| Back to Long Tests report for BioC 3.22 |
This page was generated on 2025-04-26 23:55 -0400 (Sat, 26 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4722 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4494 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4523 |
| 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 15/30 | Hostname | OS / Arch | CHECK | |||||||
| crisprScore 1.13.0 (landing page) Jean-Philippe Fortin
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | |||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
|
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. |
| Package: crisprScore |
| Version: 1.13.0 |
| 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_1.13.0.tar.gz |
| StartedAt: 2025-04-26 16:04:33 -0400 (Sat, 26 Apr 2025) |
| EndedAt: 2025-04-26 16:14:33 -0400 (Sat, 26 Apr 2025) |
| EllapsedTime: 599.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: crisprScore.Rcheck |
| Warnings: 0 |
crisprScore.Rcheck/tests/testthat.Rout
R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 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
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")
Channels:
- bioconda
- conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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/noarch::ca-certificates-2025.4.26-hbd8a1cb_0
certifi conda-forge/osx-64::certifi-2019.11.28-py27h8c360ce_1
libcxx conda-forge/osx-64::libcxx-20.1.3-hf95d169_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-h0622a9a_3
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-h7cca4af_2
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
Channels:
- bioconda
- conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.3.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- bioconda
- conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.3.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk
added / updated specs:
- biopython=1.74
- matplotlib=2.2.3
- numpy=1.11.3
- pandas=0.23.4
- pip=20.1.1
- python[version='2.7.*,2.7.*']
- scipy=1.2.1
- six=1.16.0
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
numpy-1.11.3 |py27hdf140aa_1207 3.5 MB conda-forge
pandas-0.23.4 |py27h1702cab_1000 9.1 MB conda-forge
pyparsing-2.4.7 | pyh9f0ad1d_0 60 KB conda-forge
python-dateutil-2.8.1 | py_0 220 KB conda-forge
pytz-2020.1 | pyh9f0ad1d_0 227 KB conda-forge
scipy-1.2.1 | py27hbd7caa9_1 15.7 MB conda-forge
singledispatch-3.6.1 | pyh44b312d_0 12 KB conda-forge
subprocess32-3.5.4 | py27h0b31af3_0 44 KB conda-forge
tornado-5.1.1 |py27h1de35cc_1000 642 KB conda-forge
------------------------------------------------------------
Total: 47.4 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
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
matplotlib conda-forge/osx-64::matplotlib-2.2.3-py27_1
matplotlib-base conda-forge/osx-64::matplotlib-base-2.2.3-py27hd64abcd_1
numpy conda-forge/osx-64::numpy-1.11.3-py27hdf140aa_1207
pandas conda-forge/osx-64::pandas-0.23.4-py27h1702cab_1000
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
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-1.16.0-pyh6c4a22f_0
subprocess32 conda-forge/osx-64::subprocess32-3.5.4-py27h0b31af3_0
tornado conda-forge/osx-64::tornado-5.1.1-py27h1de35cc_1000
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liblapack-3.8.0 | 10 KB | ########## | 100% [A[A[A[A[A[A[A[A[A[A[A[A[A[A[A[A[A
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matplotlib-base-2.2. | 6.4 MB | ########## | 100% [A[A[A
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Preparing transaction: - \ done
Verifying transaction: / - \ | / - \ | / - done
Executing transaction: | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - 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-3.22-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth
Requirement already satisfied: scipy<=1.2.1 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.2.1)
Requirement already satisfied: numpy<=1.14 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.11.3)
Requirement already satisfied: matplotlib in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (2.2.3)
Collecting nose
Using cached nose-1.3.7-py2-none-any.whl (154 kB)
Requirement already satisfied: scikit-learn<0.18,>=0.17.1 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (0.17.1)
Requirement already satisfied: pandas in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (0.23.4)
Requirement already satisfied: biopython<=1.76 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.74)
