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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HPAanalyze_1.26.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/HPAanalyze.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HPAanalyze/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HPAanalyze’ version ‘1.26.1’
* 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 ‘HPAanalyze’ 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 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
gene_ensembl_convert: no visible binding for global variable
  ‘lookup_df’
hpaDownload: no visible binding for global variable
  ‘hpa_histology_data’
hpaDownload: no visible binding for global variable ‘Gene’
hpaDownload: no visible binding for global variable ‘Gene name’
hpaDownload: no visible binding for global variable ‘Tissue’
hpaDownload: no visible binding for global variable ‘Cell type’
hpaDownload: no visible binding for global variable ‘Level’
hpaDownload: no visible binding for global variable ‘Reliability’
hpaDownload: no visible binding for global variable ‘Cancer’
hpaDownload: no visible binding for global variable ‘High’
hpaDownload: no visible binding for global variable ‘Medium’
hpaDownload: no visible binding for global variable ‘Low’
hpaDownload: no visible binding for global variable ‘Not detected’
hpaDownload: no visible binding for global variable ‘Main location’
hpaDownload: no visible binding for global variable ‘Additional
  location’
hpaDownload: no visible binding for global variable ‘Extracellular
  location’
hpaDownload: no visible binding for global variable ‘Enhanced’
hpaDownload: no visible binding for global variable ‘Supported’
hpaDownload: no visible binding for global variable ‘Approved’
hpaDownload: no visible binding for global variable ‘Uncertain’
hpaDownload: no visible binding for global variable ‘Single-cell
  variation intensity’
hpaDownload: no visible binding for global variable ‘Single-cell
  variation spatial’
hpaDownload: no visible binding for global variable ‘Cell cycle
  dependency’
hpaDownload: no visible binding for global variable ‘GO id’
hpaSubset : subsetting: no visible binding for global variable ‘gene’
hpaSubset : subsetting: no visible binding for global variable ‘tissue’
hpaSubset : subsetting: no visible binding for global variable
  ‘cell_type’
hpaSubset : subsetting: no visible binding for global variable ‘cancer’
hpaSubset : subsetting: no visible binding for global variable
  ‘cell_line’
hpaVis: no visible binding for global variable ‘hpa_histology_data’
hpaVisPatho: no visible binding for global variable ‘gene’
hpaVisPatho: no visible binding for global variable ‘cancer’
hpaVisPatho: no visible binding for global variable ‘high’
hpaVisPatho: no visible binding for global variable ‘medium’
hpaVisPatho: no visible binding for global variable ‘low’
hpaVisPatho: no visible binding for global variable ‘not_detected’
hpaVisPatho: no visible binding for global variable ‘patient_count’
hpaVisPatho: no visible binding for global variable ‘level’
hpaVisSubcell: no visible binding for global variable ‘gene’
hpaVisSubcell: no visible binding for global variable ‘sub_location’
hpaVisTissue: no visible binding for global variable ‘gene’
hpaVisTissue: no visible binding for global variable ‘.’
hpaVisTissue: no visible binding for global variable ‘tissue’
hpaVisTissue: no visible binding for global variable ‘cell_type’
hpaVisTissue: no visible binding for global variable ‘level’
hpaVisTissue: no visible binding for global variable ‘tissue_cell’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘patientId’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘age’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘sex’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘staining’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘intensity’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘quantity’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘imageUrl’
hpaXmlTissueExprSum: no visible binding for global variable ‘tissue’
hpaXmlTissueExprSum: no visible binding for global variable ‘imageUrl’
is_null_data: no visible binding for global variable
  ‘hpa_histology_data’
named_vector_list_to_tibble: no visible binding for global variable
  ‘index’
Undefined global functions or variables:
  . Additional location Approved Cancer Cell cycle dependency Cell type
  Enhanced Extracellular location GO id Gene Gene name High Level Low
  Main location Medium Not detected Reliability Single-cell variation
  intensity Single-cell variation spatial Supported Tissue Uncertain
  age cancer cell_line cell_type gene high hpa_histology_data imageUrl
  index intensity level lookup_df low medium not_detected patientId
  patient_count quantity sex staining sub_location tissue tissue_cell
Consider adding
  importFrom("stats", "cycle")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
hpaVisPatho 5.67  0.086   6.054
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/HPAanalyze.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HPAanalyze
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘HPAanalyze’ ...
** this is package ‘HPAanalyze’ version ‘1.26.1’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HPAanalyze)