Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 604/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
drawProteins 1.26.0 (landing page) Paul Brennan
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the drawProteins package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/drawProteins.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: drawProteins |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:drawProteins.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings drawProteins_1.26.0.tar.gz |
StartedAt: 2024-12-20 18:09:15 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 18:09:59 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 43.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: drawProteins.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:drawProteins.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings drawProteins_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/drawProteins.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘drawProteins/DESCRIPTION’ ... OK * this is package ‘drawProteins’ version ‘1.26.0’ * 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 ‘drawProteins’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: CHANGES VERSION 0.98.1 * 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘drawProteins-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: parse_gff > ### Title: Reformat file or url in gff format to allow to draw > ### Aliases: parse_gff > > ### ** Examples > > data <- parse_gff("https://www.uniprot.org/uniprot/Q04206.gff") Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) Rows: 3 Columns: 3 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "\t" chr (3): X1, X2, X3 ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. Error in `dplyr::filter()`: ℹ In argument: `begin > 0`. Caused by error: ! `..1` must be of size 3 or 1, not size 0. Backtrace: ▆ 1. ├─drawProteins::parse_gff("https://www.uniprot.org/uniprot/Q04206.gff") 2. │ ├─dplyr::filter(gff_data, begin > 0) 3. │ └─dplyr:::filter.data.frame(gff_data, begin > 0) 4. │ └─dplyr:::filter_rows(.data, dots, by) 5. │ └─dplyr:::filter_eval(...) 6. │ ├─base::withCallingHandlers(...) 7. │ └─mask$eval_all_filter(dots, env_filter) 8. │ └─dplyr (local) eval() 9. ├─dplyr:::dplyr_internal_error(...) 10. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 11. │ └─rlang:::signal_abort(cnd, .file) 12. │ └─base::signalCondition(cnd) 13. └─dplyr (local) `<fn>`(`<dpl:::__>`) 14. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 4. │ └─dplyr:::filter_rows(.data, dots, by) 5. │ └─dplyr:::filter_eval(...) 6. │ ├─base::withCallingHandlers(...) 7. │ └─mask$eval_all_filter(dots, env_filter) 8. │ └─dplyr (local) eval() 9. ├─dplyr:::dplyr_internal_error(...) 10. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 11. │ └─rlang:::signal_abort(cnd, .file) 12. │ └─base::signalCondition(cnd) 13. └─dplyr (local) `<fn>`(`<dpl:::__>`) 14. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) [ FAIL 1 | WARN 2 | SKIP 0 | PASS 165 ] Error: Test failures Execution halted * 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: 2 ERRORs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/drawProteins.Rcheck/00check.log’ for details.
drawProteins.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL drawProteins ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘drawProteins’ ... ** 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 (drawProteins)
drawProteins.Rcheck/tests/testthat.Rout.fail
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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(drawProteins) > > test_check("drawProteins") [1] "Download has worked" [1] "An error has occured. Code: 400" [ FAIL 1 | WARN 2 | SKIP 0 | PASS 165 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-parsers.R:57:3'): parse_gff ──────────────────────────────────── Error in `dplyr::filter(gff_data, begin > 0)`: ℹ In argument: `begin > 0`. Caused by error: ! `..1` must be of size 6 or 1, not size 0. Backtrace: ▆ 1. ├─drawProteins::parse_gff("https://www.uniprot.org/uniprot/P0A7B8.gff") at test-parsers.R:57:3 2. │ ├─dplyr::filter(gff_data, begin > 0) 3. │ └─dplyr:::filter.data.frame(gff_data, begin > 0) 4. │ └─dplyr:::filter_rows(.data, dots, by) 5. │ └─dplyr:::filter_eval(...) 6. │ ├─base::withCallingHandlers(...) 7. │ └─mask$eval_all_filter(dots, env_filter) 8. │ └─dplyr (local) eval() 9. ├─dplyr:::dplyr_internal_error(...) 10. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 11. │ └─rlang:::signal_abort(cnd, .file) 12. │ └─base::signalCondition(cnd) 13. └─dplyr (local) `<fn>`(`<dpl:::__>`) 14. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) [ FAIL 1 | WARN 2 | SKIP 0 | PASS 165 ] Error: Test failures Execution halted
drawProteins.Rcheck/drawProteins-Ex.timings
name | user | system | elapsed | |
draw_canvas | 0.191 | 0.011 | 0.203 | |
draw_chains | 0.285 | 0.009 | 0.293 | |
draw_domains | 0.273 | 0.006 | 0.280 | |
draw_folding | 0.487 | 0.006 | 0.493 | |
draw_motif | 0.195 | 0.003 | 0.199 | |
draw_phospho | 0.161 | 0.003 | 0.164 | |
draw_recept_dom | 0.300 | 0.006 | 0.306 | |
draw_regions | 0.224 | 0.004 | 0.229 | |
draw_repeat | 0.180 | 0.003 | 0.183 | |
extract_feat_acc | 0.016 | 0.002 | 0.018 | |
extract_names | 0.005 | 0.001 | 0.008 | |
extract_transcripts | 0.020 | 0.001 | 0.022 | |
feature_to_dataframe | 0.020 | 0.004 | 0.024 | |
get_features | 0.069 | 0.012 | 0.225 | |