Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:05 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 985/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HPAanalyze 1.27.2 (landing page) Anh Nhat Tran
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 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: 1.27.2 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HPAanalyze_1.27.2.tar.gz |
StartedAt: 2025-08-08 23:17:58 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 23:19:57 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 119.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: HPAanalyze.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HPAanalyze_1.27.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/HPAanalyze.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * 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 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 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 : <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: . 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/HPAanalyze.Rcheck/00check.log’ for details.
HPAanalyze.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL HPAanalyze ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘HPAanalyze’ ... ** this is package ‘HPAanalyze’ version ‘1.27.2’ ** 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 | 1.300 | 0.211 | 1.513 | |
hpaExport | 0.446 | 0.037 | 0.482 | |
hpaListParam | 0.106 | 0.045 | 0.151 | |
hpaVis | 1.047 | 0.039 | 1.085 | |
hpaVisPatho | 2.544 | 0.226 | 2.770 | |
hpaVisSubcell | 1.467 | 0.224 | 1.691 | |
hpaVisTissue | 1.483 | 0.222 | 1.706 | |
hpaXml | 0.232 | 0.029 | 2.986 | |
hpaXmlAntibody | 0.106 | 0.009 | 2.767 | |
hpaXmlGet | 0.053 | 0.012 | 2.503 | |
hpaXmlProtClass | 0.119 | 0.066 | 2.510 | |
hpaXmlTissueExpr | 0.000 | 0.001 | 0.000 | |
hpaXmlTissueExprSum | 0.100 | 0.031 | 2.576 | |
hpa_histology_data | 1.128 | 0.201 | 1.329 | |