Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 836/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GEOexplorer 1.12.0 (landing page) Guy Hunt
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the GEOexplorer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GEOexplorer.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: GEOexplorer |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GEOexplorer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GEOexplorer_1.12.0.tar.gz |
StartedAt: 2024-11-19 22:30:11 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 22:38:58 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 526.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GEOexplorer.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GEOexplorer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GEOexplorer_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GEOexplorer.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GEOexplorer/DESCRIPTION’ ... OK * this is package ‘GEOexplorer’ version ‘1.12.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘GEOexplorer’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘GEOexplorer’ Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘GEOexplorer’ See ‘/Users/biocbuild/bbs-3.20-bioc/meat/GEOexplorer.Rcheck/00install.out’ for details. * 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 combineExpressionData: no visible binding for global variable ‘rowname’ removeLowlyExpressedGenes: no visible binding for global variable ‘rnaExpressionData’ removeLowlyExpressedGenes: no visible binding for global variable ‘group’ Undefined global functions or variables: group rnaExpressionData rowname * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/GEOexplorer.Rcheck/00check.log’ for details.
GEOexplorer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GEOexplorer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘GEOexplorer’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘GEOexplorer’ Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘GEOexplorer’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘GEOexplorer’ Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘GEOexplorer’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘GEOexplorer’ Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘GEOexplorer’ ** testing if installed package keeps a record of temporary installation path * DONE (GEOexplorer)
GEOexplorer.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(GEOexplorer) Loading required package: shiny Loading required package: limma Loading required package: Biobase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following object is masked from 'package:limma': plotMA The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: plotly Loading required package: ggplot2 Attaching package: 'plotly' The following object is masked from 'package:ggplot2': last_plot The following object is masked from 'package:stats': filter The following object is masked from 'package:graphics': layout Loading required package: enrichR Welcome to enrichR Checking connection ... Enrichr ... Connection is Live! FlyEnrichr ... Connection is Live! WormEnrichr ... Connection is Live! YeastEnrichr ... Connection is Live! FishEnrichr ... Connection is Live! OxEnrichr ... Connection is Live! Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Warning messages: 1: replacing previous import 'shiny::dataTableOutput' by 'DT::dataTableOutput' when loading 'GEOexplorer' 2: replacing previous import 'shiny::renderDataTable' by 'DT::renderDataTable' when loading 'GEOexplorer' > > test_check("GEOexplorer") Found 1 file(s) GSE178351_series_matrix.txt.gz Annotation GPL not available, so will use submitter GPL instead Cluster size 24351 broken into 8281 16070 Cluster size 8281 broken into 6052 2229 Cluster size 6052 broken into 3427 2625 Cluster size 3427 broken into 1621 1806 Cluster size 1621 broken into 830 791 Done cluster 830 Done cluster 791 Done cluster 1621 Cluster size 1806 broken into 850 956 Done cluster 850 Done cluster 956 Done cluster 1806 Done cluster 3427 Cluster size 2625 broken into 1160 1465 Done cluster 1160 Done cluster 1465 Done cluster 2625 Done cluster 6052 Cluster size 2229 broken into 749 1480 Done cluster 749 Done cluster 1480 Done cluster 2229 Done cluster 8281 Cluster size 16070 broken into 7624 8446 Cluster size 7624 broken into 3559 4065 Cluster size 3559 broken into 1881 1678 Cluster size 1881 broken into 908 973 Done cluster 908 Done cluster 973 Done cluster 1881 Cluster size 1678 broken into 789 889 Done cluster 789 Done cluster 889 Done cluster 1678 Done cluster 3559 Cluster size 4065 broken into 1962 2103 Cluster size 1962 broken into 1058 904 Done cluster 1058 Done cluster 904 Done cluster 1962 Cluster size 2103 broken into 972 1131 Done cluster 972 Done cluster 1131 Done cluster 2103 Done cluster 4065 Done cluster 7624 Cluster size 8446 broken into 4144 4302 Cluster size 4144 broken into 2283 1861 Cluster size 2283 broken into 1197 1086 Done cluster 1197 Done cluster 1086 Done cluster 2283 Cluster size 1861 broken into 1234 627 Done cluster 1234 Done cluster 627 Done cluster 1861 Done cluster 4144 Cluster size 4302 broken into 2165 2137 Cluster size 2165 broken into 1098 1067 Done cluster 1098 Done cluster 