R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
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> library(testthat)
> library(crisprScore)
Loading required package: crisprScoreData
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> 
> test_check("crisprScore")
Saving _problems/test-ontargets-16.R

Saving _problems/test-ontargets-20.R

Saving _problems/test-ontargets-25.R
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ontargets.R:16:5'): enPAM+GB scores ────────────────────────────
<getvarError/missingArgError/error/condition>
Error in `getEnPAMGBScores(enpamgb_sequences)`: argument "condaEnv" is missing, with no default
Backtrace:
    ▆
 1. ├─testthat::expect_equal(...) at test-ontargets.R:16:5
 2. │ └─testthat::quasi_label(enquo(object), label)
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─crisprScore::getEnPAMGBScores(enpamgb_sequences)
 5.   └─reticulate::use_condaenv(condaEnv)
 6.     └─base::grepl("[/\\]", condaenv)
 7.       └─base::is.factor(x)
── Error ('test-ontargets.R:20:5'): Lindel scores ──────────────────────────────
<getvarError/missingArgError/error/condition>
Error in `getLindelScores(lindel_sequences)`: argument "condaEnv" is missing, with no default
Backtrace:
    ▆
 1. ├─testthat::expect_equal(...) at test-ontargets.R:20:5
 2. │ └─testthat::quasi_label(enquo(object), label)
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─crisprScore::getLindelScores(lindel_sequences)
 5.   └─crisprScore:::getPythonBinary(condaEnv)
 6.     └─base::file.path(envpath, suffix)
── Error ('test-ontargets.R:25:5'): DeepHF scores ──────────────────────────────
<getvarError/missingArgError/error/condition>
Error in `getDeepHFScores(deephf_sequences, enzyme = "WT")`: argument "condaEnv" is missing, with no default
Backtrace:
    ▆
 1. ├─testthat::expect_equal(...) at test-ontargets.R:25:5
 2. │ └─testthat::quasi_label(enquo(object), label)
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─crisprScore::getDeepHFScores(deephf_sequences, enzyme = "WT")
 5.   └─reticulate::use_condaenv(condaEnv)
 6.     └─base::grepl("[/\\]", condaenv)
 7.       └─base::is.factor(x)

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no crisprScore_1.15.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc-longtests/meat/crisprScore.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘crisprScore/DESCRIPTION’ ... OK
* this is package ‘crisprScore’ version ‘1.15.2’
* 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 ‘crisprScore’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.23-bioc-longtests/meat/crisprScore.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package 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 ... 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 whether startup messages can be suppressed ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... 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:
  Error in `getDeepHFScores(deephf_sequences, enzyme = "WT")`: argument "condaEnv" is missing, with no default
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-ontargets.R:25:5
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─crisprScore::getDeepHFScores(deephf_sequences, enzyme = "WT")
   5.   └─reticulate::use_condaenv(condaEnv)
   6.     └─base::grepl("[/\\]", condaenv)
   7.       └─base::is.factor(x)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc-longtests/meat/crisprScore.Rcheck/00check.log’
for details.

* installing *source* package ‘crisprScore’ ...
** this is package ‘crisprScore’ version ‘1.15.2’
** using non-staged installation via StagedInstall field
** 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
* DONE (crisprScore)