Requirement already satisfied: cycler>=0.10 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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 /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (2.4.7)
Requirement already satisfied: python-dateutil>=2.1 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (2.8.1)
Requirement already satisfied: pytz in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (2020.1)
Requirement already satisfied: six>=1.10 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (1.16.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (1.1.0)
Requirement already satisfied: backports.functools_lru_cache in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (1.6.1)
Requirement already satisfied: subprocess32 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (3.5.4)
Requirement already satisfied: setuptools in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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=b4a4b6bbff3c8be9608b36ce586f632f43d48c1a0008608f36682d546c4de541
Stored in directory: /private/tmp/pip-ephem-wheel-cache-BrDqiP/wheels/98/ad/eb/983169d0f70bb1f2597fe85418a22f6a8ea56c7e0e1a8cd7d8
Successfully built Azimuth
Installing collected packages: nose, Azimuth
Successfully installed Azimuth-2.0 nose-1.3.7
/Users/biocbuild/bbs-3.22-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-3.22-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth/getAzimuth.py", line 4, in <module>
import azimuth.model_comparison
File "/Users/biocbuild/bbs-3.22-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-3.22-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth/azimuth/predict.py", line 7, in <module>
import util
File "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth/azimuth/util.py", line 2, in <module>
import matplotlib.pylab as plt
File "/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages/matplotlib/pylab.py", line 252, in <module>
from matplotlib import cbook, mlab, pyplot as plt
File "/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/azimuth_basilisk/lib/python2.7/site-packages/matplotlib/pyplot.py", line 71, in <module>
from matplotlib.backends import pylab_setup
File "/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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')
Channels:
- conda-forge
- bioconda
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/deepcpf1_basilisk
added / updated specs:
- python=2.7
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/noarch::ca-certificates-2025.4.26-hbd8a1cb_0
certifi conda-forge/osx-64::certifi-2019.11.28-py27h8c360ce_1
libcxx conda-forge/osx-64::libcxx-20.1.3-hf95d169_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-h0622a9a_3
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-h7cca4af_2
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
Channels:
- conda-forge
- bioconda
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.3.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
- bioconda
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.3.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
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 h5py==2.10.0
Using cached h5py-2.10.0-cp27-cp27m-macosx_10_6_intel.whl (2.9 MB)
Collecting Keras==2.1.5
Using cached Keras-2.1.5-py2.py3-none-any.whl (334 kB)
Collecting numpy==1.16.5
Using cached numpy-1.16.5-cp27-cp27m-macosx_10_9_x86_64.whl (13.9 MB)
Collecting scipy==1.2.1
Using cached scipy-1.2.1-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 (27.4 MB)
Collecting tensorflow==1.0.0
Using cached tensorflow-1.0.0-cp27-cp27m-macosx_10_11_x86_64.whl (39.3 MB)
Processing /Users/biocbuild/Library/Caches/pip/wheels/3f/57/ee/3a809616477a8502944fc8ac4e2bd464a8d4e28dbe2f2696bb/Theano-1.0.1-py2-none-any.whl
Collecting six
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Collecting pyyaml
Using cached PyYAML-5.4.1-cp27-cp27m-macosx_10_9_x86_64.whl (245 kB)
Collecting mock>=2.0.0
Using cached mock-3.0.5-py2.py3-none-any.whl (25 kB)
Collecting protobuf>=3.1.0
Using cached protobuf-3.17.3-cp27-cp27m-macosx_10_9_x86_64.whl (1.0 MB)
Requirement already satisfied: wheel in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/deepcpf1_basilisk/lib/python2.7/site-packages (from tensorflow==1.0.0) (0.37.1)
Collecting funcsigs>=1; python_version < "3.3"
Using cached funcsigs-1.0.2-py2.py3-none-any.whl (17 kB)
Installing collected packages: numpy, six, h5py, scipy, pyyaml, Keras, funcsigs, mock, protobuf, tensorflow, Theano
Successfully installed Keras-2.1.5 Theano-1.0.1 funcsigs-1.0.2 h5py-2.10.0 mock-3.0.5 numpy-1.16.5 protobuf-3.17.3 pyyaml-5.4.1 scipy-1.2.1 six-1.17.0 tensorflow-1.0.0
