdashboard::valueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBoxOutput’ by ‘flexdashboard::valueBoxOutput’ when loading ‘protGear’
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      launch_protGear_interactive.Rd, launch_select.Rd,
  remove_batch_effect.Rd, rlm_normalise_matrix.Rd, rlm_normalise.Rd
* Checking package NEWS...
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 411 lines (11%) are > 80 characters
      long.
    First 6 lines:
      R/buffer_spot_functions.R:4 #' @param buffer_spot A character string co...
      R/buffer_spot_functions.R:7 #' @description A function to extract the b...
      R/buffer_spot_functions.R:13 #' bg_correct_df <- readr::read_csv(system...
      R/buffer_spot_functions.R:47 #' @param buffer_names A character string ...
      R/buffer_spot_functions.R:48 #' @param buffer_mfi A character string co...
      R/buffer_spot_functions.R:50 #' @param slide_id  A character string con...
    * NOTE: Consider 4 spaces instead of tabs; 4 lines (0%) contain
      tabs.
    First 4 lines:
      R/read_files_functions.R:186 #' @param df A 	default dataset to use for...
      R/read_files_functions.R:189 #' @param log_mfi 	a logical value indicat...
      R/read_files_functions.R:272 #' @param log_mfi 	a logical value indicat...
      R/read_files_functions.R:342 #' @param method 	a description of the bac...
    * NOTE: Consider multiples of 4 spaces for line indents, 862
      lines(23%) are not.
    First 6 lines:
      R/buffer_spot_functions.R:16   Data2_buffer <- Data1 %>%
      R/buffer_spot_functions.R:22                    antigen,
      R/buffer_spot_functions.R:23                    replicate,
      R/buffer_spot_functions.R:24                    FMedianBG_correct,
      R/buffer_spot_functions.R:25                    Block,
      R/buffer_spot_functions.R:26                    Column,
    See http://bioconductor.org/developers/how-to/coding-style/
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.


Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 12
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.

===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir protGear_0.99.542.tar.gz'
>>>>>>> 

* installing *source* package ‘protGear’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘magrittr::set_names’ by ‘rlang::set_names’ when loading ‘protGear’
Warning: replacing previous import ‘gtools::chr’ by ‘rlang::chr’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘protGear’
Warning: replacing previous import ‘magrittr::extract’ by ‘tidyr::extract’ when loading ‘protGear’
Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘protGear’
Warning: replacing previous import ‘stats::lag’ by ‘dplyr::lag’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::renderValueBox’ by ‘flexdashboard::renderValueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBox’ by ‘flexdashboard::valueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBoxOutput’ by ‘flexdashboard::valueBoxOutput’ when loading ‘protGear’
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘magrittr::set_names’ by ‘rlang::set_names’ when loading ‘protGear’
Warning: replacing previous import ‘gtools::chr’ by ‘rlang::chr’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘protGear’
Warning: replacing previous import ‘magrittr::extract’ by ‘tidyr::extract’ when loading ‘protGear’
Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘protGear’
Warning: replacing previous import ‘stats::lag’ by ‘dplyr::lag’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::renderValueBox’ by ‘flexdashboard::renderValueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBox’ by ‘flexdashboard::valueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBoxOutput’ by ‘flexdashboard::valueBoxOutput’ when loading ‘protGear’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘magrittr::set_names’ by ‘rlang::set_names’ when loading ‘protGear’
Warning: replacing previous import ‘gtools::chr’ by ‘rlang::chr’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘protGear’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘protGear’
Warning: replacing previous import ‘magrittr::extract’ by ‘tidyr::extract’ when loading ‘protGear’
Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘protGear’
Warning: replacing previous import ‘stats::lag’ by ‘dplyr::lag’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::renderValueBox’ by ‘flexdashboard::renderValueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBox’ by ‘flexdashboard::valueBox’ when loading ‘protGear’
Warning: replacing previous import ‘shinydashboard::valueBoxOutput’ by ‘flexdashboard::valueBoxOutput’ when loading ‘protGear’
** testing if installed package keeps a record of temporary installation path
* DONE (protGear)