Back to Long Tests report for BioC 3.19

This page was generated on 2024-06-22 23:55 -0400 (Sat, 22 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 18/33HostnameOS / ArchCHECK
crisprScore 1.8.0  (landing page)
Jean-Philippe Fortin
Snapshot Date: 2024-06-22 09:55 -0400 (Sat, 22 Jun 2024)
git_url: https://git.bioconductor.org/packages/crisprScore
git_branch: RELEASE_3_19
git_last_commit: af3634d
git_last_commit_date: 2024-04-30 11:39:45 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.4 Monterey / x86_64  OK  


CHECK results for crisprScore on merida1

To the developers/maintainers of the crisprScore package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: crisprScore
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2024-06-22 16:06:30 -0400 (Sat, 22 Jun 2024)
EndedAt: 2024-06-22 16:53:10 -0400 (Sat, 22 Jun 2024)
EllapsedTime: 2799.8 seconds
RetCode: 0
Status:   OK  
CheckDir: crisprScore.Rcheck
Warnings: 0

Tests output

crisprScore.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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: /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk

  added / updated specs:
    - python=2.7


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libffi-3.2.1               |                1          41 KB  bioconda
    ------------------------------------------------------------
                                           Total:          41 KB

The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
  certifi            conda-forge/osx-64::certifi-2019.11.28-py27h8c360ce_1
  libcxx             conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
  libffi             bioconda/osx-64::libffi-3.2.1-1
  libsqlite          conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0
  libzlib            conda-forge/osx-64::libzlib-1.2.13-h87427d6_6
  ncurses            conda-forge/osx-64::ncurses-6.5-h5846eda_0
  openssl            conda-forge/osx-64::openssl-1.1.1w-h8a1eda9_0
  pip                conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
  python             conda-forge/osx-64::python-2.7.15-h8e446fc_1011_cpython
  python_abi         conda-forge/osx-64::python_abi-2.7-1_cp27m
  readline           conda-forge/osx-64::readline-8.2-h9e318b2_1
  setuptools         conda-forge/osx-64::setuptools-44.0.0-py27_0
  sqlite             conda-forge/osx-64::sqlite-3.46.0-h28673e1_0
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
  zlib               conda-forge/osx-64::zlib-1.2.13-h87427d6_6


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk

  added / updated specs:
    - biopython=1.74
    - certifi=2019.11.28
    - cycler=0.10.0
    - futures=3.3.0
    - kiwisolver=1.1.0
    - matplotlib=2.2.3
    - mmtf-python=1.1.2
    - nose=1.3.7
    - numpy=1.11.3
    - olefile=0.46
    - pandas=0.23.4
    - pillow=6.2.1
    - pip=20.1.1
    - pyparsing=2.4.7
    - python-dateutil=2.8.1
    - python[version='2.7.*,2.7.*']
    - pytz=2020.1
    - reportlab=3.5.42
    - scipy=1.2.1
    - setuptools=44.0.0
    - six=1.15.0
    - subprocess32=3.5.4
    - tornado=5.1.1
    - wheel=0.36.2


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    backports-1.0              |     pyhd8ed1ab_3           6 KB  conda-forge
    backports.functools_lru_cache-1.6.1|             py_0           8 KB  conda-forge
    backports_abc-0.5          |             py_1           5 KB  conda-forge
    biopython-1.74             |   py27h0b31af3_0         2.5 MB  conda-forge
    cycler-0.10.0              |             py_2           9 KB  conda-forge
    functools32-3.2.3.2        |             py_3          15 KB  conda-forge
    futures-3.3.0              |   py27h8c360ce_1          25 KB  conda-forge
    kiwisolver-1.1.0           |   py27h5cd23e5_1          57 KB  conda-forge
    libblas-3.8.0              |      14_openblas          10 KB  conda-forge
    libcblas-3.8.0             |      14_openblas          10 KB  conda-forge
    libgfortran-3.0.1          |                0         495 KB  conda-forge
    liblapack-3.8.0            |      14_openblas          10 KB  conda-forge
    libopenblas-0.3.7          |       hd44dcd8_1         8.4 MB  conda-forge
    matplotlib-2.2.3           |           py27_1           6 KB  conda-forge
    matplotlib-base-2.2.3      |   py27hd64abcd_1         6.4 MB  conda-forge
    mmtf-python-1.1.2          |             py_0          21 KB  conda-forge
    msgpack-python-1.0.0       |   py27h5cd23e5_1          28 KB  conda-forge
    nose-1.3.7                 |py27h8c360ce_1004         214 KB  conda-forge
    numpy-1.11.3               |py27hdf140aa_1207         3.5 MB  conda-forge
    olefile-0.46               |     pyh9f0ad1d_1          32 KB  conda-forge
    pandas-0.23.4              |py27h1702cab_1000         9.1 MB  conda-forge
    pillow-6.2.1               |   py27h43b43f3_1         588 KB  conda-forge
    pyparsing-2.4.7            |     pyh9f0ad1d_0          60 KB  conda-forge
    pytz-2020.1                |     pyh9f0ad1d_0         227 KB  conda-forge
    reportlab-3.5.42           |   py27he89c811_0         2.4 MB  conda-forge
    scipy-1.2.1                |   py27hbd7caa9_1        15.7 MB  conda-forge
    singledispatch-3.6.1       |     pyh44b312d_0          12 KB  conda-forge
    six-1.15.0                 |     pyh9f0ad1d_0          14 KB  conda-forge
    subprocess32-3.5.4         |   py27h0b31af3_0          44 KB  conda-forge
    tornado-5.1.1              |py27h1de35cc_1000         642 KB  conda-forge
    wheel-0.36.2               |     pyhd3deb0d_0          31 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        50.6 MB

The following NEW packages will be INSTALLED:

  backports          conda-forge/noarch::backports-1.0-pyhd8ed1ab_3
  backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.1-py_0
  backports_abc      conda-forge/noarch::backports_abc-0.5-py_1
  biopython          conda-forge/osx-64::biopython-1.74-py27h0b31af3_0
  cycler             conda-forge/noarch::cycler-0.10.0-py_2
  freetype           conda-forge/osx-64::freetype-2.12.1-h60636b9_2
  functools32        conda-forge/noarch::functools32-3.2.3.2-py_3
  futures            conda-forge/osx-64::futures-3.3.0-py27h8c360ce_1
  jpeg               conda-forge/osx-64::jpeg-9e-hb7f2c08_3
  kiwisolver         conda-forge/osx-64::kiwisolver-1.1.0-py27h5cd23e5_1
  libblas            conda-forge/osx-64::libblas-3.8.0-14_openblas
  libcblas           conda-forge/osx-64::libcblas-3.8.0-14_openblas
  libgfortran        conda-forge/osx-64::libgfortran-3.0.1-0
  liblapack          conda-forge/osx-64::liblapack-3.8.0-14_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.7-hd44dcd8_1
  libpng             conda-forge/osx-64::libpng-1.6.43-h92b6c6a_0
  libtiff            conda-forge/osx-64::libtiff-4.2.0-h1167814_3
  libwebp-base       conda-forge/osx-64::libwebp-base-1.4.0-h10d778d_0
  matplotlib         conda-forge/osx-64::matplotlib-2.2.3-py27_1
  matplotlib-base    conda-forge/osx-64::matplotlib-base-2.2.3-py27hd64abcd_1
  mmtf-python        conda-forge/noarch::mmtf-python-1.1.2-py_0
  msgpack-python     conda-forge/osx-64::msgpack-python-1.0.0-py27h5cd23e5_1
  nose               conda-forge/osx-64::nose-1.3.7-py27h8c360ce_1004
  numpy              conda-forge/osx-64::numpy-1.11.3-py27hdf140aa_1207
  olefile            conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1
  pandas             conda-forge/osx-64::pandas-0.23.4-py27h1702cab_1000
  pillow             conda-forge/osx-64::pillow-6.2.1-py27h43b43f3_1
  pyparsing          conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  pytz               conda-forge/noarch::pytz-2020.1-pyh9f0ad1d_0
  reportlab          conda-forge/osx-64::reportlab-3.5.42-py27he89c811_0
  scipy              conda-forge/osx-64::scipy-1.2.1-py27hbd7caa9_1
  singledispatch     conda-forge/noarch::singledispatch-3.6.1-pyh44b312d_0
  six                conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
  subprocess32       conda-forge/osx-64::subprocess32-3.5.4-py27h0b31af3_0
  tornado            conda-forge/osx-64::tornado-5.1.1-py27h1de35cc_1000
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0
  zstd               conda-forge/osx-64::zstd-1.5.6-h915ae27_0

The following packages will be DOWNGRADED:

  wheel                                 0.37.1-pyhd8ed1ab_0 --> 0.36.2-pyhd3deb0d_0