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-3.22-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=bfdff9c100ab94963411f90033a896a9e6678dcaf9aeae6f6bfc2b18909632fd
Stored in directory: /private/tmp/pip-ephem-wheel-cache-9YPq9Q/wheels/7b/84/37/b41dfcb653ed98b329cd632a8c8e9e5789e1d23ea2309ee248
Successfully built DeepCpf1
Installing collected packages: DeepCpf1
Successfully installed DeepCpf1-1.0
Channels:
- conda-forge
- bioconda
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/enpamgb_basilisk
added / updated specs:
- python=3.6
The following packages will be downloaded:
package | build
---------------------------|-----------------
pip-21.3.1 | pyhd8ed1ab_0 1.2 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-58.0.4 | py36h79c6626_2 960 KB conda-forge
------------------------------------------------------------
Total: 22.8 MB
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/noarch::ca-certificates-2025.4.26-hbd8a1cb_0
libcxx conda-forge/osx-64::libcxx-20.1.3-hf95d169_0
libffi conda-forge/osx-64::libffi-3.4.6-h281671d_1
liblzma conda-forge/osx-64::liblzma-5.8.1-hd471939_0
liblzma-devel conda-forge/osx-64::liblzma-devel-5.8.1-hd471939_0
libsqlite conda-forge/osx-64::libsqlite-3.49.1-hdb6dae5_2
libzlib conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2
ncurses conda-forge/osx-64::ncurses-6.5-h0622a9a_3
openssl conda-forge/osx-64::openssl-1.1.1w-h8a1eda9_0
pip conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
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-h7cca4af_2
setuptools conda-forge/osx-64::setuptools-58.0.4-py36h79c6626_2
sqlite conda-forge/osx-64::sqlite-3.49.1-h2e4c9dc_2
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.8.1-h357f2ed_0
xz-gpl-tools conda-forge/osx-64::xz-gpl-tools-5.8.1-h357f2ed_0
xz-tools conda-forge/osx-64::xz-tools-5.8.1-hd471939_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
- bioconda
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.3.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
- bioconda
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.3.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/enpamgb_basilisk
added / updated specs:
- biopython=1.78
- h5py=2.10.0
- keras-preprocessing=1.1.2
- numpy=1.19.5
- pandas=1.1.5
- pip=21.0.1
- python[version='3.6.*,3.6.*']
- scikit-learn=0.21.2
- scipy=1.5.3
- setuptools=49.6.0
- six=1.15.0
The following packages will be downloaded:
package | build
---------------------------|-----------------
biopython-1.78 | py36hfa26744_2 2.6 MB conda-forge
certifi-2021.5.30 | py36h79c6626_0 141 KB conda-forge
h5py-2.10.0 |nompi_py36h4d7a79e_106 923 KB conda-forge
joblib-1.2.0 | pyhd8ed1ab_0 205 KB conda-forge
numpy-1.19.5 | py36h08b5fde_2 5.0 MB conda-forge
pandas-1.1.5 | py36h2be6da3_0 10.0 MB conda-forge
pip-21.0.1 | pyhd8ed1ab_0 1.1 MB conda-forge
pytz-2023.3.post1 | pyhd8ed1ab_0 183 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
setuptools-49.6.0 | py36h79c6626_3 916 KB conda-forge
six-1.15.0 | pyh9f0ad1d_0 14 KB conda-forge
------------------------------------------------------------
Total: 43.9 MB
The following NEW packages will be INSTALLED:
biopython conda-forge/osx-64::biopython-1.78-py36hfa26744_2
c-ares conda-forge/osx-64::c-ares-1.34.5-hf13058a_0
certifi conda-forge/osx-64::certifi-2021.5.30-py36h79c6626_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
joblib conda-forge/noarch::joblib-1.2.0-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-3.1.20250104-pl5321ha958ccf_0
libev conda-forge/osx-64::libev-4.33-h10d778d_2
libgfortran conda-forge/osx-64::libgfortran-14.2.0-hef36b68_105
libgfortran5 conda-forge/osx-64::libgfortran5-14.2.0-h58528f3_105
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
libssh2 conda-forge/osx-64::libssh2-1.10.0-h7535e13_3
llvm-openmp conda-forge/osx-64::llvm-openmp-20.1.3-ha54dae1_0
numpy conda-forge/osx-64::numpy-1.19.5-py36h08b5fde_2
pandas conda-forge/osx-64::pandas-1.1.5-py36h2be6da3_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
pytz conda-forge/noarch::pytz-2023.3.post1-pyhd8ed1ab_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
zlib conda-forge/osx-64::zlib-1.2.13-h87427d6_6
The following packages will be DOWNGRADED:
libsqlite 3.49.1-hdb6dae5_2 --> 3.46.0-h1b8f9f3_0
libzlib 1.3.1-hd23fc13_2 --> 1.2.13-h87427d6_6
pip 21.3.1-pyhd8ed1ab_0 --> 21.0.1-pyhd8ed1ab_0
setuptools 58.0.4-py36h79c6626_2 --> 49.6.0-py36h79c6626_3
sqlite 3.49.1-h2e4c9dc_2 --> 3.46.0-h28673e1_0
Downloading and Extracting Packages: ...working...
