############################################################################## ############################################################################## ### ### 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_1.18.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/HPAanalyze.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HPAanalyze/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HPAanalyze’ version ‘1.18.1’ * 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 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 hpaDownload: no visible binding for global variable ‘datasetnames’ hpaDownload: no visible binding for global variable ‘hpa_histology_data’ hpaDownload: no visible binding for global variable ‘.’ 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: . age cancer cell_line cell_type datasetnames gene high hpa_histology_data imageUrl index intensity level low medium not_detected patientId patient_count quantity sex staining sub_location tissue tissue_cell * 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 6.383 0.109 8.506 hpaVisTissue 3.868 0.130 5.343 hpaVisSubcell 3.717 0.086 5.094 * 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-3.17-bioc/meat/HPAanalyze.Rcheck/00check.log’ for details.