R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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Platform: x86_64-apple-darwin20

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> library(testthat)
> library(crisprScore)
Loading required package: crisprScoreData
Loading required package: ExperimentHub
Loading required package: BiocGenerics

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> 
> test_check("crisprScore")
/Users/biocbuild/bbs-3.20-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth/azimuth/predict.py:16: UserWarning: 
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

The backend was *originally* set to 'MacOSX' by the following code:
  File "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth/getAzimuth.py", line 4, in <module>
    import azimuth.model_comparison
  File "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth/azimuth/model_comparison.py", line 1, in <module>
    import azimuth.predict as pd
  File "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth/azimuth/predict.py", line 7, in <module>
    import util
  File "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth/azimuth/util.py", line 2, in <module>
    import matplotlib.pylab as plt
  File "/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/crisprScore/1.10.0/azimuth_basilisk/lib/python2.7/site-packages/matplotlib/pylab.py", line 252, in <module>
    from matplotlib import cbook, mlab, pyplot as plt
  File "/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/crisprScore/1.10.0/azimuth_basilisk/lib/python2.7/site-packages/matplotlib/pyplot.py", line 71, in <module>
    from matplotlib.backends import pylab_setup
  File "/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/crisprScore/1.10.0/azimuth_basilisk/lib/python2.7/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
    line for line in traceback.format_stack()


  matplotlib.use('TkAgg')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
 23.293   4.621 172.261 

##############################################################################
##############################################################################
###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/crisprScore.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-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 Monterey 12.7.6
* 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 ‘1.10.0’
* 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 ... NOTE
Found the following non-portable file paths:
  crisprScore/inst/python/deepspcas9/DeepCas9_Final/PreTrain-Final-False-3-5-7-100-70-40-0.001-550-True-80-60.data-00000-of-00001
  crisprScore/inst/python/deepspcas9/DeepCas9_Final/PreTrain-Final-False-3-5-7-100-70-40-0.001-550-True-80-60.index
  crisprScore/inst/python/deepspcas9/DeepCas9_Final/PreTrain-Final-False-3-5-7-100-70-40-0.001-550-True-80-60.meta

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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-3.20-bioc-longtests/meat/crisprScore.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    python   5.9Mb
* 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 ... NOTE
':::' call which should be '::': ‘basilisk.utils:::getPythonBinary’
  See the note in ?`:::` about the use of this operator.
* 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 shell scripts ... 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’
 OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/crisprScore.Rcheck/00check.log’
for details.

* installing *source* package ‘crisprScore’ ...
** 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)