Downloading and Extracting Packages

numpy-1.11.3         | 3.5 MB    |            |   0% 
numpy-1.11.3         | 3.5 MB    |            |   0% 
numpy-1.11.3         | 3.5 MB    | ########## | 100% 
numpy-1.11.3         | 3.5 MB    | ########## | 100% 

six-1.15.0           | 14 KB     |            |   0% 
six-1.15.0           | 14 KB     | ########## | 100% 

libgfortran-3.0.1    | 495 KB    |            |   0% 
libgfortran-3.0.1    | 495 KB    | ########## | 100% 
libgfortran-3.0.1    | 495 KB    | ########## | 100% 

scipy-1.2.1          | 15.7 MB   |            |   0% 
scipy-1.2.1          | 15.7 MB   |            |   0% 
scipy-1.2.1          | 15.7 MB   | ##1        |  22% 
scipy-1.2.1          | 15.7 MB   | #####5     |  56% 
scipy-1.2.1          | 15.7 MB   | ########## | 100% 
scipy-1.2.1          | 15.7 MB   | ########## | 100% 

liblapack-3.8.0      | 10 KB     |            |   0% 
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libcblas-3.8.0       | 10 KB     |            |   0% 
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singledispatch-3.6.1 | 12 KB     |            |   0% 
singledispatch-3.6.1 | 12 KB     | ########## | 100% 
singledispatch-3.6.1 | 12 KB     | ########## | 100% 

pillow-6.2.1         | 588 KB    |            |   0% 
pillow-6.2.1         | 588 KB    | ##7        |  27% 
pillow-6.2.1         | 588 KB    | ########## | 100% 
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wheel-0.36.2         | 31 KB     |            |   0% 
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mmtf-python-1.1.2    | 21 KB     |            |   0% 
mmtf-python-1.1.2    | 21 KB     | ########## | 100% 
mmtf-python-1.1.2    | 21 KB     | ########## | 100% 

subprocess32-3.5.4   | 44 KB     |            |   0% 
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backports.functools_ | 8 KB      |            |   0% 
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functools32-3.2.3.2  | 15 KB     |            |   0% 
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matplotlib-2.2.3     | 6 KB      |            |   0% 
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backports_abc-0.5    | 5 KB      |            |   0% 
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pandas-0.23.4        | 9.1 MB    |            |   0% 
pandas-0.23.4        | 9.1 MB    |            |   0% 
pandas-0.23.4        | 9.1 MB    | ##8        |  29% 
pandas-0.23.4        | 9.1 MB    | ######1    |  62% 
pandas-0.23.4        | 9.1 MB    | ########## | 100% 
pandas-0.23.4        | 9.1 MB    | ########## | 100% 

pyparsing-2.4.7      | 60 KB     |            |   0% 
pyparsing-2.4.7      | 60 KB     | ########## | 100% 
pyparsing-2.4.7      | 60 KB     | ########## | 100% 

tornado-5.1.1        | 642 KB    |            |   0% 
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kiwisolver-1.1.0     | 57 KB     |            |   0% 
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backports-1.0        | 6 KB      |            |   0% 
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backports-1.0        | 6 KB      | ########## | 100% 

msgpack-python-1.0.0 | 28 KB     |            |   0% 
msgpack-python-1.0.0 | 28 KB     | #####8     |  58% 
msgpack-python-1.0.0 | 28 KB     | ########## | 100% 

libopenblas-0.3.7    | 8.4 MB    |            |   0% 
libopenblas-0.3.7    | 8.4 MB    |            |   0% 
libopenblas-0.3.7    | 8.4 MB    | ####1      |  41% 
libopenblas-0.3.7    | 8.4 MB    | ######4    |  65% 
libopenblas-0.3.7    | 8.4 MB    | ########## | 100% 
libopenblas-0.3.7    | 8.4 MB    | ########## | 100% 

pytz-2020.1          | 227 KB    |            |   0% 
pytz-2020.1          | 227 KB    | ########## | 100% 
pytz-2020.1          | 227 KB    | ########## | 100% 

nose-1.3.7           | 214 KB    |            |   0% 
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nose-1.3.7           | 214 KB    | ########## | 100% 
nose-1.3.7           | 214 KB    | ########## | 100% 

matplotlib-base-2.2. | 6.4 MB    |            |   0% 
matplotlib-base-2.2. | 6.4 MB    |            |   0% 
matplotlib-base-2.2. | 6.4 MB    | ######3    |  64% 
matplotlib-base-2.2. | 6.4 MB    | ########## | 100% 
matplotlib-base-2.2. | 6.4 MB    | ########## | 100% 

libblas-3.8.0        | 10 KB     |            |   0% 
libblas-3.8.0        | 10 KB     | ########## | 100% 
libblas-3.8.0        | 10 KB     | ########## | 100% 

reportlab-3.5.42     | 2.4 MB    |            |   0% 
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reportlab-3.5.42     | 2.4 MB    | ########## | 100% 
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biopython-1.74       | 2.5 MB    |            |   0% 
biopython-1.74       | 2.5 MB    |            |   1% 
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futures-3.3.0        | 25 KB     |            |   0% 
futures-3.3.0        | 25 KB     | ######2    |  63% 
futures-3.3.0        | 25 KB     | ########## | 100% 

olefile-0.46         | 32 KB     |            |   0% 
olefile-0.46         | 32 KB     | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Collecting scikit-learn==0.17.1
  Using cached scikit_learn-0.17.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.9 MB)
Installing collected packages: scikit-learn
Successfully installed scikit-learn-0.17.1
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Processing /Users/biocbuild/bbs-3.19-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth
Requirement already satisfied: scipy<=1.2.1 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.2.1)
Requirement already satisfied: numpy<=1.14 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.11.3)
Requirement already satisfied: matplotlib in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (2.2.3)
Requirement already satisfied: nose in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.3.7)
Requirement already satisfied: scikit-learn<0.18,>=0.17.1 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (0.17.1)
Requirement already satisfied: pandas in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (0.23.4)
Requirement already satisfied: biopython<=1.76 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.74)
Requirement already satisfied: cycler>=0.10 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (2.4.7)
Requirement already satisfied: python-dateutil>=2.1 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (2.8.1)
Requirement already satisfied: pytz in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (2020.1)
Requirement already satisfied: six>=1.10 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (1.15.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (1.1.0)
Requirement already satisfied: backports.functools_lru_cache in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (1.6.1)
Requirement already satisfied: subprocess32 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (3.5.4)
Requirement already satisfied: setuptools in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages (from kiwisolver>=1.0.1->matplotlib->Azimuth==2.0) (44.0.0.post20200102)
Building wheels for collected packages: Azimuth
  Building wheel for Azimuth (setup.py): started
  Building wheel for Azimuth (setup.py): finished with status 'done'
  Created wheel for Azimuth: filename=Azimuth-2.0-py2-none-any.whl size=163884 sha256=21c1bd6fbbb108c17bb93653e29c39936bae04df53a24c69fb008cd997a4c327
  Stored in directory: /private/tmp/pip-ephem-wheel-cache-qTRfvL/wheels/50/0c/68/5f0c76edd14de81c954a615bbac6911c311201f9d0a99ff5ec
Successfully built Azimuth
Installing collected packages: Azimuth
Successfully installed Azimuth-2.0
/Users/biocbuild/bbs-3.19-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-3.19-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth/getAzimuth.py", line 4, in <module>
    import azimuth.model_comparison
  File "/Users/biocbuild/bbs-3.19-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-3.19-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth/azimuth/predict.py", line 7, in <module>
    import util
  File "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth/azimuth/util.py", line 2, in <module>
    import matplotlib.pylab as plt
  File "/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages/matplotlib/pylab.py", line 252, in <module>
    from matplotlib import cbook, mlab, pyplot as plt
  File "/var/cache/basilisk/1.16.0/crisprScore/1.8.0/azimuth_basilisk/lib/python2.7/site-packages/matplotlib/pyplot.py", line 71, in <module>
    from matplotlib.backends import pylab_setup
  File "/var/cache/basilisk/1.16.0/crisprScore/1.8.0/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')
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: /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deepcpf1_basilisk

  added / updated specs:
    - python=2.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
  certifi            conda-forge/osx-64::certifi-2019.11.28-py27h8c360ce_1
  libcxx             conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
  libffi             conda-forge/osx-64::libffi-3.2.1-hb1e8313_1007
  libsqlite          conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0
  libzlib            conda-forge/osx-64::libzlib-1.2.13-h87427d6_6
  ncurses            conda-forge/osx-64::ncurses-6.5-h5846eda_0
  openssl            conda-forge/osx-64::openssl-1.1.1w-h8a1eda9_0
  pip                conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
  python             conda-forge/osx-64::python-2.7.15-h8e446fc_1011_cpython
  python_abi         conda-forge/osx-64::python_abi-2.7-1_cp27m
  readline           conda-forge/osx-64::readline-8.2-h9e318b2_1
  setuptools         conda-forge/osx-64::setuptools-44.0.0-py27_0
  sqlite             conda-forge/osx-64::sqlite-3.46.0-h28673e1_0
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
  zlib               conda-forge/osx-64::zlib-1.2.13-h87427d6_6


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1
done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0
done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deepcpf1_basilisk

  added / updated specs:
    - funcsigs=1.0.2
    - h5py=2.10.0
    - keras=2.1.5
    - linecache2=1.0.0
    - mako=1.1.4
    - markupsafe=1.1.1
    - mock=3.0.5
    - numpy=1.16.5
    - pip=20.1.1
    - protobuf=3.11.4
    - pygpu=0.7.6
    - python[version='2.7.*,2.7.*']
    - pyyaml=5.3.1
    - scipy=1.2.1
    - setuptools=44.0.0
    - six=1.15.0
    - tensorflow=1.0.0
    - theano=1.0.1
    - traceback2=1.4.0
    - unittest2=1.1.0
    - wheel=0.36.2


