Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-01 11:36:10 -0400 (Wed, 01 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
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 2037/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpatialOmicsOverlay 1.4.0 (landing page) Maddy Griswold
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the SpatialOmicsOverlay package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialOmicsOverlay.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: SpatialOmicsOverlay |
Version: 1.4.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SpatialOmicsOverlay.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SpatialOmicsOverlay_1.4.0.tar.gz |
StartedAt: 2024-05-01 10:15:19 -0400 (Wed, 01 May 2024) |
EndedAt: 2024-05-01 10:16:44 -0400 (Wed, 01 May 2024) |
EllapsedTime: 84.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: SpatialOmicsOverlay.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SpatialOmicsOverlay.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SpatialOmicsOverlay_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialOmicsOverlay.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: x86_64-pc-linux-gnu * 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 ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK * this is package ‘SpatialOmicsOverlay’ version ‘1.4.0’ * 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 ‘SpatialOmicsOverlay’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... WARNING Error: package or namespace load failed for ‘SpatialOmicsOverlay’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘BiocFileCache’ Execution halted It looks like this package has a loading problem when not on .libPaths: see the messages for details. * checking dependencies in R code ... NOTE Error: there is no package called ‘Biobase’ Call sequence: 8: doWithOneRestart(return(expr), restart) 7: withOneRestart(expr, restarts[[1L]]) 6: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 1: loadNamespace(package, lib.loc) Execution halted * checking S3 generic/method consistency ... WARNING Error: there is no package called ‘Biobase’ Call sequence: 8: doWithOneRestart(return(expr), restart) 7: withOneRestart(expr, restarts[[1L]]) 6: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 1: loadNamespace(package, lib.loc) Execution halted See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Error: there is no package called ‘Biobase’ Call sequence: 8: doWithOneRestart(return(expr), restart) 7: withOneRestart(expr, restarts[[1L]]) 6: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 1: loadNamespace(package, lib.loc) Execution halted The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Error: there is no package called ‘S4Vectors’ Call sequence: 6: doWithOneRestart(return(expr), restart) 5: withOneRestart(expr, restarts[[1L]]) 4: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 1: loadNamespace(package, lib.loc) Execution halted See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called ‘S4Vectors’ Calls: <Anonymous> Execution halted * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Error: package or namespace load failed for ‘SpatialOmicsOverlay’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘S4Vectors’ Call sequence: 6: stop(msg, call. = FALSE, domain = NA) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc, Execution halted All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Error: package or namespace load failed for ‘SpatialOmicsOverlay’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘S4Vectors’ Call sequence: 6: stop(msg, call. = FALSE, domain = NA) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc, Execution halted Error: package or namespace load failed for ‘SpatialOmicsOverlay’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘S4Vectors’ Call sequence: 6: stop(msg, call. = FALSE, domain = NA) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc, Execution halted Error: package or namespace load failed for ‘SpatialOmicsOverlay’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘S4Vectors’ Call sequence: 6: stop(msg, call. = FALSE, domain = NA) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc, Execution halted * checking Rd \usage sections ... NOTE Error: there is no package called ‘S4Vectors’ Call sequence: 6: doWithOneRestart(return(expr), restart) 5: withOneRestart(expr, restarts[[1L]]) 4: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 1: loadNamespace(package, lib.loc) Execution halted The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘SpatialOmicsOverlay-Ex.R’ failed The error occurred in: R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. Natural language support but running in an English locale 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. > pkgname <- "SpatialOmicsOverlay" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > base::assign(".ExTimings", "SpatialOmicsOverlay-Ex.timings", pos = 'CheckExEnv') > base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv')) > base::assign(".format_ptime", + function(x) { + if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L] + if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L] + options(OutDec = '.') + format(x[1L:3L], digits = 7L) + }, + pos = 'CheckExEnv') > > ### * </HEADER> > library('SpatialOmicsOverlay') Error: package or namespace load failed for ‘SpatialOmicsOverlay’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘S4Vectors’ Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(vdiffr) > > options( java.parameters = "-Xmx4g" ) > library( "RBioFormats" ) Error: package or namespace load failed for 'RBioFormats' in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'S4Vectors' Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘SpatialOmicsOverlay.Rmd’ using rmarkdown Quitting from lines at lines 16-25 [setup] (SpatialOmicsOverlay.Rmd) Error: processing vignette 'SpatialOmicsOverlay.Rmd' failed with diagnostics: package or namespace load failed for 'RBioFormats' in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'S4Vectors' --- failed re-building ‘SpatialOmicsOverlay.Rmd’ SUMMARY: processing the following file failed: ‘SpatialOmicsOverlay.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 5 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialOmicsOverlay.Rcheck/00check.log’ for details.
SpatialOmicsOverlay.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SpatialOmicsOverlay ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘SpatialOmicsOverlay’ ... ** using staged installation ** R ** 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 (SpatialOmicsOverlay)
SpatialOmicsOverlay.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(vdiffr) > > options( java.parameters = "-Xmx4g" ) > library( "RBioFormats" ) Error: package or namespace load failed for 'RBioFormats' in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'S4Vectors' Execution halted
SpatialOmicsOverlay.Rcheck/SpatialOmicsOverlay-Ex.timings
name | user | system | elapsed |