R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(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...
patching file configure
patching file configure.ac
patching file Misc/NEWS.d/next/macOS/2019-06-03-05-49-49.bpo-36231.RfmW_p.rst
patching file setup.py
patching file setup.py
patching file Doc/library/ctypes.rst
patching file Lib/test/test_unicode.py
patching file Modules/_ctypes/_ctypes.c
patching file Modules/_ctypes/callproc.c
patching file Modules/_ctypes/ctypes.h
patching file setup.py
patching file Misc/NEWS.d/next/macOS/2020-06-24-13-51-57.bpo-41100.mcHdc5.rst
patching file configure
patching file configure.ac
patching file 'Misc/NEWS.d/next/Core and Builtins/2020-06-30-04-44-29.bpo-41100.PJwA6F.rst'
patching file Modules/_decimal/libmpdec/mpdecimal.h
patching file setup.py
patching file Misc/NEWS.d/next/Build/2021-10-11-16-27-38.bpo-45405.iSfdW5.rst
patching file configure
patching file configure.ac
patching file 'Misc/NEWS.d/next/Core and Builtins/2019-04-16-11-52-21.bpo-27987.n2_DcQ.rst'
patching file Objects/obmalloc.c
patching file Include/objimpl.h
patching file 'Misc/NEWS.d/next/Core and Builtins/2019-05-15-18-28-43.bpo-27987.FaxuLy.rst'
patching file Misc/NEWS.d/next/Library/2019-02-25-13-21-43.bpo-36106.VuhEiQ.rst
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 '/home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk' ... 
Done!
Installing packages: pip, wheel, setuptools
Collecting pip
  Downloading https://files.pythonhosted.org/packages/a4/6d/6463d49a933f547439d6b5b98b46af8742cc03ae83543e4d7688c2420f8b/pip-21.3.1-py3-none-any.whl (1.7MB)
Collecting wheel
  Downloading https://files.pythonhosted.org/packages/27/d6/003e593296a85fd6ed616ed962795b2f87709c3eee2bca4f6d0fe55c6d00/wheel-0.37.1-py2.py3-none-any.whl
Collecting setuptools
  Downloading https://files.pythonhosted.org/packages/b0/3a/88b210db68e56854d0bcf4b38e165e03be377e13907746f825790f3df5bf/setuptools-59.6.0-py3-none-any.whl (952kB)
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: 'biopython==1.78', 'h5py==2.10.0', 'Keras-Preprocessing==1.1.2', 'numpy==1.19.5', 'pandas==1.1.5', 'pip==21.0.1', 'scikit-learn==0.21.2', 'scipy==1.5.3', 'setuptools==49.6.0', 'six==1.15.0', 'tensorflow==2.4.1'
Collecting biopython==1.78
  Downloading biopython-1.78-cp36-cp36m-manylinux1_x86_64.whl (2.3 MB)
Collecting h5py==2.10.0
  Downloading h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9 MB)
Collecting Keras-Preprocessing==1.1.2
  Downloading Keras_Preprocessing-1.1.2-py2.py3-none-any.whl (42 kB)
Collecting numpy==1.19.5
  Using cached numpy-1.19.5-cp36-cp36m-manylinux2010_x86_64.whl (14.8 MB)
Collecting pandas==1.1.5
  Downloading pandas-1.1.5-cp36-cp36m-manylinux1_x86_64.whl (9.5 MB)
Collecting pip==21.0.1
  Downloading pip-21.0.1-py3-none-any.whl (1.5 MB)
Collecting scikit-learn==0.21.2
  Downloading scikit_learn-0.21.2-cp36-cp36m-manylinux1_x86_64.whl (6.7 MB)
Collecting scipy==1.5.3
  Downloading scipy-1.5.3-cp36-cp36m-manylinux1_x86_64.whl (25.9 MB)
Collecting setuptools==49.6.0
  Downloading setuptools-49.6.0-py3-none-any.whl (803 kB)
Collecting six==1.15.0
  Downloading six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting tensorflow==2.4.1
  Using cached tensorflow-2.4.1-cp36-cp36m-manylinux2010_x86_64.whl (394.3 MB)
Collecting pytz>=2017.2
  Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
Collecting python-dateutil>=2.7.3
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Collecting joblib>=0.11
  Downloading joblib-1.1.1-py2.py3-none-any.whl (309 kB)
Collecting tensorboard~=2.4
  Using cached tensorboard-2.10.1-py3-none-any.whl (5.9 MB)
Collecting gast==0.3.3
  Using cached gast-0.3.3-py2.py3-none-any.whl (9.7 kB)
Collecting absl-py~=0.10
  Using cached absl_py-0.15.0-py3-none-any.whl (132 kB)
Collecting protobuf>=3.9.2
  Using cached protobuf-3.19.6-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
Collecting tensorflow-estimator<2.5.0,>=2.4.0
  Using cached tensorflow_estimator-2.4.0-py2.py3-none-any.whl (462 kB)
Collecting wrapt~=1.12.1
  Using cached wrapt-1.12.1-cp36-cp36m-linux_x86_64.whl
Collecting flatbuffers~=1.12.0
  Using cached flatbuffers-1.12-py2.py3-none-any.whl (15 kB)
Collecting google-pasta~=0.2
  Using cached google_pasta-0.2.0-py3-none-any.whl (57 kB)