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    funcsigs-1.0.2             |             py_3          14 KB  conda-forge
    h5py-2.10.0                |nompi_py27h106b333_102         996 KB  conda-forge
    hdf5-1.10.5                |nompi_h3e39495_1104         3.0 MB  conda-forge
    keras-2.1.5                |           py27_0         491 KB  conda-forge
    libblas-3.9.0              |       8_openblas          11 KB  conda-forge
    libcblas-3.9.0             |       8_openblas          11 KB  conda-forge
    libgfortran-4.0.0          |7_5_0_h1a10cd1_23          19 KB  conda-forge
    libgfortran4-7.5.0         |      h1a10cd1_23         1.1 MB  conda-forge
    libgpuarray-0.7.6          |    h0d85af4_1003         191 KB  conda-forge
    liblapack-3.9.0            |       8_openblas          11 KB  conda-forge
    libopenblas-0.3.12         |openmp_h63d9170_1         8.7 MB  conda-forge
    libprotobuf-3.11.4         |       hd174df1_0         4.4 MB  conda-forge
    linecache2-1.0.0           |             py_1          13 KB  conda-forge
    mako-1.1.4                 |     pyh44b312d_0          58 KB  conda-forge
    markupsafe-1.1.1           |   py27h89ed719_1          24 KB  conda-forge
    mock-3.0.5                 |   py27h8c360ce_1          43 KB  conda-forge
    numpy-1.16.5               |   py27hde6bac1_0         4.2 MB  conda-forge
    protobuf-3.11.4            |   py27h4a8c4bd_0         684 KB  conda-forge
    pygpu-0.7.6                |py27h3b54f70_1000         624 KB  conda-forge
    pyyaml-5.3.1               |   py27h89ed719_0         171 KB  conda-forge
    scipy-1.2.1                |   py27h7e0e109_2        17.8 MB  conda-forge
    tensorflow-1.0.0           |           py27_0        32.0 MB  conda-forge
    theano-1.0.1               |           py27_1         3.6 MB  conda-forge
    traceback2-1.4.0           |           py27_0          28 KB  conda-forge
    unittest2-1.1.0            |             py_0          68 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        78.2 MB

The following NEW packages will be INSTALLED:

  funcsigs           conda-forge/noarch::funcsigs-1.0.2-py_3
  h5py               conda-forge/osx-64::h5py-2.10.0-nompi_py27h106b333_102
  hdf5               conda-forge/osx-64::hdf5-1.10.5-nompi_h3e39495_1104
  keras              conda-forge/osx-64::keras-2.1.5-py27_0
  libblas            conda-forge/osx-64::libblas-3.9.0-8_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-8_openblas
  libgfortran        conda-forge/osx-64::libgfortran-4.0.0-7_5_0_h1a10cd1_23
  libgfortran4       conda-forge/osx-64::libgfortran4-7.5.0-h1a10cd1_23
  libgpuarray        conda-forge/osx-64::libgpuarray-0.7.6-h0d85af4_1003
  liblapack          conda-forge/osx-64::liblapack-3.9.0-8_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.12-openmp_h63d9170_1
  libprotobuf        conda-forge/osx-64::libprotobuf-3.11.4-hd174df1_0
  linecache2         conda-forge/noarch::linecache2-1.0.0-py_1
  llvm-openmp        conda-forge/osx-64::llvm-openmp-18.1.8-h15ab845_0
  mako               conda-forge/noarch::mako-1.1.4-pyh44b312d_0
  markupsafe         conda-forge/osx-64::markupsafe-1.1.1-py27h89ed719_1
  mock               conda-forge/osx-64::mock-3.0.5-py27h8c360ce_1
  numpy              conda-forge/osx-64::numpy-1.16.5-py27hde6bac1_0
  protobuf           conda-forge/osx-64::protobuf-3.11.4-py27h4a8c4bd_0
  pygpu              conda-forge/osx-64::pygpu-0.7.6-py27h3b54f70_1000
  pyyaml             conda-forge/osx-64::pyyaml-5.3.1-py27h89ed719_0
  scipy              conda-forge/osx-64::scipy-1.2.1-py27h7e0e109_2
  six                conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
  tensorflow         conda-forge/osx-64::tensorflow-1.0.0-py27_0
  theano             conda-forge/osx-64::theano-1.0.1-py27_1
  traceback2         conda-forge/osx-64::traceback2-1.4.0-py27_0
  unittest2          conda-forge/noarch::unittest2-1.1.0-py_0
  yaml               conda-forge/osx-64::yaml-0.2.5-h0d85af4_2

The following packages will be DOWNGRADED:

  wheel                                 0.37.1-pyhd8ed1ab_0 --> 0.36.2-pyhd3deb0d_0



Downloading and Extracting Packages

libopenblas-0.3.12   | 8.7 MB    |            |   0% 
libopenblas-0.3.12   | 8.7 MB    |            |   0% 
libopenblas-0.3.12   | 8.7 MB    | #######9   |  79% 
libopenblas-0.3.12   | 8.7 MB    | ########## | 100% 

mock-3.0.5           | 43 KB     |            |   0% 
mock-3.0.5           | 43 KB     | ###6       |  37% 
mock-3.0.5           | 43 KB     | ########## | 100% 

markupsafe-1.1.1     | 24 KB     |            |   0% 
markupsafe-1.1.1     | 24 KB     | ######5    |  66% 
markupsafe-1.1.1     | 24 KB     | ########## | 100% 

mako-1.1.4           | 58 KB     |            |   0% 
mako-1.1.4           | 58 KB     | ##7        |  28% 
mako-1.1.4           | 58 KB     | ########## | 100% 

pyyaml-5.3.1         | 171 KB    |            |   0% 
pyyaml-5.3.1         | 171 KB    | 9          |   9% 
pyyaml-5.3.1         | 171 KB    | ########## | 100% 

traceback2-1.4.0     | 28 KB     |            |   0% 
traceback2-1.4.0     | 28 KB     | ########## | 100% 
traceback2-1.4.0     | 28 KB     | ########## | 100% 

tensorflow-1.0.0     | 32.0 MB   |            |   0% 
tensorflow-1.0.0     | 32.0 MB   |            |   0% 
tensorflow-1.0.0     | 32.0 MB   | 7          |   8% 
tensorflow-1.0.0     | 32.0 MB   | #6         |  16% 
tensorflow-1.0.0     | 32.0 MB   | ###3       |  33% 
tensorflow-1.0.0     | 32.0 MB   | ####3      |  44% 
tensorflow-1.0.0     | 32.0 MB   | #####3     |  54% 
tensorflow-1.0.0     | 32.0 MB   | ######6    |  66% 
tensorflow-1.0.0     | 32.0 MB   | ########7  |  87% 
tensorflow-1.0.0     | 32.0 MB   | ########## | 100% 

libcblas-3.9.0       | 11 KB     |            |   0% 
libcblas-3.9.0       | 11 KB     | ########## | 100% 

libgfortran4-7.5.0   | 1.1 MB    |            |   0% 
libgfortran4-7.5.0   | 1.1 MB    | ########## | 100% 
libgfortran4-7.5.0   | 1.1 MB    | ########## | 100% 

linecache2-1.0.0     | 13 KB     |            |   0% 
linecache2-1.0.0     | 13 KB     | ########## | 100% 

funcsigs-1.0.2       | 14 KB     |            |   0% 
funcsigs-1.0.2       | 14 KB     | ########## | 100% 

numpy-1.16.5         | 4.2 MB    |            |   0% 
numpy-1.16.5         | 4.2 MB    | ##         |  21% 
numpy-1.16.5         | 4.2 MB    | ########## | 100% 
numpy-1.16.5         | 4.2 MB    | ########## | 100% 

theano-1.0.1         | 3.6 MB    |            |   0% 
theano-1.0.1         | 3.6 MB    |            |   0% 
theano-1.0.1         | 3.6 MB    | ########## | 100% 
theano-1.0.1         | 3.6 MB    | ########## | 100% 

libblas-3.9.0        | 11 KB     |            |   0% 
libblas-3.9.0        | 11 KB     | ########## | 100% 

unittest2-1.1.0      | 68 KB     |            |   0% 
unittest2-1.1.0      | 68 KB     | ##3        |  24% 
unittest2-1.1.0      | 68 KB     | ########## | 100% 

pygpu-0.7.6          | 624 KB    |            |   0% 
pygpu-0.7.6          | 624 KB    | 2          |   3% 
pygpu-0.7.6          | 624 KB    | ########## | 100% 
pygpu-0.7.6          | 624 KB    | ########## | 100% 

h5py-2.10.0          | 996 KB    |            |   0% 
h5py-2.10.0          | 996 KB    | ########5  |  85% 
h5py-2.10.0          | 996 KB    | ########## | 100% 

libgpuarray-0.7.6    | 191 KB    |            |   0% 
libgpuarray-0.7.6    | 191 KB    | ########## | 100% 
libgpuarray-0.7.6    | 191 KB    | ########## | 100% 

