############################################################################## ############################################################################## ### ### Running command: ### ### /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_1.27.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/HPAanalyze.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HPAanalyze/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HPAanalyze’ version ‘1.27.2’ * 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 : : no visible binding for global variable ‘patientId’ hpaXmlTissueExpr : : no visible binding for global variable ‘age’ hpaXmlTissueExpr : : no visible binding for global variable ‘sex’ hpaXmlTissueExpr : : no visible binding for global variable ‘staining’ hpaXmlTissueExpr : : no visible binding for global variable ‘intensity’ hpaXmlTissueExpr : : no visible binding for global variable ‘quantity’ hpaXmlTissueExpr : : 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 * 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-3.22-bioc/meat/HPAanalyze.Rcheck/00check.log’ for details.