Collecting grpcio~=1.32.0
  Using cached grpcio-1.32.0-cp36-cp36m-manylinux2014_x86_64.whl (3.8 MB)
Collecting astunparse~=1.6.3
  Using cached astunparse-1.6.3-py2.py3-none-any.whl (12 kB)
Collecting termcolor~=1.1.0
  Using cached termcolor-1.1.0-py3-none-any.whl
Collecting typing-extensions~=3.7.4
  Using cached typing_extensions-3.7.4.3-py3-none-any.whl (22 kB)
Collecting opt-einsum~=3.3.0
  Using cached opt_einsum-3.3.0-py3-none-any.whl (65 kB)
Requirement already satisfied: wheel~=0.35 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow==2.4.1) (0.37.1)
Collecting tensorboard-plugin-wit>=1.6.0
  Using cached tensorboard_plugin_wit-1.8.1-py3-none-any.whl (781 kB)
Collecting werkzeug>=1.0.1
  Using cached Werkzeug-2.0.3-py3-none-any.whl (289 kB)
Collecting google-auth<3,>=1.6.3
  Using cached google_auth-2.22.0-py2.py3-none-any.whl (181 kB)
Collecting tensorboard-data-server<0.7.0,>=0.6.0
  Using cached tensorboard_data_server-0.6.1-py3-none-manylinux2010_x86_64.whl (4.9 MB)
Collecting requests<3,>=2.21.0
  Using cached requests-2.27.1-py2.py3-none-any.whl (63 kB)
Collecting markdown>=2.6.8
  Using cached Markdown-3.3.7-py3-none-any.whl (97 kB)
Collecting google-auth-oauthlib<0.5,>=0.4.1
  Using cached google_auth_oauthlib-0.4.6-py2.py3-none-any.whl (18 kB)
Collecting cachetools<6.0,>=2.0.0
  Using cached cachetools-4.2.4-py3-none-any.whl (10 kB)
Collecting pyasn1-modules>=0.2.1
  Using cached pyasn1_modules-0.3.0-py2.py3-none-any.whl (181 kB)
Collecting rsa<5,>=3.1.4
  Using cached rsa-4.9.1-py3-none-any.whl (34 kB)
Collecting urllib3<2.0
  Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
Collecting requests-oauthlib>=0.7.0
  Using cached requests_oauthlib-2.0.0-py2.py3-none-any.whl (24 kB)
Collecting importlib-metadata>=4.4
  Using cached importlib_metadata-4.8.3-py3-none-any.whl (17 kB)
Collecting certifi>=2017.4.17
  Downloading certifi-2025.4.26-py3-none-any.whl (159 kB)
Collecting idna<4,>=2.5
  Using cached idna-3.10-py3-none-any.whl (70 kB)
Collecting charset-normalizer~=2.0.0
  Using cached charset_normalizer-2.0.12-py3-none-any.whl (39 kB)
Collecting dataclasses
  Using cached dataclasses-0.8-py3-none-any.whl (19 kB)
Collecting zipp>=0.5
  Using cached zipp-3.6.0-py3-none-any.whl (5.3 kB)
Collecting pyasn1<0.6.0,>=0.4.6
  Using cached pyasn1-0.5.1-py2.py3-none-any.whl (84 kB)
Collecting oauthlib>=3.0.0
  Using cached oauthlib-3.2.2-py3-none-any.whl (151 kB)
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
  Attempting uninstall: setuptools
    Found existing installation: setuptools 59.6.0
    Uninstalling setuptools-59.6.0:
      Successfully uninstalled setuptools-59.6.0
  Attempting uninstall: pip
    Found existing installation: pip 21.3.1
    Uninstalling pip-21.3.1:
      Successfully uninstalled pip-21.3.1
Successfully installed Keras-Preprocessing-1.1.2 absl-py-0.15.0 astunparse-1.6.3 biopython-1.78 cachetools-4.2.4 certifi-2025.4.26 charset-normalizer-2.0.12 dataclasses-0.8 flatbuffers-1.12 gast-0.3.3 google-auth-2.22.0 google-auth-oauthlib-0.4.6 google-pasta-0.2.0 grpcio-1.32.0 h5py-2.10.0 idna-3.10 importlib-metadata-4.8.3 joblib-1.1.1 markdown-3.3.7 numpy-1.19.5 oauthlib-3.2.2 opt-einsum-3.3.0 pandas-1.1.5 pip-21.0.1 protobuf-3.19.6 pyasn1-0.5.1 pyasn1-modules-0.3.0 python-dateutil-2.9.0.post0 pytz-2025.2 requests-2.27.1 requests-oauthlib-2.0.0 rsa-4.9.1 scikit-learn-0.21.2 scipy-1.5.3 setuptools-49.6.0 six-1.15.0 tensorboard-2.10.1 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.1 tensorflow-2.4.1 tensorflow-estimator-2.4.0 termcolor-1.1.0 typing-extensions-3.7.4.3 urllib3-1.26.20 werkzeug-2.0.3 wrapt-1.12.1 zipp-3.6.0
Virtual environment '/home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk' successfully created.
Processing /home/biocbuild/bbs-3.22-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/enpamgb
Requirement already satisfied: biopython>=1.74 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (1.78)
Requirement already satisfied: joblib>=0.13.2 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (1.1.1)
Requirement already satisfied: numpy>=1.16.4 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (1.19.5)
Requirement already satisfied: pandas>=0.24.2 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (1.1.5)