protobuf-3.11.4      | 684 KB    |            |   0% 
protobuf-3.11.4      | 684 KB    | 2          |   2% 
protobuf-3.11.4      | 684 KB    | ########## | 100% 
protobuf-3.11.4      | 684 KB    | ########## | 100% 

keras-2.1.5          | 491 KB    |            |   0% 
keras-2.1.5          | 491 KB    | 3          |   3% 
keras-2.1.5          | 491 KB    | ########## | 100% 
keras-2.1.5          | 491 KB    | ########## | 100% 

libprotobuf-3.11.4   | 4.4 MB    |            |   0% 
libprotobuf-3.11.4   | 4.4 MB    | ##2        |  22% 
libprotobuf-3.11.4   | 4.4 MB    | ########## | 100% 
libprotobuf-3.11.4   | 4.4 MB    | ########## | 100% 

scipy-1.2.1          | 17.8 MB   |            |   0% 
scipy-1.2.1          | 17.8 MB   |            |   0% 
scipy-1.2.1          | 17.8 MB   | ##8        |  29% 
scipy-1.2.1          | 17.8 MB   | ###9       |  39% 
scipy-1.2.1          | 17.8 MB   | ########4  |  85% 
scipy-1.2.1          | 17.8 MB   | ########## | 100% 

hdf5-1.10.5          | 3.0 MB    |            |   0% 
hdf5-1.10.5          | 3.0 MB    |            |   1% 
hdf5-1.10.5          | 3.0 MB    | ########## | 100% 
hdf5-1.10.5          | 3.0 MB    | ########## | 100% 

libgfortran-4.0.0    | 19 KB     |            |   0% 
libgfortran-4.0.0    | 19 KB     | ########3  |  83% 
libgfortran-4.0.0    | 19 KB     | ########## | 100% 

liblapack-3.9.0      | 11 KB     |            |   0% 
liblapack-3.9.0      | 11 KB     | ########## | 100% 
liblapack-3.9.0      | 11 KB     | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Processing /Users/biocbuild/bbs-3.19-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/deepcpf1
Building wheels for collected packages: DeepCpf1
  Building wheel for DeepCpf1 (setup.py): started
  Building wheel for DeepCpf1 (setup.py): finished with status 'done'
  Created wheel for DeepCpf1: filename=DeepCpf1-1.0-py2-none-any.whl size=768630 sha256=0d38d63595d573f4f3b96bed1b23e1ace31a5034ad4de5b64305ca431adb3bb0
  Stored in directory: /private/tmp/pip-ephem-wheel-cache-JltqqT/wheels/78/4e/de/36d21731afa46357ea2dd8cab932c00be9ad24b8e72b95d141
Successfully built DeepCpf1
Installing collected packages: DeepCpf1
Successfully installed DeepCpf1-1.0
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/enpamgb_basilisk

  added / updated specs:
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2016.9.26          |           py36_0         217 KB  conda-forge
    pip-20.0.2                 |           py36_1         1.9 MB  conda-forge
    python-3.6.15              |haf480d7_0_cpython        20.6 MB  conda-forge
    python_abi-3.6             |          2_cp36m           4 KB  conda-forge
    setuptools-49.6.0          |   py36h79c6626_3         916 KB  conda-forge
    wheel-0.34.2               |           py36_0          43 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        23.7 MB

The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
  certifi            conda-forge/osx-64::certifi-2016.9.26-py36_0
  libcxx             conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
  libffi             conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
  libsqlite          conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0
  libzlib            conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
  ncurses            conda-forge/osx-64::ncurses-6.5-h5846eda_0
  openssl            conda-forge/osx-64::openssl-1.1.1w-h8a1eda9_0
  pip                conda-forge/osx-64::pip-20.0.2-py36_1
  python             conda-forge/osx-64::python-3.6.15-haf480d7_0_cpython
  python_abi         conda-forge/osx-64::python_abi-3.6-2_cp36m
  readline           conda-forge/osx-64::readline-8.2-h9e318b2_1
  setuptools         conda-forge/osx-64::setuptools-49.6.0-py36h79c6626_3
  sqlite             conda-forge/osx-64::sqlite-3.46.0-h28673e1_0
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1
  wheel              conda-forge/osx-64::wheel-0.34.2-py36_0
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1
done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0
WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/enpamgb_basilisk

  added / updated specs:
    - absl-py=0.12.0
    - astunparse=1.6.3
    - biopython=1.78
    - cachetools=4.2.1
    - certifi=2020.12.5
    - chardet=4.0.0
    - flatbuffers=1.12
    - gast=0.3.3
    - google-auth-oauthlib=0.4.3
    - google-auth=1.27.1
    - google-pasta=0.2.0
    - grpcio=1.32.0
    - h5py=2.10.0
    - idna=2.10
    - importlib-metadata=3.7.2
    - joblib=1.0.1
    - keras-preprocessing=1.1.2
    - markdown=3.3.4
    - numpy=1.19.5
    - oauthlib=3.1.0
    - pandas=1.1.5
    - pip=21.0.1
    - protobuf=3.15.5
    - pyasn1-modules=0.2.8
    - pyasn1=0.4.8
    - python-dateutil=2.8.1
    - python[version='3.6.*,3.6.*']
    - pytz=2021.1
    - requests-oauthlib=1.3.0
    - requests=2.25.1
    - rsa=4.7.2
    - scikit-learn=0.21.2
    - scipy=1.5.3
    - setuptools=49.6.0
    - six=1.15.0
    - termcolor=1.1.0
    - typing-extensions=3.7.4.3
    - urllib3=1.26.3
    - werkzeug=1.0.1
    - wheel=0.36.2
    - wrapt=1.12.1
    - zipp=3.4.1


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    absl-py-0.12.0             |     pyhd8ed1ab_0          96 KB  conda-forge
    aiohttp-3.7.4.post0        |   py36hfa26744_0         608 KB  conda-forge
    async-timeout-3.0.1        |          py_1000          11 KB  conda-forge
    biopython-1.78             |   py36hfa26744_2         2.6 MB  conda-forge
    blinker-1.5                |     pyhd8ed1ab_0          15 KB  conda-forge
    brotlipy-0.7.0             |py36hfa26744_1001         357 KB  conda-forge
    cachetools-4.2.1           |     pyhd8ed1ab_0          13 KB  conda-forge
    certifi-2020.12.5          |   py36h79c6626_1         143 KB  conda-forge
    cffi-1.14.6                |   py36hbc36220_1         217 KB  conda-forge
    chardet-4.0.0              |   py36h79c6626_1         219 KB  conda-forge
    click-8.0.1                |   py36h79c6626_0         144 KB  conda-forge
    cryptography-35.0.0        |   py36ha6a00b0_0         1.2 MB  conda-forge
    flatbuffers-1.12.1         |       he49afe7_0         996 KB  conda-forge
    gast-0.3.3                 |             py_0          12 KB  conda-forge
    google-auth-1.27.1         |     pyhd3eb1b0_0          72 KB
    google-auth-oauthlib-0.4.3 |     pyhd8ed1ab_0          19 KB  conda-forge
    grpcio-1.32.0              |   py36h9799307_0         1.8 MB  conda-forge
    h5py-2.10.0                |nompi_py36h4d7a79e_106         923 KB  conda-forge
    idna-2.10                  |     pyh9f0ad1d_0          52 KB  conda-forge
    idna_ssl-1.1.0             |  pyhd8ed1ab_1002           7 KB  conda-forge
    importlib-metadata-3.7.2   |   py36h79c6626_0          23 KB  conda-forge
    joblib-1.0.1               |     pyhd8ed1ab_0         206 KB  conda-forge
    libprotobuf-3.15.5         |       hcf210ce_0         2.1 MB  conda-forge
    markdown-3.3.4             |     pyhd8ed1ab_0          67 KB  conda-forge
    multidict-5.2.0            |   py36hfa26744_0          56 KB  conda-forge
    numpy-1.19.5               |   py36h08b5fde_2         5.0 MB  conda-forge
    oauthlib-3.1.0             |     pyhd8ed1ab_0          86 KB  conda-forge
    pandas-1.1.5               |   py36h2be6da3_0        10.0 MB  conda-forge
    pip-21.0.1                 |     pyhd8ed1ab_0         1.1 MB  conda-forge
    protobuf-3.15.5            |   py36hefe7e0e_0         321 KB  conda-forge
    pyasn1-modules-0.2.8       |             py_0          72 KB
    pyjwt-2.8.0                |     pyhd8ed1ab_0          24 KB  conda-forge
    pyopenssl-22.0.0           |     pyhd8ed1ab_1         120 KB  conda-forge
    pysocks-1.7.1              |   py36h79c6626_3          27 KB  conda-forge
    pytz-2021.1                |     pyhd8ed1ab_0         239 KB  conda-forge
    requests-2.25.1            |     pyhd3deb0d_0          51 KB  conda-forge
    requests-oauthlib-1.3.0    |     pyh9f0ad1d_0          21 KB  conda-forge
    rsa-4.7.2                  |     pyh44b312d_0          28 KB  conda-forge
    scikit-learn-0.21.2        |   py36hd4ffd6c_1         5.9 MB  conda-forge
    scipy-1.5.3                |   py36h4f136de_1        16.9 MB  conda-forge
    termcolor-1.1.0            |     pyhd8ed1ab_3           8 KB  conda-forge
    typing-extensions-3.7.4.3  |                0           8 KB  conda-forge
    typing_extensions-3.7.4.3  |             py_0          25 KB  conda-forge
    urllib3-1.26.3             |     pyhd8ed1ab_0          99 KB  conda-forge
    werkzeug-1.0.1             |     pyh9f0ad1d_0         239 KB  conda-forge
    wrapt-1.12.1               |   py36hfa26744_3          42 KB  conda-forge
    yarl-1.6.3                 |   py36hfa26744_2         132 KB  conda-forge
    zipp-3.4.1                 |     pyhd8ed1ab_0          11 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        52.4 MB

