Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:01 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 971/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HPAanalyze 1.20.0 (landing page) Anh Nhat Tran
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.20.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings HPAanalyze_1.20.0.tar.gz |
StartedAt: 2024-04-15 23:49:37 -0400 (Mon, 15 Apr 2024) |
EndedAt: 2024-04-15 23:52:32 -0400 (Mon, 15 Apr 2024) |
EllapsedTime: 174.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: HPAanalyze.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings HPAanalyze_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/HPAanalyze.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘HPAanalyze/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HPAanalyze’ version ‘1.20.0’ * 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 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 loading without being on the library search path ... 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘a_HPAanalyze_quick_start.Rmd’ using ‘UTF-8’... OK ‘b_HPAanalyze_indepth.Rmd’ using ‘UTF-8’... OK ‘c_HPAanalyze_case_query.Rmd’ using ‘UTF-8’... failed ‘d_HPAanalyze_case_offline_xml.Rmd’ using ‘UTF-8’... OK ‘e_HPAanalyze_case_json.Rmd’ using ‘UTF-8’... OK ‘f_HPAanalyze_case_images.Rmd’ using ‘UTF-8’... OK ‘z_HPAanalyze_paper_figures.Rmd’ using ‘UTF-8’... failed WARNING Errors in running code in vignettes: when running code in ‘c_HPAanalyze_case_query.Rmd’ ... intersect, setdiff, setequal, union > library(tibble) > library(readr) When sourcing ‘c_HPAanalyze_case_query.R’: Error: there is no package called ‘readr’ Execution halted when running code in ‘z_HPAanalyze_paper_figures.Rmd’ ... > plot_2a <- hpaVisTissue(data = data, targetGene = gene_list_2, + targetTissue = tissue_list_2, color = c("#eff3ff", "#bdd7e7", + "#6ba ..." ... [TRUNCATED] * WARNING: targetCellType variable not specified, visualize all. >> Use hpaListParam() to list possible values for target variables. When sourcing ‘z_HPAanalyze_paper_figures.R’: Error: no applicable method for 'filter' applied to an object of class "NULL" Execution halted * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/HPAanalyze.Rcheck/00check.log’ for details.
HPAanalyze.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL HPAanalyze ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 | 1.597 | 0.212 | 1.809 | |
hpaExport | 0.416 | 0.060 | 0.476 | |
hpaListParam | 0.100 | 0.044 | 0.144 | |
hpaVis | 1.152 | 0.047 | 1.200 | |
hpaVisPatho | 3.014 | 0.276 | 3.291 | |
hpaVisSubcell | 1.871 | 0.264 | 2.136 | |
hpaVisTissue | 1.856 | 0.296 | 2.152 | |
hpaXml | 0.243 | 0.017 | 4.068 | |
hpaXmlAntibody | 0 | 0 | 0 | |
hpaXmlGet | 0 | 0 | 0 | |
hpaXmlProtClass | 0 | 0 | 0 | |
hpaXmlTissueExpr | 0 | 0 | 0 | |
hpaXmlTissueExprSum | 0 | 0 | 0 | |
hpa_histology_data | 1.437 | 0.223 | 1.660 | |