scipy-1.5.3 | 16.9 MB | | 0%
pandas-1.1.5 | 10.0 MB | | 0% [A
scikit-learn-0.21.2 | 5.9 MB | | 0% [A[A
numpy-1.19.5 | 5.0 MB | | 0% [A[A[A
biopython-1.78 | 2.6 MB | | 0% [A[A[A[A
pip-21.0.1 | 1.1 MB | | 0% [A[A[A[A[A
h5py-2.10.0 | 923 KB | | 0% [A[A[A[A[A[A
setuptools-49.6.0 | 916 KB | | 0% [A[A[A[A[A[A[A
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Building wheels for collected packages: wrapt
Building wheel for wrapt (setup.py): started
Building wheel for wrapt (setup.py): finished with status 'done'
Created wheel for wrapt: filename=wrapt-1.12.1-cp36-cp36m-macosx_11_0_x86_64.whl size=32713 sha256=2adb22460e6c1299bec110764e09bb0d5faae1065b8ff58a7cf2b836d1b7e9b8
Stored in directory: /Users/biocbuild/Library/Caches/pip/wheels/32/42/7f/23cae9ff6ef66798d00dc5d659088e57dbba01566f6c60db63
Successfully built wrapt
Installing collected packages: urllib3, pyasn1, idna, charset-normalizer, zipp, typing-extensions, rsa, requests, pyasn1-modules, oauthlib, cachetools, requests-oauthlib, importlib-metadata, google-auth, dataclasses, werkzeug, tensorboard-plugin-wit, tensorboard-data-server, protobuf, markdown, grpcio, google-auth-oauthlib, absl-py, wrapt, termcolor, tensorflow-estimator, tensorboard, opt-einsum, google-pasta, gast, flatbuffers, astunparse, tensorflow
Successfully installed absl-py-0.15.0 astunparse-1.6.3 cachetools-4.2.4 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 idna-3.10 importlib-metadata-4.8.3 markdown-3.3.7 oauthlib-3.2.2 opt-einsum-3.3.0 protobuf-3.19.6 pyasn1-0.5.1 pyasn1-modules-0.3.0 requests-2.27.1 requests-oauthlib-2.0.0 rsa-4.9.1 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
Processing /Users/biocbuild/bbs-3.22-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/enpamgb
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Requirement already satisfied: markdown>=2.6.8 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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: tensorboard-plugin-wit>=1.6.0 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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: tensorboard-data-server<0.7.0,>=0.6.0 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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: werkzeug>=1.0.1 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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: google-auth<3,>=1.6.3 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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: cachetools<6.0,>=2.0.0 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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: rsa<5,>=3.1.4 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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: urllib3<2.0 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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: pyasn1-modules>=0.2.1 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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: requests-oauthlib>=0.7.0 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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) (2.0.0)
Requirement already satisfied: importlib-metadata>=4.4 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/enpamgb_basilisk/lib/python3.6/site-packages (from markdown>=2.6.8->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (4.8.3)
Requirement already satisfied: zipp>=0.5 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/enpamgb_basilisk/lib/python3.6/site-packages (from importlib-metadata>=4.4->markdown>=2.6.8->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (3.6.0)
Requirement already satisfied: pyasn1<0.6.0,>=0.4.6 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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) (0.5.1)
Requirement already satisfied: charset-normalizer~=2.0.0 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/enpamgb_basilisk/lib/python3.6/site-packages (from requests<3,>=2.21.0->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.0.12)
Requirement already satisfied: certifi>=2017.4.17 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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) (2021.5.30)
