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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")
Downloading Python-3.6.15.tar.xz...
-> https://www.python.org/ftp/python/3.6.15/Python-3.6.15.tar.xz
Installing Python-3.6.15...
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patching file Modules/mathmodule.c
Hunk #1 succeeded at 67 with fuzz 1 (offset -33 lines).
Hunk #2 succeeded at 296 (offset -32 lines).
Hunk #3 succeeded at 320 (offset -32 lines).
Hunk #4 succeeded at 390 (offset -33 lines).
Installed Python-3.6.15 to /home/biocbuild/.pyenv/versions/3.6.15
Using Python: /home/biocbuild/.pyenv/versions/3.6.15/bin/python3.6
Creating virtual environment '/var/cache/basilisk/1.23.0/crisprScore/1.15.0/enpamgb_basilisk' ... 
Done!
Installing packages: pip, wheel, setuptools
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Installing collected packages: urllib3, pyasn1, idna, charset-normalizer, certifi, zipp, typing-extensions, six, rsa, requests, pyasn1-modules, oauthlib, cachetools, requests-oauthlib, importlib-metadata, google-auth, dataclasses, werkzeug, tensorboard-plugin-wit, tensorboard-data-server, setuptools, protobuf, numpy, markdown, grpcio, google-auth-oauthlib, absl-py, wrapt, termcolor, tensorflow-estimator, tensorboard, scipy, pytz, python-dateutil, opt-einsum, Keras-Preprocessing, joblib, h5py, google-pasta, gast, flatbuffers, astunparse, tensorflow, scikit-learn, pip, pandas, biopython
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Requirement already satisfied: zipp>=0.5 in /var/cache/basilisk/1.23.0/crisprScore/1.15.0/enpamgb_basilisk/lib/python3.6/site-packages (from importlib-metadata>=4.4->markdown>=2.6.8->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (3.6.0)
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Requirement already satisfied: certifi>=2017.4.17 in /var/cache/basilisk/1.23.0/crisprScore/1.15.0/enpamgb_basilisk/lib/python3.6/site-packages (from requests<3,>=2.21.0->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2025.4.26)
Requirement already satisfied: charset-normalizer~=2.0.0 in /var/cache/basilisk/1.23.0/crisprScore/1.15.0/enpamgb_basilisk/lib/python3.6/site-packages (from requests<3,>=2.21.0->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.0.12)
Requirement already satisfied: oauthlib>=3.0.0 in /var/cache/basilisk/1.23.0/crisprScore/1.15.0/enpamgb_basilisk/lib/python3.6/site-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<0.5,>=0.4.1->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (3.2.2)
Requirement already satisfied: dataclasses in /var/cache/basilisk/1.23.0/crisprScore/1.15.0/enpamgb_basilisk/lib/python3.6/site-packages (from werkzeug>=1.0.1->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.8)
Building wheels for collected packages: sgrna-modeler
  Building wheel for sgrna-modeler (setup.py): started
  Building wheel for sgrna-modeler (setup.py): finished with status 'done'
  Created wheel for sgrna-modeler: filename=sgrna_modeler-0.1.0-py3-none-any.whl size=459415 sha256=035855ae975cc531b2b354d53c263ac80f9c431993b8c5c7b6dd8d5d156aeaca
  Stored in directory: /tmp/pip-ephem-wheel-cache-s9kq6lay/wheels/95/cc/9d/1b976c0bcbea9920199a115a5c514cea529d8ba8ad6bdf7c25
Successfully built sgrna-modeler
Installing collected packages: sgrna-modeler
Successfully installed sgrna-modeler-0.1.0
WARNING: You are using pip version 21.0.1; however, version 21.3.1 is available.
You should consider upgrading via the '/var/cache/basilisk/1.23.0/crisprScore/1.15.0/enpamgb_basilisk/bin/python -m pip install --upgrade pip' command.
2025-11-08 16:31:01.781534: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /var/cache/basilisk/1.23.0/crisprScore/1.15.0/enpamgb_basilisk/lib:/home/biocbuild/.pyenv/versions/3.6.15/lib:/home/biocbuild/bbs-3.23-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/var/cache/basilisk/1.23.0/crisprScore/1.15.0/enpamgb_basilisk/lib:/home/biocbuild/.pyenv/versions/3.6.15/lib:/home/biocbuild/bbs-3.23-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.23-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.23-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.23-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.23-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server
2025-11-08 16:31:01.781678: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
Using Python: /home/biocbuild/.pyenv/versions/3.6.15/bin/python3.6
Creating virtual environment '/var/cache/basilisk/1.23.0/crisprScore/1.15.0/lindel_basilisk' ... 
