Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:53 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the slinky package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/slinky.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1790/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
slinky 1.10.2 (landing page) Eric Kort
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
Package: slinky |
Version: 1.10.2 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:slinky.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings slinky_1.10.2.tar.gz |
StartedAt: 2021-10-14 11:39:52 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:43:09 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 196.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: slinky.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:slinky.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings slinky_1.10.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/slinky.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘slinky/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘slinky’ version ‘1.10.2’ * 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 ‘slinky’ can be installed ... OK * 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 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 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘slinky-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: clue > ### Title: clue > ### Aliases: clue clue,Slinky-method > > ### ** Examples > > # for build/demo only. You MUST use your own key when using the slinky > # package. > user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'), + as='parsed')$user_key > sl <- Slinky(user_key, + system.file('extdata', 'demo.gctx', + package='slinky'), + system.file('extdata', 'demo_inst_info.txt', + package = 'slinky')) > amox <- clue(sl, where_clause = list("pert_iname" = "amoxicillin", + "cell_id" = "MCF7", + "is_gold" = TRUE)) Error: Problem with `mutate()` column `distil_id`. ℹ `distil_id = strsplit(distil_id, "\\|")`. ✖ non-character argument Backtrace: █ 1. ├─slinky::clue(...) 2. ├─slinky::clue(...) 3. │ └─dat %>% mutate(distil_id = strsplit(distil_id, "\\|")) %>% unnest(distil_id) 4. ├─tidyr::unnest(., distil_id) 5. ├─dplyr::mutate(., distil_id = strsplit(distil_id, "\\|")) 6. ├─dplyr:::mutate.data.frame(...) 7. │ └─dplyr:::mutate_cols(.data, ..., caller_env = caller_env()) 8. │ ├─base::withCallingHandlers(...) 9. │ └─mask$eval_all_mutate(quo) 10. ├─base::strsplit(distil_id, "\\|") 11. └─base::.handleSimpleError(...) 12. └─dplyr:::h(simpleError(msg, 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: > library(testthat) > library(slinky) > > test_check("slinky") ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure (test_clue.R:17:3): A gene can be retrieved ───────────────────────── nrow(tt) not equal to 1. target is NULL, current is numeric ── Failure (test_clue.R:22:3): Limit working correctly on genes API ──────────── nrow(tt) not equal to 1. target is NULL, current is numeric [ FAIL 2 | WARN 0 | SKIP 0 | PASS 44 ] 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: 2 ERRORs See ‘/home/biocbuild/bbs-3.13-bioc/meat/slinky.Rcheck/00check.log’ for details.
slinky.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL slinky ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘slinky’ ... ** 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 (slinky)
slinky.Rcheck/tests/testthat.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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. > library(testthat) > library(slinky) > > test_check("slinky") ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure (test_clue.R:17:3): A gene can be retrieved ───────────────────────── nrow(tt) not equal to 1. target is NULL, current is numeric ── Failure (test_clue.R:22:3): Limit working correctly on genes API ──────────── nrow(tt) not equal to 1. target is NULL, current is numeric [ FAIL 2 | WARN 0 | SKIP 0 | PASS 44 ] Error: Test failures Execution halted
slinky.Rcheck/slinky-Ex.timings
name | user | system | elapsed | |
Slinky-class | 0.351 | 0.025 | 1.208 | |
closeAll | 0.028 | 0.004 | 0.060 | |