Requirement already satisfied: idna<4,>=2.5 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/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) (3.10)
Requirement already satisfied: oauthlib>=3.0.0 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/enpamgb_basilisk/lib/python3.6/site-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<0.5,>=0.4.1->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (3.2.2)
Requirement already satisfied: dataclasses in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/enpamgb_basilisk/lib/python3.6/site-packages (from werkzeug>=1.0.1->tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.8)
Building wheels for collected packages: sgrna-modeler
Building wheel for sgrna-modeler (setup.py): started
Building wheel for sgrna-modeler (setup.py): finished with status 'done'
Created wheel for sgrna-modeler: filename=sgrna_modeler-0.1.0-py3-none-any.whl size=459415 sha256=6906bee2c7c7e5de8bb6b7c191e0848eb7574a3d8f4c9a3460b0ae07c55e1f3c
Stored in directory: /private/tmp/pip-ephem-wheel-cache-y67equ4b/wheels/37/2e/fc/bee98ee2abca5a7c383d760ea51b57e35297cf3107424d7a06
Successfully built sgrna-modeler
Installing collected packages: sgrna-modeler
Successfully installed sgrna-modeler-0.1.0
Channels:
- conda-forge
- bioconda
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/lindel_basilisk
added / updated specs:
- python=3.6
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/noarch::ca-certificates-2025.4.26-hbd8a1cb_0
libcxx conda-forge/osx-64::libcxx-20.1.3-hf95d169_0
libffi conda-forge/osx-64::libffi-3.4.6-h281671d_1
liblzma conda-forge/osx-64::liblzma-5.8.1-hd471939_0
liblzma-devel conda-forge/osx-64::liblzma-devel-5.8.1-hd471939_0
libsqlite conda-forge/osx-64::libsqlite-3.49.1-hdb6dae5_2
libzlib conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2
ncurses conda-forge/osx-64::ncurses-6.5-h0622a9a_3
openssl conda-forge/osx-64::openssl-1.1.1w-h8a1eda9_0
pip conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
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-h7cca4af_2
setuptools conda-forge/osx-64::setuptools-58.0.4-py36h79c6626_2
sqlite conda-forge/osx-64::sqlite-3.49.1-h2e4c9dc_2
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.8.1-h357f2ed_0
xz-gpl-tools conda-forge/osx-64::xz-gpl-tools-5.8.1-h357f2ed_0
xz-tools conda-forge/osx-64::xz-tools-5.8.1-hd471939_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
- bioconda
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.3.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
- bioconda
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.3.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/lindel_basilisk
added / updated specs:
- numpy=1.19.5
- pip=21.0.1
- python[version='3.6.*,3.6.*']
- scipy=1.5.3
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-14.2.0-hef36b68_105
libgfortran5 conda-forge/osx-64::libgfortran5-14.2.0-h58528f3_105
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-20.1.3-ha54dae1_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 DOWNGRADED:
pip 21.3.1-pyhd8ed1ab_0 --> 21.0.1-pyhd8ed1ab_0
Downloading and Extracting Packages: ...working... done
Preparing transaction: - done
Verifying transaction: | / - \ | / done
Executing transaction: \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
Processing /Users/biocbuild/bbs-3.22-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/lindel
Requirement already satisfied: numpy in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/lindel_basilisk/lib/python3.6/site-packages (from Lindel==1.0) (1.19.5)
Requirement already satisfied: scipy in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/lindel_basilisk/lib/python3.6/site-packages (from Lindel==1.0) (1.5.3)
Building wheels for collected packages: Lindel
Building wheel for Lindel (setup.py): started
Building wheel for Lindel (setup.py): finished with status 'done'
Created wheel for Lindel: filename=Lindel-1.0-py3-none-any.whl size=33618 sha256=74cd8915628c8bf21c2928fc763b718f9229291b7c3fb605c3e83aa4fc65dd7a
Stored in directory: /private/tmp/pip-ephem-wheel-cache-6rgmelgw/wheels/5e/4c/b5/63d0510bb10b7087aa0d2eaef0bde61197195ccb4a46a84816
Successfully built Lindel