The following NEW packages will be INSTALLED:

  absl-py            conda-forge/noarch::absl-py-0.12.0-pyhd8ed1ab_0
  aiohttp            conda-forge/osx-64::aiohttp-3.7.4.post0-py36hfa26744_0
  astunparse         conda-forge/noarch::astunparse-1.6.3-pyhd8ed1ab_0
  async-timeout      conda-forge/noarch::async-timeout-3.0.1-py_1000
  attrs              conda-forge/noarch::attrs-22.2.0-pyh71513ae_0
  biopython          conda-forge/osx-64::biopython-1.78-py36hfa26744_2
  blinker            conda-forge/noarch::blinker-1.5-pyhd8ed1ab_0
  brotlipy           conda-forge/osx-64::brotlipy-0.7.0-py36hfa26744_1001
  c-ares             conda-forge/osx-64::c-ares-1.28.1-h10d778d_0
  cachetools         conda-forge/noarch::cachetools-4.2.1-pyhd8ed1ab_0
  cffi               conda-forge/osx-64::cffi-1.14.6-py36hbc36220_1
  chardet            conda-forge/osx-64::chardet-4.0.0-py36h79c6626_1
  click              conda-forge/osx-64::click-8.0.1-py36h79c6626_0
  cryptography       conda-forge/osx-64::cryptography-35.0.0-py36ha6a00b0_0
  flatbuffers        conda-forge/osx-64::flatbuffers-1.12.1-he49afe7_0
  gast               conda-forge/noarch::gast-0.3.3-py_0
  google-auth        pkgs/main/noarch::google-auth-1.27.1-pyhd3eb1b0_0
  google-auth-oauth~ conda-forge/noarch::google-auth-oauthlib-0.4.3-pyhd8ed1ab_0
  google-pasta       conda-forge/noarch::google-pasta-0.2.0-pyh8c360ce_0
  grpcio             conda-forge/osx-64::grpcio-1.32.0-py36h9799307_0
  h5py               conda-forge/osx-64::h5py-2.10.0-nompi_py36h4d7a79e_106
  hdf5               conda-forge/osx-64::hdf5-1.10.6-nompi_hc5d9132_1114
  idna               conda-forge/noarch::idna-2.10-pyh9f0ad1d_0
  idna_ssl           conda-forge/noarch::idna_ssl-1.1.0-pyhd8ed1ab_1002
  importlib-metadata conda-forge/osx-64::importlib-metadata-3.7.2-py36h79c6626_0
  joblib             conda-forge/noarch::joblib-1.0.1-pyhd8ed1ab_0
  keras-preprocessi~ conda-forge/noarch::keras-preprocessing-1.1.2-pyhd8ed1ab_0
  krb5               conda-forge/osx-64::krb5-1.20.1-h0165f36_0
  libblas            conda-forge/osx-64::libblas-3.9.0-20_osx64_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-20_osx64_openblas
  libcurl            conda-forge/osx-64::libcurl-7.87.0-haf73cf8_0
  libedit            conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2
  libev              conda-forge/osx-64::libev-4.33-h10d778d_2
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
  libgfortran5       conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
  liblapack          conda-forge/osx-64::liblapack-3.9.0-20_osx64_openblas
  libnghttp2         conda-forge/osx-64::libnghttp2-1.51.0-h0dd9d14_0
  libopenblas        conda-forge/osx-64::libopenblas-0.3.25-openmp_hfef2a42_0
  libprotobuf        conda-forge/osx-64::libprotobuf-3.15.5-hcf210ce_0
  libssh2            conda-forge/osx-64::libssh2-1.10.0-h7535e13_3
  llvm-openmp        conda-forge/osx-64::llvm-openmp-18.1.8-h15ab845_0
  markdown           conda-forge/noarch::markdown-3.3.4-pyhd8ed1ab_0
  multidict          conda-forge/osx-64::multidict-5.2.0-py36hfa26744_0
  numpy              conda-forge/osx-64::numpy-1.19.5-py36h08b5fde_2
  oauthlib           conda-forge/noarch::oauthlib-3.1.0-pyhd8ed1ab_0
  pandas             conda-forge/osx-64::pandas-1.1.5-py36h2be6da3_0
  protobuf           conda-forge/osx-64::protobuf-3.15.5-py36hefe7e0e_0
  pyasn1             conda-forge/noarch::pyasn1-0.4.8-py_0
  pyasn1-modules     pkgs/main/noarch::pyasn1-modules-0.2.8-py_0
  pycparser          conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
  pyjwt              conda-forge/noarch::pyjwt-2.8.0-pyhd8ed1ab_0
  pyopenssl          conda-forge/noarch::pyopenssl-22.0.0-pyhd8ed1ab_1
  pysocks            conda-forge/osx-64::pysocks-1.7.1-py36h79c6626_3
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  pytz               conda-forge/noarch::pytz-2021.1-pyhd8ed1ab_0
  requests           conda-forge/noarch::requests-2.25.1-pyhd3deb0d_0
  requests-oauthlib  conda-forge/noarch::requests-oauthlib-1.3.0-pyh9f0ad1d_0
  rsa                conda-forge/noarch::rsa-4.7.2-pyh44b312d_0
  scikit-learn       conda-forge/osx-64::scikit-learn-0.21.2-py36hd4ffd6c_1
  scipy              conda-forge/osx-64::scipy-1.5.3-py36h4f136de_1
  six                conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
  termcolor          conda-forge/noarch::termcolor-1.1.0-pyhd8ed1ab_3
  typing-extensions  conda-forge/noarch::typing-extensions-3.7.4.3-0
  typing_extensions  conda-forge/noarch::typing_extensions-3.7.4.3-py_0
  urllib3            conda-forge/noarch::urllib3-1.26.3-pyhd8ed1ab_0
  werkzeug           conda-forge/noarch::werkzeug-1.0.1-pyh9f0ad1d_0
  wrapt              conda-forge/osx-64::wrapt-1.12.1-py36hfa26744_3
  yarl               conda-forge/osx-64::yarl-1.6.3-py36hfa26744_2
  zipp               conda-forge/noarch::zipp-3.4.1-pyhd8ed1ab_0
  zlib               conda-forge/osx-64::zlib-1.2.13-h87427d6_6

The following packages will be UPDATED:

  certifi                                  2016.9.26-py36_0 --> 2020.12.5-py36h79c6626_1
  pip                 conda-forge/osx-64::pip-20.0.2-py36_1 --> conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0
  wheel              conda-forge/osx-64::wheel-0.34.2-py36~ --> conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0

The following packages will be DOWNGRADED:

  libzlib                                  1.3.1-h87427d6_1 --> 1.2.13-h87427d6_6



Downloading and Extracting Packages

typing_extensions-3. | 25 KB     |            |   0% 
typing_extensions-3. | 25 KB     | ######3    |  64% 
typing_extensions-3. | 25 KB     | ########## | 100% 

zipp-3.4.1           | 11 KB     |            |   0% 
zipp-3.4.1           | 11 KB     | ########## | 100% 
zipp-3.4.1           | 11 KB     | ########## | 100% 

requests-oauthlib-1. | 21 KB     |            |   0% 
requests-oauthlib-1. | 21 KB     | ########## | 100% 

flatbuffers-1.12.1   | 996 KB    |            |   0% 
flatbuffers-1.12.1   | 996 KB    | 1          |   2% 
flatbuffers-1.12.1   | 996 KB    | ########## | 100% 
flatbuffers-1.12.1   | 996 KB    | ########## | 100% 

google-auth-1.27.1   | 72 KB     |            |   0% 
google-auth-1.27.1   | 72 KB     | ##2        |  22% 
google-auth-1.27.1   | 72 KB     | ########## | 100% 
google-auth-1.27.1   | 72 KB     | ########## | 100% 

cachetools-4.2.1     | 13 KB     |            |   0% 
cachetools-4.2.1     | 13 KB     | ########## | 100% 
cachetools-4.2.1     | 13 KB     | ########## | 100% 

async-timeout-3.0.1  | 11 KB     |            |   0% 
async-timeout-3.0.1  | 11 KB     | ########## | 100% 

idna_ssl-1.1.0       | 7 KB      |            |   0% 
idna_ssl-1.1.0       | 7 KB      | ########## | 100% 

joblib-1.0.1         | 206 KB    |            |   0% 
joblib-1.0.1         | 206 KB    | #######7   |  77% 
joblib-1.0.1         | 206 KB    | ########## | 100% 

brotlipy-0.7.0       | 357 KB    |            |   0% 
brotlipy-0.7.0       | 357 KB    | ########## | 100% 
brotlipy-0.7.0       | 357 KB    | ########## | 100% 

