Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2023-08-14 11:32:16 -0400 (Mon, 14 Aug 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.3.1 Ventura | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4334 |
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 198/2216 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biodbMirbase 1.5.0 (landing page) Pierrick Roger
| kjohnson1 | macOS 13.3.1 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
To the developers/maintainers of the biodbMirbase package: - 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: biodbMirbase |
Version: 1.5.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbMirbase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbMirbase_1.5.0.tar.gz |
StartedAt: 2023-08-11 10:55:11 -0400 (Fri, 11 Aug 2023) |
EndedAt: 2023-08-11 10:55:58 -0400 (Fri, 11 Aug 2023) |
EllapsedTime: 46.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biodbMirbase.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbMirbase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbMirbase_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/biodbMirbase.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * 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 13.3.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘biodbMirbase/DESCRIPTION’ ... OK * this is package ‘biodbMirbase’ version ‘1.5.0’ * 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 ‘biodbMirbase’ can be installed ... OK * checking installed package size ... OK * checking package 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 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 ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘MirbaseMatureConn’ ‘MirbaseMatureEntry’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa' Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`) 3. └─conn$getEntryIds(max.results = max) 4. └─private$doGetEntryIds(max.results = max.results, ...) 5. └─self$download() 6. └─private$doDownload() 7. └─sched$downloadFile(url = url, dest.file = self$getDownloadPath()) 8. └─utils::download.file(...) [ FAIL 6 | WARN 6 | SKIP 0 | PASS 40 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/biodbMirbase.Rcheck/00check.log’ for details.
biodbMirbase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbMirbase ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘biodbMirbase’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help No man pages found in package ‘biodbMirbase’ *** 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 (biodbMirbase)
biodbMirbase.Rcheck/tests/testthat.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 (64-bit) 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. > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbMirbase) > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbMirbase") trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa' trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa' trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa' trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa' trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa' trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa' [ FAIL 6 | WARN 6 | SKIP 0 | PASS 40 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error (???): RT unit is defined when there is an RT value. ────────────────── Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa' Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`) 3. └─conn$getBiodb()$getFactory()$getEntry(...) 4. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 5. └─conn$getEntryContent(ids) 6. └─self$download() 7. └─private$doDownload() 8. └─sched$downloadFile(url = url, dest.file = self$getDownloadPath()) 9. └─utils::download.file(...) ── Error (???): We can load an entry from the database. ──────────────────────── Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa' Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`) 3. └─opt$refEntries$getRealEntry(id) 4. └─self$getRealEntries(ids = id) 5. └─private$bdb$getFactory()$getEntry(...) 6. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 7. └─conn$getEntryContent(ids) 8. └─self$download() 9. └─private$doDownload() 10. └─sched$downloadFile(url = url, dest.file = self$getDownloadPath()) 11. └─utils::download.file(...) ── Error (???): Wrong entry gives NULL ───────────────────────────────────────── Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa' Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`) 3. └─biodb$getFactory()$getEntry(db.name, id = "WRONGA") 4. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 5. └─conn$getEntryContent(ids) 6. └─self$download() 7. └─private$doDownload() 8. └─sched$downloadFile(url = url, dest.file = self$getDownloadPath()) 9. └─utils::download.file(...) ── Error (???): One wrong entry does not block the retrieval of good ones ────── Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa' Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`) 3. └─biodb$getFactory()$getEntry(db.name, id = ids) 4. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 5. └─conn$getEntryContent(ids) 6. └─self$download() 7. └─private$doDownload() 8. └─sched$downloadFile(url = url, dest.file = self$getDownloadPath()) 9. └─utils::download.file(...) ── Error (???): The peak table is correct. ───────────────────────────────────── Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa' Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`) 3. └─biodb$getFactory()$getEntry(...) 4. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 5. └─conn$getEntryContent(ids) 6. └─self$download() 7. └─private$doDownload() 8. └─sched$downloadFile(url = url, dest.file = self$getDownloadPath()) 9. └─utils::download.file(...) ── Error (???): We can get a list of entry ids. ──────────────────────────────── Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa' Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`) 3. └─conn$getEntryIds(max.results = max) 4. └─private$doGetEntryIds(max.results = max.results, ...) 5. └─self$download() 6. └─private$doDownload() 7. └─sched$downloadFile(url = url, dest.file = self$getDownloadPath()) 8. └─utils::download.file(...) [ FAIL 6 | WARN 6 | SKIP 0 | PASS 40 ] Error: Test failures Execution halted