Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 959/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HPAanalyze 1.23.0 (landing page) Anh Nhat Tran
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the HPAanalyze package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HPAanalyze.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: HPAanalyze |
Version: 1.23.0 |
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_1.23.0.tar.gz |
StartedAt: 2024-06-10 22:22:18 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 22:24:10 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 112.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: HPAanalyze.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/HPAanalyze.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HPAanalyze/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HPAanalyze’ version ‘1.23.0’ * 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 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 : <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: . 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 * 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-3.20-bioc/meat/HPAanalyze.Rcheck/00check.log’ for details.
HPAanalyze.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HPAanalyze ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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 | 2.173 | 0.107 | 2.290 | |
hpaExport | 0.460 | 0.048 | 0.512 | |
hpaListParam | 0.126 | 0.022 | 0.148 | |
hpaVis | 1.151 | 0.035 | 1.191 | |
hpaVisPatho | 3.747 | 0.163 | 3.940 | |
hpaVisSubcell | 2.431 | 0.122 | 2.564 | |
hpaVisTissue | 2.493 | 0.116 | 2.617 | |
hpaXml | 0.180 | 0.031 | 0.901 | |
hpaXmlAntibody | 0.000 | 0.001 | 0.000 | |
hpaXmlGet | 0 | 0 | 0 | |
hpaXmlProtClass | 0 | 0 | 0 | |
hpaXmlTissueExpr | 0 | 0 | 0 | |
hpaXmlTissueExprSum | 0 | 0 | 0 | |
hpa_histology_data | 1.830 | 0.110 | 1.954 | |