pyasn1-modules-0.2.8 | 72 KB     |            |   0% 
pyasn1-modules-0.2.8 | 72 KB     | ########## | 100% 
pyasn1-modules-0.2.8 | 72 KB     | ########## | 100% 

aiohttp-3.7.4.post0  | 608 KB    |            |   0% 
aiohttp-3.7.4.post0  | 608 KB    | 2          |   3% 
aiohttp-3.7.4.post0  | 608 KB    | ########## | 100% 
aiohttp-3.7.4.post0  | 608 KB    | ########## | 100% 

h5py-2.10.0          | 923 KB    |            |   0% 
h5py-2.10.0          | 923 KB    | 1          |   2% 
h5py-2.10.0          | 923 KB    | ########## | 100% 
h5py-2.10.0          | 923 KB    | ########## | 100% 

typing-extensions-3. | 8 KB      |            |   0% 
typing-extensions-3. | 8 KB      | ########## | 100% 

grpcio-1.32.0        | 1.8 MB    |            |   0% 
grpcio-1.32.0        | 1.8 MB    |            |   1% 
grpcio-1.32.0        | 1.8 MB    | ########## | 100% 
grpcio-1.32.0        | 1.8 MB    | ########## | 100% 

multidict-5.2.0      | 56 KB     |            |   0% 
multidict-5.2.0      | 56 KB     | ########## | 100% 
multidict-5.2.0      | 56 KB     | ########## | 100% 

protobuf-3.15.5      | 321 KB    |            |   0% 
protobuf-3.15.5      | 321 KB    | 4          |   5% 
protobuf-3.15.5      | 321 KB    | ########## | 100% 
protobuf-3.15.5      | 321 KB    | ########## | 100% 

scikit-learn-0.21.2  | 5.9 MB    |            |   0% 
scikit-learn-0.21.2  | 5.9 MB    |            |   0% 
scikit-learn-0.21.2  | 5.9 MB    | ########## | 100% 
scikit-learn-0.21.2  | 5.9 MB    | ########## | 100% 

pip-21.0.1           | 1.1 MB    |            |   0% 
pip-21.0.1           | 1.1 MB    | ########## | 100% 
pip-21.0.1           | 1.1 MB    | ########## | 100% 

cryptography-35.0.0  | 1.2 MB    |            |   0% 
cryptography-35.0.0  | 1.2 MB    | #2         |  13% 
cryptography-35.0.0  | 1.2 MB    | ########## | 100% 
cryptography-35.0.0  | 1.2 MB    | ########## | 100% 

requests-2.25.1      | 51 KB     |            |   0% 
requests-2.25.1      | 51 KB     | ########## | 100% 

pysocks-1.7.1        | 27 KB     |            |   0% 
pysocks-1.7.1        | 27 KB     | ########## | 100% 

importlib-metadata-3 | 23 KB     |            |   0% 
importlib-metadata-3 | 23 KB     | ######8    |  68% 
importlib-metadata-3 | 23 KB     | ########## | 100% 

pyopenssl-22.0.0     | 120 KB    |            |   0% 
pyopenssl-22.0.0     | 120 KB    | ########## | 100% 
pyopenssl-22.0.0     | 120 KB    | ########## | 100% 

cffi-1.14.6          | 217 KB    |            |   0% 
cffi-1.14.6          | 217 KB    | ########## | 100% 
cffi-1.14.6          | 217 KB    | ########## | 100% 

oauthlib-3.1.0       | 86 KB     |            |   0% 
oauthlib-3.1.0       | 86 KB     | #8         |  19% 
oauthlib-3.1.0       | 86 KB     | ########## | 100% 

urllib3-1.26.3       | 99 KB     |            |   0% 
urllib3-1.26.3       | 99 KB     | ########## | 100% 
urllib3-1.26.3       | 99 KB     | ########## | 100% 

blinker-1.5          | 15 KB     |            |   0% 
blinker-1.5          | 15 KB     | ########## | 100% 

certifi-2020.12.5    | 143 KB    |            |   0% 
certifi-2020.12.5    | 143 KB    | #1         |  11% 
certifi-2020.12.5    | 143 KB    | ########## | 100% 

wrapt-1.12.1         | 42 KB     |            |   0% 
wrapt-1.12.1         | 42 KB     | ########## | 100% 
wrapt-1.12.1         | 42 KB     | ########## | 100% 

pandas-1.1.5         | 10.0 MB   |            |   0% 
pandas-1.1.5         | 10.0 MB   | 2          |   3% 
pandas-1.1.5         | 10.0 MB   | #####6     |  57% 
pandas-1.1.5         | 10.0 MB   | ########## | 100% 
pandas-1.1.5         | 10.0 MB   | ########## | 100% 

idna-2.10            | 52 KB     |            |   0% 
idna-2.10            | 52 KB     | ########## | 100% 

markdown-3.3.4       | 67 KB     |            |   0% 
markdown-3.3.4       | 67 KB     | ########## | 100% 
markdown-3.3.4       | 67 KB     | ########## | 100% 

rsa-4.7.2            | 28 KB     |            |   0% 
rsa-4.7.2            | 28 KB     | ########## | 100% 

absl-py-0.12.0       | 96 KB     |            |   0% 
absl-py-0.12.0       | 96 KB     | #6         |  17% 
absl-py-0.12.0       | 96 KB     | ########## | 100% 

werkzeug-1.0.1       | 239 KB    |            |   0% 
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Requirement already satisfied: requests-oauthlib>=0.7.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/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) (1.3.0)
Requirement already satisfied: importlib-metadata in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/enpamgb_basilisk/lib/python3.6/site-packages (from markdown>=2.6.8->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (3.7.2)
Requirement already satisfied: pyasn1<0.5.0,>=0.4.6 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/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) (0.4.8)
Requirement already satisfied: certifi>=2017.4.17 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/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) (2020.12.5)
Requirement already satisfied: chardet<5,>=3.0.2 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/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) (4.0.0)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/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) (1.26.3)
Requirement already satisfied: idna<3,>=2.5 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/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) (2.10)
Requirement already satisfied: oauthlib>=3.0.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/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) (3.1.0)
Requirement already satisfied: zipp>=0.5 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/enpamgb_basilisk/lib/python3.6/site-packages (from importlib-metadata->markdown>=2.6.8->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (3.4.1)
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=459416 sha256=1fb80e62be775b56b7aa6995f9b8e9bc1f87a564386376a1d78e07eff86d3b25
  Stored in directory: /private/tmp/pip-ephem-wheel-cache-qa8pxgjz/wheels/c3/12/f4/5d906eaf63a631451e46e516f2249648f084e71b4ee8dc58b6
Successfully built sgrna-modeler
Installing collected packages: sgrna-modeler
Successfully installed sgrna-modeler-0.1.0
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/lindel_basilisk

  added / updated specs:
    - python=3.6


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
  certifi            conda-forge/osx-64::certifi-2016.9.26-py36_0
  libcxx             conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
  libffi             conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
  libsqlite          conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0
  libzlib            conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
  ncurses            conda-forge/osx-64::ncurses-6.5-h5846eda_0
  openssl            conda-forge/osx-64::openssl-1.1.1w-h8a1eda9_0
  pip                conda-forge/osx-64::pip-20.0.2-py36_1
  python             conda-forge/osx-64::python-3.6.15-haf480d7_0_cpython
  python_abi         conda-forge/osx-64::python_abi-3.6-2_cp36m
  readline           conda-forge/osx-64::readline-8.2-h9e318b2_1
  setuptools         conda-forge/osx-64::setuptools-49.6.0-py36h79c6626_3
  sqlite             conda-forge/osx-64::sqlite-3.46.0-h28673e1_0
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1
  wheel              conda-forge/osx-64::wheel-0.34.2-py36_0
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/lindel_basilisk

  added / updated specs:
    - certifi=2020.12.5
    - numpy=1.19.5
    - pip=21.0.1
    - python[version='3.6.*,3.6.*']
    - scipy=1.5.3
    - setuptools=49.6.0
    - wheel=0.36.2


The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-64::libblas-3.9.0-20_osx64_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-20_osx64_openblas
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
  libgfortran5       conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
  liblapack          conda-forge/osx-64::liblapack-3.9.0-20_osx64_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.25-openmp_hfef2a42_0
  llvm-openmp        conda-forge/osx-64::llvm-openmp-18.1.8-h15ab845_0
  numpy              conda-forge/osx-64::numpy-1.19.5-py36h08b5fde_2
  scipy              conda-forge/osx-64::scipy-1.5.3-py36h4f136de_1