Requirement already satisfied: scikit-learn==0.21.2 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (0.21.2)
Requirement already satisfied: scipy>=1.3.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (1.5.3)
Requirement already satisfied: tensorflow>=1.14.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (2.4.1)
Requirement already satisfied: pytz>=2017.2 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from pandas>=0.24.2->sgrna-modeler==0.1.0) (2025.2)
Requirement already satisfied: python-dateutil>=2.7.3 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from pandas>=0.24.2->sgrna-modeler==0.1.0) (2.9.0.post0)
Requirement already satisfied: six>=1.5 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from python-dateutil>=2.7.3->pandas>=0.24.2->sgrna-modeler==0.1.0) (1.15.0)
Requirement already satisfied: h5py~=2.10.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.10.0)
Requirement already satisfied: google-pasta~=0.2 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.2.0)
Requirement already satisfied: keras-preprocessing~=1.1.2 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.1.2)
Requirement already satisfied: typing-extensions~=3.7.4 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (3.7.4.3)
Requirement already satisfied: grpcio~=1.32.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.32.0)
Requirement already satisfied: flatbuffers~=1.12.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.12)
Requirement already satisfied: opt-einsum~=3.3.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (3.3.0)
Requirement already satisfied: gast==0.3.3 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.3.3)
Requirement already satisfied: astunparse~=1.6.3 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.6.3)
Requirement already satisfied: tensorflow-estimator<2.5.0,>=2.4.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.4.0)
Requirement already satisfied: absl-py~=0.10 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.15.0)
Requirement already satisfied: termcolor~=1.1.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.1.0)
Requirement already satisfied: protobuf>=3.9.2 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (3.19.6)
Requirement already satisfied: wheel~=0.35 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.37.1)
Requirement already satisfied: wrapt~=1.12.1 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.12.1)
Requirement already satisfied: tensorboard~=2.4 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.10.1)
Requirement already satisfied: werkzeug>=1.0.1 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.0.3)
Requirement already satisfied: markdown>=2.6.8 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (3.3.7)
Requirement already satisfied: requests<3,>=2.21.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.27.1)
Requirement already satisfied: tensorboard-data-server<0.7.0,>=0.6.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.6.1)
Requirement already satisfied: google-auth<3,>=1.6.3 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.22.0)
Requirement already satisfied: google-auth-oauthlib<0.5,>=0.4.1 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.4.6)
Requirement already satisfied: tensorboard-plugin-wit>=1.6.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.8.1)
Requirement already satisfied: setuptools>=41.0.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (49.6.0)
Requirement already satisfied: pyasn1-modules>=0.2.1 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from google-auth<3,>=1.6.3->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.3.0)
Requirement already satisfied: cachetools<6.0,>=2.0.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from google-auth<3,>=1.6.3->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (4.2.4)
Requirement already satisfied: urllib3<2.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from google-auth<3,>=1.6.3->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.26.20)
Requirement already satisfied: rsa<5,>=3.1.4 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from google-auth<3,>=1.6.3->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (4.9.1)
