Back to Long Tests report for BioC 3.19 |
This page was generated on 2024-05-11 23:55:02 -0400 (Sat, 11 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
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 13/33 | Hostname | OS / Arch | CHECK | |||||||
biodbUniprot 1.10.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
To the developers/maintainers of the biodbUniprot 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: biodbUniprot |
Version: 1.10.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbUniprot_1.10.0.tar.gz |
StartedAt: 2024-05-11 16:10:24 -0400 (Sat, 11 May 2024) |
EndedAt: 2024-05-11 16:11:48 -0400 (Sat, 11 May 2024) |
EllapsedTime: 83.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biodbUniprot.Rcheck |
Warnings: NA |
biodbUniprot.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(biodbUniprot) > Sys.setenv(TESTTHAT_REPORTER="summary") > test_check("biodbUniprot") [ FAIL 13 | WARN 12 | SKIP 0 | PASS 497 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_long_100_generic.R:16:1'): RT unit is defined when there is an RT value. ── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`) 3. └─conn$getBiodb()$getFactory()$getEntry(...) 4. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 5. └─conn$getEntryContent(ids) 6. └─self$getEntryContentFromDb(ch.missing.ids) 7. └─private$doGetEntryContentFromDb(entry.id) 8. └─private$doGetEntryContentOneByOne(id) 9. └─scheduler$sendRequest(requests[[i]]) 10. └─cch$saveContentToFile(...) 11. └─private$doSaveContentToFile(...) 12. └─biodb:::saveContentsToFiles(file.paths, content) 13. └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files) 14. └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 15. └─base::cat(cnt, file = f) 16. └─base::file(file, ifelse(append, "a", "w")) ── Error ('test_long_100_generic.R:16:1'): We can search for an entry by searchable field ── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`) 3. └─conn$getEntry(id, drop = TRUE) 4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop) 5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 6. └─conn$getEntryContent(ids) 7. └─cch$saveContentToFile(...) 8. └─private$doSaveContentToFile(...) 9. └─biodb:::saveContentsToFiles(file.paths, content) 10. └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files) 11. └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 12. └─base::cat(cnt, file = f) 13. └─base::file(file, ifelse(append, "a", "w")) ── Error ('test_long_100_generic.R:16:1'): We can search for an entry by name. ── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`) 3. └─conn$getEntry(id, drop = TRUE) 4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop) 5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 6. └─conn$getEntryContent(ids) 7. └─cch$saveContentToFile(...) 8. └─private$doSaveContentToFile(...) 9. └─biodb:::saveContentsToFiles(file.paths, content) 10. └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files) 11. └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 12. └─base::cat(cnt, file = f) 13. └─base::file(file, ifelse(append, "a", "w")) ── Error ('test_long_100_generic.R:16:1'): We can load an entry from the database. ── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, 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$getEntryContent(ids) 8. └─cch$saveContentToFile(...) 9. └─private$doSaveContentToFile(...) 10. └─biodb:::saveContentsToFiles(file.paths, content) 11. └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files) 12. └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 13. └─base::cat(cnt, file = f) 14. └─base::file(file, ifelse(append, "a", "w")) ── Error ('test_long_100_generic.R:16:1'): We can search for a compound ──────── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(db = `<UnprtCnn>`, opt = `<named list>`) 3. └─db$getEntry(id, drop = TRUE) 4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop) 5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 6. └─conn$getEntryContent(ids) 7. └─cch$saveContentToFile(...) 8. └─private$doSaveContentToFile(...) 9. └─biodb:::saveContentsToFiles(file.paths, content) 10. └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files) 11. └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 12. └─base::cat(cnt, file = f) 13. └─base::file(file, ifelse(append, "a", "w")) ── Error ('test_long_100_generic.R:16:1'): annotateMzValues() accepts a single vector. ── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`) 3. └─conn$getEntry(ids, drop = FALSE) 4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop) 5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 6. └─conn$getEntryContent(ids) 7. └─self$getEntryContentFromDb(ch.missing.ids) 8. └─private$doGetEntryContentFromDb(entry.id) 9. └─private$doGetEntryContentOneByOne(id) 10. └─scheduler$sendRequest(requests[[i]]) 11. └─cch$saveContentToFile(...) 12. └─private$doSaveContentToFile(...) 13. └─biodb:::saveContentsToFiles(file.paths, content) 14. └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files) 15. └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 16. └─base::cat(cnt, file = f) 17. └─base::file(file, ifelse(append, "a", "w")) ── Error ('test_long_100_generic.R:16:1'): ppm tolerance works in annotateMzValues() ── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`) 3. └─conn$getEntry(ids, drop = FALSE) 4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop) 5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 6. └─conn$getEntryContent(ids) 7. └─self$getEntryContentFromDb(ch.missing.ids) 8. └─private$doGetEntryContentFromDb(entry.id) 9. └─private$doGetEntryContentOneByOne(id) 10. └─scheduler$sendRequest(requests[[i]]) 11. └─cch$saveContentToFile(...) 12. └─private$doSaveContentToFile(...) 