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_0.99.2.tar.gz’

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 BiocCheckGitClone('protGear')

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This is BiocCheckGitClone version 1.31.29. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
    * ERROR: System Files found that should not be git tracked:
        protGear.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...


Summary:
ERROR count: 1
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
BiocCheckGitClone FAILED.




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2460/fd64ad63a2999048ed3b60ce1ee35a0500bf6089/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 ‘0.99.2’
* 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', '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 ... [49s/49s] 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/fd64ad63a2999048ed3b60ce1ee35a0500bf6089/protGear.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 20.9Mb
  sub-directories of 1Mb or more:
    doc              4.6Mb
    extdata         14.5Mb
    shiny-examples   1.5Mb
* 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 ... [42s/42s] 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 ... [55s/55s] OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
plot_bg 7.452  0.046   7.545
* 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/fd64ad63a2999048ed3b60ce1ee35a0500bf6089/protGear.Rcheck/00check.log’
for details.






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 BiocCheck('protGear_0.99.2.tar.gz')

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This is BiocCheck version 1.31.29. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
  cmd: /Library/Frameworks/R.framework/Resources/bin/R
  args: --vanilla CMD INSTALL --no-test-load --library=/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp0bg5y4/file193210b72e38/lib '/Users/pkgbuild/packagebuilder/workers/jobs/2460/fd64ad63a2999048ed3b60ce1ee35a0500bf6089/protGear_0.99.2.tar.gz'
  stderr:
  ERROR: dependency ‘trend’ is not available for package ‘protGear’
  * removing ‘/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/Rtmp0bg5y4/file193210b72e38/lib/protGear’

    * ERROR:
      /Users/pkgbuild/packagebuilder/workers/jobs/2460/fd64ad63a2999048ed3b60ce1ee35a0500bf6089/protGear_0.99.2.tar.gz
      must be installable.
  cmd: /Library/Frameworks/R.framework/Resources/bin/R
  args: --vanilla -e 'library(protGear)'
  stderr:
  Error in library(protGear) : there is no package called ‘protGear’
  Execution halted

    * ERROR:
      /Users/pkgbuild/packagebuilder/workers/jobs/2460/fd64ad63a2999048ed3b60ce1ee35a0500bf6089/protGear_0.99.2.tar.gz
      must be loadable.
* Checking Package Dependencies...
Warning in packageDescription(pkgname, lib.loc = lib.loc) :
  no package 'protGear' was found
Error: $ operator is invalid for atomic vectors
Execution halted

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir protGear_0.99.2.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)