1067 Done cluster 2165 Cluster size 2137 broken into 990 1147 Done cluster 990 Done cluster 1147 Done cluster 2137 Done cluster 4302 Done cluster 8446 Done cluster 16070 Uploading data to Enrichr... Done. Querying GO_Biological_Process_2015... Done. Parsing results... Done. Uploading data to Enrichr... Done. Querying GO_Biological_Process_2015... Done. Parsing results... Done. Uploading data to Enrichr... Done. Querying GO_Biological_Process_2015... Done. Parsing results... Done. Found 2 file(s) GSE18380-GPL4694_series_matrix.txt.gz Annotation GPL not available, so will use submitter GPL instead GSE18380-GPL9270_series_matrix.txt.gz Annotation GPL not available, so will use submitter GPL instead Cluster size 3877 broken into 207 3670 Done cluster 207 Cluster size 3670 broken into 2511 1159 Cluster size 2511 broken into 631 1880 Done cluster 631 Cluster size 1880 broken into 862 1018 Done cluster 862 Done cluster 1018 Done cluster 1880 Done cluster 2511 Done cluster 1159 Done cluster 3670 Uploading data to Enrichr... Done. Querying GO_Biological_Process_2015... Done. Parsing results... Done. Uploading data to Enrichr... Done. Querying GO_Biological_Process_2015... Done. Parsing results... Done. Uploading data to Enrichr... Done. Querying GO_Biological_Process_2015... Done. Parsing results... Done. Found 1 file(s) GSE2_series_matrix.txt.gz Uploading data to Enrichr... Done. Querying GO_Biological_Process_2015... Done. Parsing results... Done. Uploading data to Enrichr... Done. Querying GO_Biological_Process_2015... Done. Parsing results... Done. Uploading data to Enrichr... Done. Querying GO_Biological_Process_2015... Done. Parsing results... Done. Found 1 file(s) GSE25758_series_matrix.txt.gz Annotation GPL not available, so will use submitter GPL instead Found 1 file(s) GSE25743_series_matrix.txt.gz Coefficients not estimable: Group2 Found 1 file(s) GSE18388_series_matrix.txt.gz Cluster size 35557 broken into 16183 19374 Cluster size 16183 broken into 11259 4924 Cluster size 11259 broken into 5209 6050 Cluster size 5209 broken into 2416 2793 Cluster size 2416 broken into 1584 832 Cluster size 1584 broken into 1008 576 Done cluster 1008 Done cluster 576 Done cluster 1584 Done cluster 832 Done cluster 2416 Cluster size 2793 broken into 1244 1549 Done cluster 1244 Cluster size 1549 broken into 679 870 Done cluster 679 Done cluster 870 Done cluster 1549 Done cluster 2793 Done cluster 5209 Cluster size 6050 broken into 3104 2946 Cluster size 3104 broken into 2426 678 Cluster size 2426 broken into 1633 793 Cluster size 1633 broken into 867 766 Done cluster 867 Done cluster 766 Done cluster 1633 Done cluster 793 Done cluster 2426 Done cluster 678 Done cluster 3104 Cluster size 2946 broken into 956 1990 Done cluster 956 Cluster size 1990 broken into 931 1059 Done cluster 931 Done cluster 1059 Done cluster 1990 Done cluster 2946 Done cluster 6050 Done cluster 11259 Cluster size 4924 broken into 3516 1408 Cluster size 3516 broken into 2071 1445 Cluster size 2071 broken into 1035 1036 Done cluster 1035 Done cluster 1036 Done cluster 2071 Done cluster 1445 Done cluster 3516 Done cluster 1408 Done cluster 4924 Done cluster 16183 Cluster size 19374 broken into 11322 8052 Cluster size 11322 broken into 5302 6020 Cluster size 5302 broken into 2454 2848 Cluster size 2454 broken into 1303 1151 Done cluster 1303 Done cluster 1151 Done cluster 2454 Cluster size 2848 broken into 1028 1820 Done cluster 1028 Cluster size 1820 broken into 436 1384 Done cluster 436 Done cluster 1384 Done cluster 1820 Done cluster 2848 Done cluster 5302 Cluster size 6020 broken into 3023 2997 Cluster size 3023 broken into 1295 1728 Done cluster 1295 Cluster size 1728 broken into 572 1156 Done cluster 572 Done cluster 1156 Done cluster 1728 Done cluster 3023 Cluster size 2997 broken into 1614 1383 Cluster size 1614 broken into 647 967 Done cluster 647 Done cluster 967 Done cluster 1614 Done cluster 1383 Done cluster 2997 Done cluster 6020 Done cluster 11322 Cluster size 8052 broken into 3117 4935 Cluster size 3117 broken into 1804 1313 Cluster size 1804 broken into 972 832 Done cluster 972 Done cluster 832 Done cluster 1804 Done cluster 1313 Done cluster 3117 Cluster size 4935 broken into 2290 2645 Cluster size 2290 broken into 1648 642 Cluster size 1648 broken into 912 736 Done cluster 912 Done cluster 736 Done cluster 1648 Done cluster 642 Done cluster 2290 Cluster size 2645 broken into 1263 1382 Done cluster 1263 Done cluster 1382 Done cluster 2645 Done cluster 4935 Done cluster 8052 Done cluster 19374 Uploading data to Enrichr... Done. Querying GO_Biological_Process_2015... Done. Parsing results... Done. Uploading data to Enrichr... Done. Querying GO_Biological_Process_2015... Done. Parsing results... Done. Uploading data to Enrichr... Done. Querying GO_Biological_Process_2015... Done. Parsing results... Done. Uploading data to Enrichr... Done. Querying GO_Biological_Process_2015... Done. Parsing results... Done. [ FAIL 0 | WARN 49 | SKIP 1 | PASS 2001 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'testGeoSearch.R:3:1' [ FAIL 0 | WARN 49 | SKIP 1 | PASS 2001 ] > > proc.time() user system elapsed 68.966 6.237 91.886
GEOexplorer.Rcheck/GEOexplorer-Ex.timings
name | user | system | elapsed | |
loadApp | 0.514 | 0.046 | 0.564 | |