Done!
Installing packages: pip, wheel, setuptools
Collecting pip
  Using cached https://files.pythonhosted.org/packages/a4/6d/6463d49a933f547439d6b5b98b46af8742cc03ae83543e4d7688c2420f8b/pip-21.3.1-py3-none-any.whl
Collecting wheel
  Using cached https://files.pythonhosted.org/packages/27/d6/003e593296a85fd6ed616ed962795b2f87709c3eee2bca4f6d0fe55c6d00/wheel-0.37.1-py2.py3-none-any.whl
Collecting setuptools
  Using cached https://files.pythonhosted.org/packages/b0/3a/88b210db68e56854d0bcf4b38e165e03be377e13907746f825790f3df5bf/setuptools-59.6.0-py3-none-any.whl
Installing collected packages: pip, wheel, setuptools
  Found existing installation: pip 18.1
    Uninstalling pip-18.1:
      Successfully uninstalled pip-18.1
  Found existing installation: setuptools 40.6.2
    Uninstalling setuptools-40.6.2:
      Successfully uninstalled setuptools-40.6.2
Successfully installed pip-21.3.1 setuptools-59.6.0 wheel-0.37.1
Installing packages: 'numpy==1.19.5', 'pip==21.0.1', 'scipy==1.5.3'
Collecting numpy==1.19.5
  Using cached numpy-1.19.5-cp36-cp36m-manylinux2010_x86_64.whl (14.8 MB)
Collecting pip==21.0.1
  Using cached pip-21.0.1-py3-none-any.whl (1.5 MB)
Collecting scipy==1.5.3
  Using cached scipy-1.5.3-cp36-cp36m-manylinux1_x86_64.whl (25.9 MB)
Installing collected packages: numpy, scipy, pip
  Attempting uninstall: pip
    Found existing installation: pip 21.3.1
    Uninstalling pip-21.3.1:
      Successfully uninstalled pip-21.3.1
Successfully installed numpy-1.19.5 pip-21.0.1 scipy-1.5.3
Virtual environment '/var/cache/basilisk/1.23.0/crisprScore/1.15.0/lindel_basilisk' successfully created.
Processing /home/biocbuild/bbs-3.23-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/lindel
Requirement already satisfied: numpy in /var/cache/basilisk/1.23.0/crisprScore/1.15.0/lindel_basilisk/lib/python3.6/site-packages (from Lindel==1.0) (1.19.5)
Requirement already satisfied: scipy in /var/cache/basilisk/1.23.0/crisprScore/1.15.0/lindel_basilisk/lib/python3.6/site-packages (from Lindel==1.0) (1.5.3)
Building wheels for collected packages: Lindel
  Building wheel for Lindel (setup.py): started
  Building wheel for Lindel (setup.py): finished with status 'done'
  Created wheel for Lindel: filename=Lindel-1.0-py3-none-any.whl size=33618 sha256=67d53a4ca14ed9c519de9abac1bc814ec8593de2c27212350201d6402303697f
  Stored in directory: /tmp/pip-ephem-wheel-cache-8jry21qa/wheels/67/84/e8/1579f4a5f13dae983e31552b763cd9d9e504fcb329a2e91c13
Successfully built Lindel
Installing collected packages: Lindel
Successfully installed Lindel-1.0
WARNING: You are using pip version 21.0.1; however, version 21.3.1 is available.
You should consider upgrading via the '/var/cache/basilisk/1.23.0/crisprScore/1.15.0/lindel_basilisk/bin/python -m pip install --upgrade pip' command.
Using Python: /home/biocbuild/.pyenv/versions/3.6.15/bin/python3.6
Creating virtual environment '/var/cache/basilisk/1.23.0/crisprScore/1.15.0/deephf_basilisk' ... 
Done!