Installing collected packages: Lindel
Successfully installed Lindel-1.0
Channels:
- conda-forge
- bioconda
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/deephf_basilisk
added / updated specs:
- python=3.6
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/noarch::ca-certificates-2025.4.26-hbd8a1cb_0
libcxx conda-forge/osx-64::libcxx-20.1.3-hf95d169_0
libffi conda-forge/osx-64::libffi-3.4.6-h281671d_1
liblzma conda-forge/osx-64::liblzma-5.8.1-hd471939_0
liblzma-devel conda-forge/osx-64::liblzma-devel-5.8.1-hd471939_0
libsqlite conda-forge/osx-64::libsqlite-3.49.1-hdb6dae5_2
libzlib conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2
ncurses conda-forge/osx-64::ncurses-6.5-h0622a9a_3
openssl conda-forge/osx-64::openssl-1.1.1w-h8a1eda9_0
pip conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
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-h7cca4af_2
setuptools conda-forge/osx-64::setuptools-58.0.4-py36h79c6626_2
sqlite conda-forge/osx-64::sqlite-3.49.1-h2e4c9dc_2
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.8.1-h357f2ed_0
xz-gpl-tools conda-forge/osx-64::xz-gpl-tools-5.8.1-h357f2ed_0
xz-tools conda-forge/osx-64::xz-tools-5.8.1-hd471939_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
- bioconda
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.3.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
- bioconda
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.3.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/deephf_basilisk
added / updated specs:
- python[version='3.6.*,3.6.*']
- viennarna=2.4.5
The following packages will be downloaded:
package | build
---------------------------|-----------------
viennarna-2.4.5 | hd28b015_3 13.9 MB bioconda
------------------------------------------------------------
Total: 13.9 MB
The following NEW packages will be INSTALLED:
viennarna bioconda/osx-64::viennarna-2.4.5-hd28b015_3
zlib conda-forge/osx-64::zlib-1.2.13-h87427d6_6
The following packages will be DOWNGRADED:
libsqlite 3.49.1-hdb6dae5_2 --> 3.46.0-h1b8f9f3_0
libzlib 1.3.1-hd23fc13_2 --> 1.2.13-h87427d6_6
sqlite 3.49.1-h2e4c9dc_2 --> 3.46.0-h28673e1_0
Downloading and Extracting Packages: ...working...
viennarna-2.4.5 | 13.9 MB | | 0%
viennarna-2.4.5 | 13.9 MB | | 0%
viennarna-2.4.5 | 13.9 MB | ######3 | 64%
viennarna-2.4.5 | 13.9 MB | ########## | 100%
viennarna-2.4.5 | 13.9 MB | ########## | 100%
done
Preparing transaction: - done
Verifying transaction: | done
Executing transaction: - done
Collecting biopython==1.71
Using cached biopython-1.71-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (2.1 MB)
Collecting h5py==2.9.0
Using cached h5py-2.9.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (6.3 MB)
Collecting dotmap==1.2.20
Using cached dotmap-1.2.20-py3-none-any.whl
Collecting numpy==1.14.0
Using cached numpy-1.14.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.7 MB)
Collecting scipy==1.1.0
Using cached scipy-1.1.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (16.7 MB)
Collecting pandas==0.25.3
Using cached pandas-0.25.3-cp36-cp36m-macosx_10_9_x86_64.whl (10.4 MB)
Collecting Keras==2.1.6
Using cached Keras-2.1.6-py2.py3-none-any.whl (339 kB)
Collecting gpy==1.9.8
Using cached GPy-1.9.8-cp36-cp36m-macosx_10_7_x86_64.whl (1.5 MB)
Collecting scikit-learn==0.19.1
Using cached scikit_learn-0.19.1-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (7.6 MB)
Collecting matplotlib==3.1.1
Using cached matplotlib-3.1.1-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (14.4 MB)
Collecting tensorboard==1.8.0
Using cached tensorboard-1.8.0-py3-none-any.whl (3.1 MB)
Collecting tensorflow==1.8.0
Using cached tensorflow-1.8.0-cp36-cp36m-macosx_10_11_x86_64.whl (46.5 MB)
Collecting Theano==1.0.5
Using cached Theano-1.0.5-py3-none-any.whl
Collecting six
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Collecting python-dateutil>=2.6.1
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Collecting pytz>=2017.2
Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
Collecting pyyaml
Using cached PyYAML-6.0.1-cp36-cp36m-macosx_10_9_x86_64.whl (189 kB)
Collecting paramz>=0.9.0
Using cached paramz-0.9.6-py3-none-any.whl (103 kB)
Collecting cycler>=0.10
Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
Using cached pyparsing-3.1.4-py3-none-any.whl (104 kB)
Collecting kiwisolver>=1.0.1
Using cached kiwisolver-1.3.1-cp36-cp36m-macosx_10_9_x86_64.whl (61 kB)
Collecting protobuf>=3.4.0
Using cached protobuf-3.19.6-cp36-cp36m-macosx_10_9_x86_64.whl (979 kB)
Collecting html5lib==0.9999999
Using cached html5lib-0.9999999-py3-none-any.whl
Collecting bleach==1.5.0
Using cached bleach-1.5.0-py2.py3-none-any.whl (17 kB)
Requirement already satisfied: wheel>=0.26 in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.0/crisprScore/1.13.0/deephf_basilisk/lib/python3.6/site-packages (from tensorboard==1.8.0) (0.37.1)
Collecting markdown>=2.6.8
Using cached Markdown-3.3.7-py3-none-any.whl (97 kB)
Collecting werkzeug>=0.11.10
Using cached Werkzeug-2.0.3-py3-none-any.whl (289 kB)
Collecting grpcio>=1.8.6
Using cached grpcio-1.48.2-cp36-cp36m-macosx_10_10_x86_64.whl (4.4 MB)
Collecting termcolor>=1.1.0
Using cached termcolor-1.1.0-py3-none-any.whl
Collecting astor>=0.6.0
Using cached astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting absl-py>=0.1.6
Using cached absl_py-1.4.0-py3-none-any.whl (126 kB)
Collecting gast>=0.2.0
Using cached gast-0.6.0-py3-none-any.whl (21 kB)
Collecting importlib-metadata>=4.4
Using cached importlib_metadata-4.8.3-py3-none-any.whl (17 kB)
Collecting decorator>=4.0.10
Using cached decorator-5.1.1-py3-none-any.whl (9.1 kB)
Collecting dataclasses
Using cached dataclasses-0.8-py3-none-any.whl (19 kB)
Collecting typing-extensions>=3.6.4
Using cached typing_extensions-4.1.1-py3-none-any.whl (26 kB)
Collecting zipp>=0.5
Using cached zipp-3.6.0-py3-none-any.whl (5.3 kB)
Installing collected packages: zipp, typing-extensions, six, numpy, importlib-metadata, html5lib, dataclasses, werkzeug, scipy, protobuf, markdown, decorator, bleach, termcolor, tensorboard, pyyaml, pytz, python-dateutil, pyparsing, paramz, kiwisolver, h5py, grpcio, gast, cycler, astor, absl-py, Theano, tensorflow, scikit-learn, pandas, matplotlib, Keras, gpy, dotmap, biopython
Successfully installed Keras-2.1.6 Theano-1.0.5 absl-py-1.4.0 astor-0.8.1 biopython-1.71 bleach-1.5.0 cycler-0.11.0 dataclasses-0.8 decorator-5.1.1 dotmap-1.2.20 gast-0.6.0 gpy-1.9.8 grpcio-1.48.2 h5py-2.9.0 html5lib-0.9999999 importlib-metadata-4.8.3 kiwisolver-1.3.1 markdown-3.3.7 matplotlib-3.1.1 numpy-1.14.0 pandas-0.25.3 paramz-0.9.6 protobuf-3.19.6 pyparsing-3.1.4 python-dateutil-2.9.0.post0 pytz-2025.2 pyyaml-6.0.1 scikit-learn-0.19.1 scipy-1.1.0 six-1.17.0 tensorboard-1.8.0 tensorflow-1.8.0 termcolor-1.1.0 typing-extensions-4.1.1 werkzeug-2.0.3 zipp-3.6.0
Processing /Users/biocbuild/bbs-3.22-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/deephf
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
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=10512 sha256=a1b846d957528c567733956b1839cda1f3ab2c141468ccfdf18101cb0a60c529
Stored in directory: /private/tmp/pip-ephem-wheel-cache-bepf_lvu/wheels/05/09/f3/ec8da7161c142810fa90fb40805b44fe164bda7c4d892675e3
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
208.342 100.336 505.479
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###
### 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_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/crisprScore.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘crisprScore/DESCRIPTION’ ... OK
* this is package ‘crisprScore’ version ‘1.13.0’
* 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-3.22-bioc-longtests/meat/crisprScore.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
installed size is 7.2Mb
sub-directories of 1Mb or more:
python 5.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘basilisk.utils:::getPythonBinary’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in shell scripts ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
Running ‘testthat.R’
OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/crisprScore.Rcheck/00check.log’
for details.
crisprScore.Rcheck/00install.out
* installing *source* package ‘crisprScore’ ... ** this is package ‘crisprScore’ version ‘1.13.0’ ** using non-staged installation via StagedInstall field ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (crisprScore)