Requirement already satisfied: requests-oauthlib>=0.7.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from google-auth-oauthlib<0.5,>=0.4.1->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.0.0)
Requirement already satisfied: importlib-metadata>=4.4 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from markdown>=2.6.8->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (4.8.3)
Requirement already satisfied: zipp>=0.5 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/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)
Requirement already satisfied: pyasn1<0.6.0,>=0.4.6 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib/python3.6/site-packages (from pyasn1-modules>=0.2.1->google-auth<3,>=1.6.3->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.5.1)
Requirement already satisfied: idna<4,>=2.5 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/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) (3.10)
Requirement already satisfied: charset-normalizer~=2.0.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/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: certifi>=2017.4.17 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/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: oauthlib>=3.0.0 in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/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 /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/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=39a0254fedbe2dded46170527899165b96542a21fc1921704578c0849366bf70
  Stored in directory: /tmp/pip-ephem-wheel-cache-nh8foov1/wheels/3f/4c/86/1c3daecc0cd3afd58ca844e1aff30d4a547bb1d18e527c0457
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 '/home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/bin/python -m pip install --upgrade pip' command.
2025-07-12 16:31:51.769024: 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: /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib:/home/biocbuild/.pyenv/versions/3.6.15/lib:/home/biocbuild/bbs-3.22-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/enpamgb_basilisk/lib:/home/biocbuild/.pyenv/versions/3.6.15/lib:/home/biocbuild/bbs-3.22-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.22-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.22-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.22-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.22-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server
2025-07-12 16:31:51.769086: 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 '/home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/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 '/home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/lindel_basilisk' successfully created.
Processing /home/biocbuild/bbs-3.22-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/lindel
Requirement already satisfied: numpy in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/lindel_basilisk/lib/python3.6/site-packages (from Lindel==1.0) (1.19.5)
Requirement already satisfied: scipy in /home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/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=15e2842a7e43df9934a4a1b7519d4682480ca4fb5ca6e2402187085dd3521b83
  Stored in directory: /tmp/pip-ephem-wheel-cache-kldk6rdq/wheels/20/03/df/2cc35faa8b99cd2631ed892e4d179b360049181d537f265e6f
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 '/home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/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 '/home/biocbuild/.cache/R/basilisk/1.21.5/crisprScore/1.13.1/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-3.22-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_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/crisprScore.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 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 ‘1.13.1’
* 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-3.22-bioc-longtests/meat/crisprScore.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    python   6.0Mb
* 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-3.22-bioc-longtests/meat/crisprScore.Rcheck/00check.log’
for details.

* installing *source* package ‘crisprScore’ ...
** this is package ‘crisprScore’ version ‘1.13.1’
** 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)