R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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Platform: x86_64-w64-mingw32/x64

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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, 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")
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.17.0\crisprScore\1.9.0\azimuth_basilisk

  added / updated specs:
    - python=2.7


The following NEW packages will be INSTALLED:

  certifi            conda-forge/win-64::certifi-2019.11.28-py27h8c360ce_1
  pip                conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
  python             conda-forge/win-64::python-2.7.15-h2880e7c_1011_cpython
  python_abi         conda-forge/win-64::python_abi-2.7-1_cp27m
  setuptools         conda-forge/win-64::setuptools-44.0.0-py27_0
  vc                 pkgs/main/win-64::vc-9-h2eaa2aa_6
  vs2008_runtime     conda-forge/win-64::vs2008_runtime-9.0.30729.6161-0
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
  wincertstore       conda-forge/noarch::wincertstore-0.2-pyhd8ed1ab_1009


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Rolling back transaction: ...working... done

[Errno 28] No space left on device
()

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

CondaError: Failed to write to C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\0\pkgs\python-3.6.15-h39d44d4_0_cpython.tar.bz2
  errno: 28


## Package Plan ##

  environment location: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.17.0\crisprScore\1.9.0\lindel_basilisk

  added / updated specs:
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2020.6.20          |     pyhd3eb1b0_3         155 KB
    python-3.6.15              |h39d44d4_0_cpython        18.9 MB  conda-forge
    wheel-0.34.2               |           py36_0          60 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        19.1 MB

The following NEW packages will be INSTALLED:

  certifi            pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
  pip                conda-forge/win-64::pip-20.0.2-py36_1
  python             conda-forge/win-64::python-3.6.15-h39d44d4_0_cpython
  python_abi         conda-forge/win-64::python_abi-3.6-2_cp36m
  setuptools         conda-forge/win-64::setuptools-49.6.0-py36ha15d459_3
  ucrt               conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.3-h8a93ad2_20
  vc14_runtime       conda-forge/win-64::vc14_runtime-14.40.33810-ha82c5b3_20
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.40.33810-h3bf8584_20
  wheel              conda-forge/win-64::wheel-0.34.2-py36_0
  wincertstore       conda-forge/noarch::wincertstore-0.2-pyhd8ed1ab_1009


[ FAIL 2 | WARN 4 | SKIP 3 | PASS 0 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On Windows (3): 'test-ontargets.R:23:5', 'test-ontargets.R:28:5',
  'test-ontargets.R:37:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ontargets.R:19:5'): Azimuth scores ─────────────────────────────
Error: Error creating conda environment 'C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/crisprScore/1.9.0/azimuth_basilisk' [exit code 1]
Backtrace:
    ▆
 1. ├─testthat::expect_equal(...) at test-ontargets.R:19:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─crisprScore::getAzimuthScores(azimuth_sequences)
 5.   └─basilisk::obtainEnvironmentPath(env_azimuth)
 6.     └─basilisk::setupBasiliskEnv(...)
 7.       └─reticulate::conda_install(...)
 8.         └─reticulate::conda_create(...)
 9.           └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
── Error ('test-ontargets.R:33:5'): Lindel scores ──────────────────────────────
Error: Error creating conda environment 'C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/crisprScore/1.9.0/lindel_basilisk' [exit code 1]
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test-ontargets.R:33:5
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─crisprScore::getLindelScores(lindel_sequences)
  5.   └─basilisk::basiliskRun(...)
  6.     └─basilisk::basiliskStart(...)
  7.       └─basilisk::obtainEnvironmentPath(env)
  8.         └─basilisk::setupBasiliskEnv(...)
  9.           └─reticulate::conda_install(...)
 10.             └─reticulate::conda_create(...)
 11.               └─reticulate:::stopf(fmt, envname, result, call. = FALSE)

[ FAIL 2 | WARN 4 | SKIP 3 | PASS 0 ]
Error: Test failures
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no crisprScore_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/crisprScore.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 '1.9.0'
* 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 whether package 'crisprScore' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/crisprScore.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    python   5.8Mb
* 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'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
    1. ├─testthat::expect_equal(...) at test-ontargets.R:33:5
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─crisprScore::getLindelScores(lindel_sequences)
    5.   └─basilisk::basiliskRun(...)
    6.     └─basilisk::basiliskStart(...)
    7.       └─basilisk::obtainEnvironmentPath(env)
    8.         └─basilisk::setupBasiliskEnv(...)
    9.           └─reticulate::conda_install(...)
   10.             └─reticulate::conda_create(...)
   11.               └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
  
  [ FAIL 2 | WARN 4 | SKIP 3 | PASS 0 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 5 NOTEs
See
  'F:/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)