Installing packages: pip, wheel, setuptools
Collecting pip
  Using cached https://files.pythonhosted.org/packages/a4/6d/6463d49a933f547439d6b5b98b46af8742cc03ae83543e4d7688c2420f8b/pip-21.3.1-py3-none-any.whl
Collecting wheel
  Using cached https://files.pythonhosted.org/packages/27/d6/003e593296a85fd6ed616ed962795b2f87709c3eee2bca4f6d0fe55c6d00/wheel-0.37.1-py2.py3-none-any.whl
Collecting setuptools
  Using cached https://files.pythonhosted.org/packages/b0/3a/88b210db68e56854d0bcf4b38e165e03be377e13907746f825790f3df5bf/setuptools-59.6.0-py3-none-any.whl
Installing collected packages: pip, wheel, setuptools
  Found existing installation: pip 18.1
    Uninstalling pip-18.1:
      Successfully uninstalled pip-18.1
  Found existing installation: setuptools 40.6.2
    Uninstalling setuptools-40.6.2:
      Successfully uninstalled setuptools-40.6.2
Successfully installed pip-21.3.1 setuptools-59.6.0 wheel-0.37.1
Installing packages: 'viennarna==2.4.5', 'biopython==1.71', 'h5py==2.9.0', 'dotmap==1.2.20', 'numpy==1.14.0', 'scipy==1.1.0', 'pandas==0.25.3', 'Keras==2.1.6', 'gpy==1.9.8', 'scikit-learn==0.19.1', 'matplotlib==3.1.1', 'tensorboard==1.8.0', 'tensorflow==1.8.0', 'Theano==1.0.5'
ERROR: Could not find a version that satisfies the requirement viennarna==2.4.5 (from versions: 2.5.0a5)
ERROR: No matching distribution found for viennarna==2.4.5
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 2 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ontargets.R:19:5'): Azimuth scores ─────────────────────────────
Error in `pyenv_python(version = version)`: Python 2.7 does not appear to be installed.
Try installing it with install_python(version = '2.7').
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.       ├─base::suppressMessages(install_python(version))
  8.       │ └─base::withCallingHandlers(...)
  9.       └─reticulate::install_python(version)
 10.         └─reticulate:::pyenv_python(version = version)
── Error ('test-ontargets.R:24:5'): DeepCpf1 scores ────────────────────────────
Error in `pyenv_python(version = version)`: Python 2.7 does not appear to be installed.
Try installing it with install_python(version = '2.7').
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test-ontargets.R:24:5
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─crisprScore::getDeepCpf1Scores(deepcpf1_sequences)
  5.   └─basilisk::obtainEnvironmentPath(env_deepcpf1)
  6.     └─basilisk::setupBasiliskEnv(...)
  7.       ├─base::suppressMessages(install_python(version))
  8.       │ └─base::withCallingHandlers(...)
  9.       └─reticulate::install_python(version)
 10.         └─reticulate:::pyenv_python(version = version)
── Error ('test-ontargets.R:38:5'): DeepHF scores ──────────────────────────────
Error: Error installing package(s): "'viennarna==2.4.5'", "'biopython==1.71'", "'h5py==2.9.0'", "'dotmap==1.2.20'", "'numpy==1.14.0'", "'scipy==1.1.0'", "'pandas==0.25.3'", "'Keras==2.1.6'", "'gpy==1.9.8'", "'scikit-learn==0.19.1'", "'matplotlib==3.1.1'", "'tensorboard==1.8.0'", "'tensorflow==1.8.0'", "'Theano==1.0.5'"
Backtrace:
    ▆
 1. ├─testthat::expect_equal(...) at test-ontargets.R:38:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─crisprScore::getDeepHFScores(deephf_sequences, enzyme = "WT")
 5.   └─basilisk::obtainEnvironmentPath(env_deephf)
 6.     └─basilisk::setupBasiliskEnv(...)
 7.       └─reticulate::virtualenv_create(...)
 8.         └─reticulate:::pip_install(python, packages)

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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no crisprScore_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc-longtests/meat/crisprScore.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* 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 ‘1.15.0’
* 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 ‘/home/biocbuild/bbs-3.23-bioc-longtests/meat/crisprScore.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    python   4.2Mb
* 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 loading without being on the library search path ... 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 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:
  Error: Error installing package(s): "'viennarna==2.4.5'", "'biopython==1.71'", "'h5py==2.9.0'", "'dotmap==1.2.20'", "'numpy==1.14.0'", "'scipy==1.1.0'", "'pandas==0.25.3'", "'Keras==2.1.6'", "'gpy==1.9.8'", "'scikit-learn==0.19.1'", "'matplotlib==3.1.1'", "'tensorboard==1.8.0'", "'tensorflow==1.8.0'", "'Theano==1.0.5'"
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-ontargets.R:38:5
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─crisprScore::getDeepHFScores(deephf_sequences, enzyme = "WT")
   5.   └─basilisk::obtainEnvironmentPath(env_deephf)
   6.     └─basilisk::setupBasiliskEnv(...)
   7.       └─reticulate::virtualenv_create(...)
   8.         └─reticulate:::pip_install(python, packages)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc-longtests/meat/crisprScore.Rcheck/00check.log’
for details.

* installing *source* package ‘crisprScore’ ...
** this is package ‘crisprScore’ version ‘1.15.0’
** 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)