Anh Nhat Tran
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/HPAanalyze |
| Branch: RELEASE_3_9 |
| Last Commit: 75c6aa5 |
| Last Changed Date: 2019-06-19 17:29:31 -0400 (Wed, 19 Jun 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:03:10 -0400 (Wed, 16 Oct 2019).
| Package 768/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| HPAanalyze 1.2.1 Anh Nhat Tran
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: HPAanalyze |
| Version: 1.2.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HPAanalyze_1.2.1.tar.gz |
| StartedAt: 2019-10-16 03:42:13 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:43:51 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 98.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HPAanalyze.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HPAanalyze_1.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/HPAanalyze.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HPAanalyze/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HPAanalyze’ version ‘1.2.1’ * 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 ‘hpaNormalTissue’ hpaDownload: no visible binding for global variable ‘hpaCancer’ hpaDownload: no visible binding for global variable ‘Total.patients’ hpaDownload: no visible binding for global variable ‘Level’ hpaDownload: no visible binding for global variable ‘Count.patients’ hpaDownload: no visible binding for global variable ‘hpaSubcellularLoc’ hpaDownload: no visible binding for global variable ‘rnaGeneTissue’ hpaDownload: no visible binding for global variable ‘rnaGeneCellLine’ hpaSubset: no visible binding for global variable ‘gene’ hpaSubset: no visible binding for global variable ‘tissue’ hpaSubset: no visible binding for global variable ‘cell_type’ hpaSubset: no visible binding for global variable ‘cancer’ hpaSubset: no visible binding for global variable ‘cell_line’ 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’ hpaVisSubcell: no visible binding for global variable ‘enhanced’ hpaVisSubcell: no visible binding for global variable ‘supported’ hpaVisSubcell: no visible binding for global variable ‘approved’ hpaVisSubcell: no visible binding for global variable ‘uncertain’ hpaVisTissue: no visible binding for global variable ‘gene’ 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’ named_vector_list_to_tibble: no visible binding for global variable ‘index’ named_vector_list_to_tibble: no visible binding for global variable ‘value’ Undefined global functions or variables: Count.patients Level Total.patients age approved cancer cell_line cell_type enhanced gene high hpaCancer hpaNormalTissue hpaSubcellularLoc imageUrl index intensity level low medium not_detected patientId patient_count quantity rnaGeneCellLine rnaGeneTissue sex staining sub_location supported tissue tissue_cell uncertain value * 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 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 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-3.9-bioc/meat/HPAanalyze.Rcheck/00check.log’ for details.
HPAanalyze.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HPAanalyze ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘HPAanalyze’ ... ** 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)
HPAanalyze.Rcheck/HPAanalyze-Ex.timings
| name | user | system | elapsed | |
| hpaDownload | 1.754 | 0.328 | 2.081 | |
| hpaExport | 0.500 | 0.112 | 0.616 | |
| hpaListParam | 0.115 | 0.047 | 0.162 | |
| hpaVis | 1.732 | 0.107 | 1.841 | |
| hpaVisPatho | 4.000 | 0.349 | 4.484 | |
| hpaVisSubcell | 1.729 | 0.135 | 1.863 | |
| hpaVisTissue | 1.804 | 0.155 | 1.958 | |
| hpaXml | 0.540 | 0.047 | 2.307 | |
| hpaXmlAntibody | 0.000 | 0.000 | 0.001 | |
| hpaXmlGet | 0.001 | 0.001 | 0.001 | |
| hpaXmlProtClass | 0.000 | 0.000 | 0.001 | |
| hpaXmlTissueExpr | 0.001 | 0.000 | 0.000 | |
| hpaXmlTissueExprSum | 0.000 | 0.001 | 0.000 | |
| hpa_downloaded_histology_v18 | 1.293 | 0.238 | 1.530 | |