13. └─biodb:::saveContentsToFiles(file.paths, content) 14. └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files) 15. └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 16. └─base::cat(cnt, file = f) 17. └─base::file(file, ifelse(append, "a", "w")) ── Error ('test_long_100_generic.R:16:1'): Input data frame is not modified by annotateMzValues() ── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`) 3. └─conn$getEntry(ids, drop = FALSE) 4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop) 5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 6. └─conn$getEntryContent(ids) 7. └─self$getEntryContentFromDb(ch.missing.ids) 8. └─private$doGetEntryContentFromDb(entry.id) 9. └─private$doGetEntryContentOneByOne(id) 10. └─scheduler$sendRequest(requests[[i]]) 11. └─cch$saveContentToFile(...) 12. └─private$doSaveContentToFile(...) 13. └─biodb:::saveContentsToFiles(file.paths, content) 14. └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files) 15. └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 16. └─base::cat(cnt, file = f) 17. └─base::file(file, ifelse(append, "a", "w")) ── Error ('test_long_100_generic.R:16:1'): annotateMzValues() works correctly with real values. ── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`) 3. └─conn$getEntry(ids, drop = FALSE) 4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop) 5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 6. └─conn$getEntryContent(ids) 7. └─self$getEntryContentFromDb(ch.missing.ids) 8. └─private$doGetEntryContentFromDb(entry.id) 9. └─private$doGetEntryContentOneByOne(id) 10. └─scheduler$sendRequest(requests[[i]]) 11. └─cch$saveContentToFile(...) 12. └─private$doSaveContentToFile(...) 13. └─biodb:::saveContentsToFiles(file.paths, content) 14. └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files) 15. └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 16. └─base::cat(cnt, file = f) 17. └─base::file(file, ifelse(append, "a", "w")) ── Error ('test_long_100_generic.R:16:1'): Additional fields are accepted in annotateMzValues() ── Error in `e$hasField(mf)`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) ── Error ('test_long_200_conversions.R:98:1'): We can convert gene symbols to UniProt IDs. ── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodbUniprot (local) `<fn>`(conn = `<UnprtCnn>`) 3. └─conn$geneSymbolToUniprotIds(names(expected_ids)) at test_long_200_conversions.R:14:5 4. └─self$wsSearch(query, retfmt = "ids", size = limit) 5. └─self$getBiodb()$getRequestScheduler()$sendRequest(request) 6. └─cch$saveContentToFile(...) 7. └─private$doSaveContentToFile(...) 8. └─biodb:::saveContentsToFiles(file.paths, content) 9. └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files) 10. └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 11. └─base::cat(cnt, file = f) 12. └─base::file(file, ifelse(append, "a", "w")) ── Error ('test_long_200_conversions.R:100:1'): We can convert gene symbols to UniProt IDs. ── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodbUniprot (local) `<fn>`(conn = `<UnprtCnn>`) 3. └─conn$geneSymbolToUniprotIds(names(expected_ids)) at test_long_200_conversions.R:28:5 4. └─self$wsSearch(query, retfmt = "ids", size = limit) 5. └─self$getBiodb()$getRequestScheduler()$sendRequest(request) 6. └─cch$saveContentToFile(...) 7. └─private$doSaveContentToFile(...) 8. └─biodb:::saveContentsToFiles(file.paths, content) 9. └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files) 10. └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 11. └─base::cat(cnt, file = f) 12. └─base::file(file, ifelse(append, "a", "w")) ── Error ('test_long_200_conversions.R:102:1'): We can convert gene symbols to UniProt IDs. ── Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodbUniprot (local) `<fn>`(conn = `<UnprtCnn>`) 3. └─conn$geneSymbolToUniprotIds(names(expected_ids), ignore.nonalphanum = TRUE) at test_long_200_conversions.R:42:5 4. └─self$wsSearch(query, retfmt = "ids", size = limit) 5. └─self$getBiodb()$getRequestScheduler()$sendRequest(request) 6. └─cch$saveContentToFile(...) 7. └─private$doSaveContentToFile(...) 8. └─biodb:::saveContentsToFiles(file.paths, content) 9. └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files) 10. └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 11. └─base::cat(cnt, file = f) 12. └─base::file(file, ifelse(append, "a", "w")) [ FAIL 13 | WARN 12 | SKIP 0 | PASS 497 ] Error: Test failures Execution halted
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbUniprot_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbUniprot.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error' * checking for file 'biodbUniprot/DESCRIPTION' ... OK * this is package 'biodbUniprot' version '1.10.0' * 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 whether package 'biodbUniprot' 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 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... SKIPPED * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... SKIPPED * checking examples ... SKIPPED * checking for unstated dependencies in 'longtests' ... OK * checking tests in 'longtests' ... Running 'testthat.R' ERROR Running the tests in 'longtests/testthat.R' failed. Last 13 lines of output: 2. └─biodbUniprot (local) `<fn>`(conn = `<UnprtCnn>`) 3. └─conn$geneSymbolToUniprotIds(names(expected_ids), ignore.nonalphanum = TRUE) at test_long_200_conversions.R:42:5 4. └─self$wsSearch(query, retfmt = "ids", size = limit) 5. └─self$getBiodb()$getRequestScheduler()$sendRequest(request) 6. └─cch$saveContentToFile(...) 7. └─private$doSaveContentToFile(...) 8. └─biodb:::saveContentsToFiles(file.paths, content) 9. └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files) 10. └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 11. └─base::cat(cnt, file = f) 12. └─base::file(file, ifelse(append, "a", "w")) [ FAIL 13 | WARN 12 | SKIP 0 | PASS 497 ] Error: Test failures Execution halted * DONE Status: 1 ERROR See 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbUniprot.Rcheck/00check.log' for details.
biodbUniprot.Rcheck/00install.out
* installing *source* package 'biodbUniprot' ... ** 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 (biodbUniprot)