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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:slinky.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings slinky_1.10.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/slinky.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/slinky.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL slinky
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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