The following packages will be UPDATED:

  certifi                                  2016.9.26-py36_0 --> 2020.12.5-py36h79c6626_1
  pip                 conda-forge/osx-64::pip-20.0.2-py36_1 --> conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0
  wheel              conda-forge/osx-64::wheel-0.34.2-py36~ --> conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Processing /Users/biocbuild/bbs-3.19-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/lindel
Requirement already satisfied: numpy in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/lindel_basilisk/lib/python3.6/site-packages (from Lindel==1.0) (1.19.5)
Requirement already satisfied: scipy in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/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=33602 sha256=17293b8a26d64b718111a254f245cee9d704667a243e2f2e14d51fef8b84000d
  Stored in directory: /private/tmp/pip-ephem-wheel-cache-je4h8pt7/wheels/94/92/4f/006eb0dd15880fbf04db687faa2e749fef98d5f848fc5fe3ad
Successfully built Lindel
Installing collected packages: Lindel
Successfully installed Lindel-1.0
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk

  added / updated specs:
    - python=3.6


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
  certifi            conda-forge/osx-64::certifi-2016.9.26-py36_0
  libcxx             conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
  libffi             conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
  libsqlite          conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0
  libzlib            conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
  ncurses            conda-forge/osx-64::ncurses-6.5-h5846eda_0
  openssl            conda-forge/osx-64::openssl-1.1.1w-h8a1eda9_0
  pip                conda-forge/osx-64::pip-20.0.2-py36_1
  python             conda-forge/osx-64::python-3.6.15-haf480d7_0_cpython
  python_abi         conda-forge/osx-64::python_abi-3.6-2_cp36m
  readline           conda-forge/osx-64::readline-8.2-h9e318b2_1
  setuptools         conda-forge/osx-64::setuptools-49.6.0-py36h79c6626_3
  sqlite             conda-forge/osx-64::sqlite-3.46.0-h28673e1_0
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1
  wheel              conda-forge/osx-64::wheel-0.34.2-py36_0
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1
done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0
WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk

  added / updated specs:
    - absl-py=0.12.0
    - astor=0.8.1
    - biopython=1.71
    - bleach=1.5.0
    - certifi=2020.12.5
    - cycler=0.10.0
    - decorator=4.4.2
    - dotmap=1.2.20
    - gast=0.4.0
    - gpy=1.9.8
    - gpyopt=1.2.6
    - grpcio=1.36.1
    - h5py=2.9.0
    - html5lib=0.9999999
    - importlib-metadata=3.7.2
    - keras=2.1.6
    - kiwisolver=1.3.1
    - mako=1.1.4
    - markdown=3.3.4
    - markupsafe=1.1.1
    - matplotlib=3.1.1
    - numpy=1.14.0
    - pandas=0.25.3
    - paramz=0.9.5
    - pip=21.0.1
    - protobuf=3.15.5
    - pygpu=0.7.6
    - pyparsing=2.4.7
    - python-dateutil=2.8.1
    - python[version='3.6.*,3.6.*']
    - pytz=2021.1
    - pyyaml=5.4.1
    - scikit-learn=0.19.1
    - scipy=1.1.0
    - setuptools=49.6.0
    - six=1.15.0
    - tensorboard=1.8.0
    - tensorflow=1.8.0
    - termcolor=1.1.0
    - theano=1.0.5
    - tornado=6.1
    - typing-extensions=3.7.4.3
    - viennarna=2.4.5
    - webencodings=0.5.1
    - werkzeug=1.0.1
    - wheel=0.36.2
    - zipp=3.4.1


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    astor-0.8.1                |     pyh9f0ad1d_0          25 KB  conda-forge
    biopython-1.71             |           py36_0         2.4 MB  conda-forge
    blas-1.1                   |         openblas           1 KB  conda-forge
    bleach-1.5.0               |           py36_0          23 KB  conda-forge
    cctools_osx-64-973.0.1     |      hcc6d90d_12         1.1 MB  conda-forge
    clang-11.1.0               |       h694c41f_1         125 KB  conda-forge
    clang-11-11.1.0            |default_he082bbe_1         684 KB  conda-forge
    clang_osx-64-11.1.0        |       hc8532ff_7          16 KB  conda-forge
    clangxx-11.1.0             |default_he082bbe_1         125 KB  conda-forge
    clangxx_osx-64-11.1.0      |       h2c55bc3_7          16 KB  conda-forge
    compiler-rt-11.1.0         |       h654b07c_0          78 KB  conda-forge
    compiler-rt_osx-64-11.1.0  |       h8c5fa43_0         5.6 MB  conda-forge
    decorator-4.4.2            |             py_0          11 KB  conda-forge
    dotmap-1.2.20              |             py_0           8 KB  conda-forge
    gpy-1.9.8                  |   py36h1e5eb4f_0         1.5 MB  conda-forge
    gpyopt-1.2.6               |     pyh8c360ce_0          56 KB  conda-forge
    grpcio-1.36.1              |   py36h8d587b5_0         2.0 MB  conda-forge
    h5py-2.9.0                 |nompi_py36h35dc34b_1102         965 KB  conda-forge
    hdf5-1.10.4                |nompi_h0cbb7df_1106         4.5 MB  conda-forge
    html5lib-0.9999999         |           py36_0         181 KB  conda-forge
    keras-2.1.6                |           py36_0         500 KB  conda-forge
    kiwisolver-1.3.1           |   py36hc61eee1_1          58 KB  conda-forge
    ld64_osx-64-609            |      h6adca69_10         1.5 MB  conda-forge
    libclang-cpp11.1-11.1.0    |default_he082bbe_1        12.6 MB  conda-forge
    libllvm11-11.1.0           |       h8fb7429_5        22.2 MB  conda-forge
    llvm-tools-11.1.0          |       h8fb7429_5        11.7 MB  conda-forge
    markupsafe-1.1.1           |   py36hfa26744_3          25 KB  conda-forge
    matplotlib-3.1.1           |   py36h54f8f79_0         4.9 MB
    numpy-1.14.0               |py36_blas_openblas_200         3.9 MB  conda-forge
    openblas-0.2.20            |                8        20.1 MB  conda-forge
    pandas-0.25.3              |   py36h0a44026_0         8.0 MB
    paramz-0.9.5               |             py_0          60 KB  conda-forge
    pygpu-0.7.6                |py36h917ab60_1000         604 KB  conda-forge
    pyparsing-2.4.7            |     pyhd8ed1ab_1          60 KB  conda-forge
    pyyaml-5.4.1               |   py36hfa26744_1         167 KB  conda-forge
    scikit-learn-0.19.1        |py36_blas_openblas_201         5.2 MB  conda-forge
    scipy-1.1.0                |py36_blas_openblash7943236_201        16.0 MB  conda-forge
    sigtool-0.1.3              |       h57ddcff_0         209 KB  conda-forge
    tapi-1100.0.11             |       h9ce4665_0         196 KB  conda-forge
    tensorboard-1.8.0          |           py36_1         3.1 MB  conda-forge
    tensorflow-1.8.0           |           py36_1        39.3 MB  conda-forge
    theano-1.0.5               |   py36hefe7e0e_1         3.7 MB  conda-forge
    tornado-6.1                |   py36hfa26744_1         643 KB  conda-forge
    viennarna-2.4.5            |       hd28b015_3        13.9 MB  bioconda
    webencodings-0.5.1         |     pyhd8ed1ab_2          15 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       187.9 MB

The following NEW packages will be INSTALLED:

  absl-py            conda-forge/noarch::absl-py-0.12.0-pyhd8ed1ab_0
  astor              conda-forge/noarch::astor-0.8.1-pyh9f0ad1d_0
  biopython          conda-forge/osx-64::biopython-1.71-py36_0
  blas               conda-forge/osx-64::blas-1.1-openblas
  bleach             conda-forge/osx-64::bleach-1.5.0-py36_0
  c-ares             conda-forge/osx-64::c-ares-1.28.1-h10d778d_0
  cctools_osx-64     conda-forge/osx-64::cctools_osx-64-973.0.1-hcc6d90d_12
  clang              conda-forge/osx-64::clang-11.1.0-h694c41f_1
  clang-11           conda-forge/osx-64::clang-11-11.1.0-default_he082bbe_1
  clang_osx-64       conda-forge/osx-64::clang_osx-64-11.1.0-hc8532ff_7
  clangxx            conda-forge/osx-64::clangxx-11.1.0-default_he082bbe_1
  clangxx_osx-64     conda-forge/osx-64::clangxx_osx-64-11.1.0-h2c55bc3_7
  compiler-rt        conda-forge/osx-64::compiler-rt-11.1.0-h654b07c_0
  compiler-rt_osx-64 conda-forge/noarch::compiler-rt_osx-64-11.1.0-h8c5fa43_0
  cycler             conda-forge/noarch::cycler-0.10.0-py_2
  decorator          conda-forge/noarch::decorator-4.4.2-py_0
  dotmap             conda-forge/noarch::dotmap-1.2.20-py_0
  freetype           conda-forge/osx-64::freetype-2.12.1-h60636b9_2
  gast               conda-forge/noarch::gast-0.4.0-pyh9f0ad1d_0
  gpy                conda-forge/osx-64::gpy-1.9.8-py36h1e5eb4f_0
  gpyopt             conda-forge/noarch::gpyopt-1.2.6-pyh8c360ce_0
  grpcio             conda-forge/osx-64::grpcio-1.36.1-py36h8d587b5_0
  h5py               conda-forge/osx-64::h5py-2.9.0-nompi_py36h35dc34b_1102
  hdf5               conda-forge/osx-64::hdf5-1.10.4-nompi_h0cbb7df_1106
  html5lib           conda-forge/osx-64::html5lib-0.9999999-py36_0
  importlib-metadata conda-forge/osx-64::importlib-metadata-3.7.2-py36h79c6626_0
  keras              conda-forge/osx-64::keras-2.1.6-py36_0
  kiwisolver         conda-forge/osx-64::kiwisolver-1.3.1-py36hc61eee1_1
  ld64_osx-64        conda-forge/osx-64::ld64_osx-64-609-h6adca69_10
  libclang-cpp11.1   conda-forge/osx-64::libclang-cpp11.1-11.1.0-default_he082bbe_1
  libgfortran        conda-forge/osx-64::libgfortran-3.0.1-0
  libgpuarray        conda-forge/osx-64::libgpuarray-0.7.6-h0d85af4_1003
  libllvm11          conda-forge/osx-64::libllvm11-11.1.0-h8fb7429_5
  libllvm14          conda-forge/osx-64::libllvm14-14.0.6-hc8e404f_4
  libpng             conda-forge/osx-64::libpng-1.6.43-h92b6c6a_0
  libprotobuf        conda-forge/osx-64::libprotobuf-3.15.5-hcf210ce_0
  llvm-tools         conda-forge/osx-64::llvm-tools-11.1.0-h8fb7429_5
  mako               conda-forge/noarch::mako-1.1.4-pyh44b312d_0
  markdown           conda-forge/noarch::markdown-3.3.4-pyhd8ed1ab_0
  markupsafe         conda-forge/osx-64::markupsafe-1.1.1-py36hfa26744_3
  matplotlib         pkgs/main/osx-64::matplotlib-3.1.1-py36h54f8f79_0
  numpy              conda-forge/osx-64::numpy-1.14.0-py36_blas_openblas_200
  openblas           conda-forge/osx-64::openblas-0.2.20-8
  pandas             pkgs/main/osx-64::pandas-0.25.3-py36h0a44026_0
  paramz             conda-forge/noarch::paramz-0.9.5-py_0
  protobuf           conda-forge/osx-64::protobuf-3.15.5-py36hefe7e0e_0
  pygpu              conda-forge/osx-64::pygpu-0.7.6-py36h917ab60_1000
  pyparsing          conda-forge/noarch::pyparsing-2.4.7-pyhd8ed1ab_1
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  pytz               conda-forge/noarch::pytz-2021.1-pyhd8ed1ab_0
  pyyaml             conda-forge/osx-64::pyyaml-5.4.1-py36hfa26744_1
  scikit-learn       conda-forge/osx-64::scikit-learn-0.19.1-py36_blas_openblas_201
  scipy              conda-forge/osx-64::scipy-1.1.0-py36_blas_openblash7943236_201
  sigtool            conda-forge/osx-64::sigtool-0.1.3-h57ddcff_0
  six                conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
  tapi               conda-forge/osx-64::tapi-1100.0.11-h9ce4665_0
  tensorboard        conda-forge/osx-64::tensorboard-1.8.0-py36_1
  tensorflow         conda-forge/osx-64::tensorflow-1.8.0-py36_1
  termcolor          conda-forge/noarch::termcolor-1.1.0-pyhd8ed1ab_3
  theano             conda-forge/osx-64::theano-1.0.5-py36hefe7e0e_1
  tornado            conda-forge/osx-64::tornado-6.1-py36hfa26744_1
  typing-extensions  conda-forge/noarch::typing-extensions-3.7.4.3-0
  typing_extensions  conda-forge/noarch::typing_extensions-3.7.4.3-py_0
  viennarna          bioconda/osx-64::viennarna-2.4.5-hd28b015_3
  webencodings       conda-forge/noarch::webencodings-0.5.1-pyhd8ed1ab_2
  werkzeug           conda-forge/noarch::werkzeug-1.0.1-pyh9f0ad1d_0
  yaml               conda-forge/osx-64::yaml-0.2.5-h0d85af4_2
  zipp               conda-forge/noarch::zipp-3.4.1-pyhd8ed1ab_0
  zlib               conda-forge/osx-64::zlib-1.2.13-h87427d6_6

The following packages will be UPDATED:

  certifi                                  2016.9.26-py36_0 --> 2020.12.5-py36h79c6626_1
  pip                 conda-forge/osx-64::pip-20.0.2-py36_1 --> conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0
  wheel              conda-forge/osx-64::wheel-0.34.2-py36~ --> conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0

The following packages will be DOWNGRADED:

  libzlib                                  1.3.1-h87427d6_1 --> 1.2.13-h87427d6_6



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openblas-0.2.20      | 20.1 MB   |            |   0% 
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matplotlib-3.1.1     | 4.9 MB    |            |   0% 
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Preparing transaction: ...working... done
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Processing /Users/biocbuild/bbs-3.19-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/deephf
Requirement already satisfied: scipy==1.1.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from DeepHF==1.0) (1.1.0)
Requirement already satisfied: numpy==1.14.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from DeepHF==1.0) (1.14.0)
Requirement already satisfied: h5py==2.9.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from DeepHF==1.0) (2.9.0)
Requirement already satisfied: tensorflow==1.8.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from DeepHF==1.0) (1.8.0)
Requirement already satisfied: keras==2.1.6 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from DeepHF==1.0) (2.1.6)
Requirement already satisfied: scikit-learn==0.19.1 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from DeepHF==1.0) (0.19.1)
Requirement already satisfied: biopython==1.71 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from DeepHF==1.0) (1.71)
Requirement already satisfied: matplotlib in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from DeepHF==1.0) (3.1.1)
Requirement already satisfied: DotMap in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from DeepHF==1.0) (1.2.20)
Requirement already satisfied: GPyOpt in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from DeepHF==1.0) (1.2.6)
Requirement already satisfied: pandas in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from DeepHF==1.0) (0.25.3)
Requirement already satisfied: six in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from h5py==2.9.0->DeepHF==1.0) (1.15.0)
Requirement already satisfied: pyyaml in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from keras==2.1.6->DeepHF==1.0) (5.4.1)
Requirement already satisfied: termcolor>=1.1.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from tensorflow==1.8.0->DeepHF==1.0) (1.1.0)
Requirement already satisfied: protobuf>=3.4.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from tensorflow==1.8.0->DeepHF==1.0) (3.15.5)
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Requirement already satisfied: astor>=0.6.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from tensorflow==1.8.0->DeepHF==1.0) (0.8.1)
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Requirement already satisfied: tensorboard<1.9.0,>=1.8.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from tensorflow==1.8.0->DeepHF==1.0) (1.8.0)
Requirement already satisfied: grpcio>=1.8.6 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from tensorflow==1.8.0->DeepHF==1.0) (1.36.1)
Requirement already satisfied: html5lib==0.9999999 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from tensorboard<1.9.0,>=1.8.0->tensorflow==1.8.0->DeepHF==1.0) (0.9999999)
Requirement already satisfied: markdown>=2.6.8 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from tensorboard<1.9.0,>=1.8.0->tensorflow==1.8.0->DeepHF==1.0) (3.3.4)
Requirement already satisfied: bleach==1.5.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from tensorboard<1.9.0,>=1.8.0->tensorflow==1.8.0->DeepHF==1.0) (1.5.0)
Requirement already satisfied: werkzeug>=0.11.10 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from tensorboard<1.9.0,>=1.8.0->tensorflow==1.8.0->DeepHF==1.0) (1.0.1)
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Requirement already satisfied: typing-extensions>=3.6.4 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from importlib-metadata->markdown>=2.6.8->tensorboard<1.9.0,>=1.8.0->tensorflow==1.8.0->DeepHF==1.0) (3.7.4.3)
Requirement already satisfied: zipp>=0.5 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from importlib-metadata->markdown>=2.6.8->tensorboard<1.9.0,>=1.8.0->tensorflow==1.8.0->DeepHF==1.0) (3.4.1)
Requirement already satisfied: cycler>=0.10 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from matplotlib->DeepHF==1.0) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from matplotlib->DeepHF==1.0) (1.3.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from matplotlib->DeepHF==1.0) (2.4.7)
Requirement already satisfied: python-dateutil>=2.1 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from matplotlib->DeepHF==1.0) (2.8.1)
Requirement already satisfied: pytz>=2017.2 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from pandas->DeepHF==1.0) (2021.1)
Building wheels for collected packages: DeepHF
  Building wheel for DeepHF (setup.py): started
  Building wheel for DeepHF (setup.py): finished with status 'done'
  Created wheel for DeepHF: filename=DeepHF-1.0-py3-none-any.whl size=10632 sha256=13d63641e29326f04392358dfa4f94a580fa3c86c804a9850cac06e51b5ffe31
  Stored in directory: /private/tmp/pip-ephem-wheel-cache-3_6na1wg/wheels/43/41/86/f1fed025011abde8e5afb809830162732f53e44dd40b28a164
Successfully built DeepHF
Installing collected packages: DeepHF
Successfully installed DeepHF-1.0
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 8 ]

[ FAIL 0 | WARN 10 | SKIP 0 | PASS 8 ]
> 
> proc.time()
    user   system  elapsed 
1955.747  184.458 2664.329 

'R CMD check' output

##############################################################################
##############################################################################
###
### 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/crisprScore.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.4
* 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 ‘1.8.0’
* 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-3.19-bioc-longtests/meat/crisprScore.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  7.1Mb
  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-3.19-bioc-longtests/meat/crisprScore.Rcheck/00check.log’
for details.


Installation output

crisprScore.Rcheck/00install.out

* 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)