Back to Long Tests report for BioC 3.19 |
This page was generated on 2024-06-22 23:55 -0400 (Sat, 22 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4758 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (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 18/33 | Hostname | OS / Arch | CHECK | |||||||
crisprScore 1.8.0 (landing page) Jean-Philippe Fortin
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | ||||||||
merida1 | macOS 12.7.4 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: 1.8.0 |
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 |
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% liblapack-3.8.0 | 10 KB | ########## | 100% liblapack-3.8.0 | 10 KB | ########## | 100% libcblas-3.8.0 | 10 KB | | 0% libcblas-3.8.0 | 10 KB | ########## | 100% libcblas-3.8.0 | 10 KB | ########## | 100% 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% pillow-6.2.1 | 588 KB | ########## | 100% wheel-0.36.2 | 31 KB | | 0% wheel-0.36.2 | 31 KB | ########## | 100% 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% subprocess32-3.5.4 | 44 KB | ###6 | 36% subprocess32-3.5.4 | 44 KB | ########## | 100% backports.functools_ | 8 KB | | 0% backports.functools_ | 8 KB | ########## | 100% functools32-3.2.3.2 | 15 KB | | 0% functools32-3.2.3.2 | 15 KB | ########## | 100% matplotlib-2.2.3 | 6 KB | | 0% matplotlib-2.2.3 | 6 KB | ########## | 100% matplotlib-2.2.3 | 6 KB | ########## | 100% cycler-0.10.0 | 9 KB | | 0% cycler-0.10.0 | 9 KB | ########## | 100% backports_abc-0.5 | 5 KB | | 0% backports_abc-0.5 | 5 KB | ########## | 100% 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% tornado-5.1.1 | 642 KB | 2 | 2% tornado-5.1.1 | 642 KB | ########## | 100% tornado-5.1.1 | 642 KB | ########## | 100% kiwisolver-1.1.0 | 57 KB | | 0% kiwisolver-1.1.0 | 57 KB | ########## | 100% backports-1.0 | 6 KB | | 0% backports-1.0 | 6 KB | ########## | 100% 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% nose-1.3.7 | 214 KB | 7 | 7% 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% reportlab-3.5.42 | 2.4 MB | | 1% reportlab-3.5.42 | 2.4 MB | ########## | 100% reportlab-3.5.42 | 2.4 MB | ########## | 100% biopython-1.74 | 2.5 MB | | 0% biopython-1.74 | 2.5 MB | | 1% biopython-1.74 | 2.5 MB | ########## | 100% biopython-1.74 | 2.5 MB | ########## | 100% 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% werkzeug-1.0.1 | 239 KB | ########## | 100% werkzeug-1.0.1 | 239 KB | ########## | 100% scipy-1.5.3 | 16.9 MB | | 0% scipy-1.5.3 | 16.9 MB | | 0% scipy-1.5.3 | 16.9 MB | ###4 | 35% scipy-1.5.3 | 16.9 MB | ######9 | 70% scipy-1.5.3 | 16.9 MB | #########6 | 97% scipy-1.5.3 | 16.9 MB | ########## | 100% chardet-4.0.0 | 219 KB | | 0% chardet-4.0.0 | 219 KB | ########## | 100% chardet-4.0.0 | 219 KB | ########## | 100% libprotobuf-3.15.5 | 2.1 MB | | 0% libprotobuf-3.15.5 | 2.1 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########## | 100% termcolor-1.1.0 | 8 KB | | 0% termcolor-1.1.0 | 8 KB | ########## | 100% Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting tensorflow==2.4.1 Using cached tensorflow-2.4.1-cp36-cp36m-macosx_10_11_x86_64.whl (173.9 MB) Requirement already satisfied: six~=1.15.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow==2.4.1) (1.15.0) Requirement already satisfied: wheel~=0.35 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow==2.4.1) (0.36.2) Collecting tensorboard~=2.4 Using cached tensorboard-2.10.1-py3-none-any.whl (5.9 MB) Requirement already satisfied: gast==0.3.3 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow==2.4.1) (0.3.3) Requirement already satisfied: google-pasta~=0.2 in 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/private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.4.3) Requirement already satisfied: werkzeug>=1.0.1 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.0.1) Requirement already satisfied: google-auth<3,>=1.6.3 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.27.1) Requirement already satisfied: setuptools>=41.0.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (49.6.0.post20210108) Requirement already satisfied: tensorboard-plugin-wit>=1.6.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/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: requests<3,>=2.21.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.25.1) Requirement already satisfied: rsa<5,>=3.1.4 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/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) (4.7.2) Requirement already satisfied: pyasn1-modules>=0.2.1 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/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) (0.2.8) Requirement already satisfied: cachetools<5.0,>=2.0.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/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) (4.2.1) 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 Downloading and Extracting Packages clang-11.1.0 | 125 KB | | 0% clang-11.1.0 | 125 KB | #2 | 13% clang-11.1.0 | 125 KB | ########## | 100% tensorboard-1.8.0 | 3.1 MB | | 0% tensorboard-1.8.0 | 3.1 MB | | 1% tensorboard-1.8.0 | 3.1 MB | ########## | 100% tensorboard-1.8.0 | 3.1 MB | ########## | 100% libllvm11-11.1.0 | 22.2 MB | | 0% libllvm11-11.1.0 | 22.2 MB | | 0% libllvm11-11.1.0 | 22.2 MB | #9 | 19% libllvm11-11.1.0 | 22.2 MB | ##### | 50% libllvm11-11.1.0 | 22.2 MB | #######1 | 72% libllvm11-11.1.0 | 22.2 MB | ########## | 100% libllvm11-11.1.0 | 22.2 MB | ########## | 100% grpcio-1.36.1 | 2.0 MB | | 0% grpcio-1.36.1 | 2.0 MB | | 1% grpcio-1.36.1 | 2.0 MB | ########## | 100% grpcio-1.36.1 | 2.0 MB | ########## | 100% sigtool-0.1.3 | 209 KB | | 0% sigtool-0.1.3 | 209 KB | ########## | 100% sigtool-0.1.3 | 209 KB | ########## | 100% 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/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) Requirement already satisfied: absl-py>=0.1.6 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) (0.12.0) Requirement already satisfied: gast>=0.2.0 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) (0.4.0) 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) Requirement already satisfied: wheel>=0.26 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) (0.36.2) 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) Requirement already satisfied: importlib-metadata in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from markdown>=2.6.8->tensorboard<1.9.0,>=1.8.0->tensorflow==1.8.0->DeepHF==1.0) (3.7.2) Requirement already satisfied: GPy>=1.8 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from GPyOpt->DeepHF==1.0) (1.9.8) Requirement already satisfied: paramz>=0.9.0 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from GPy>=1.8->GPyOpt->DeepHF==1.0) (0.9.5) Requirement already satisfied: decorator>=4.0.10 in /private/var/cache/basilisk/1.16.0/crisprScore/1.8.0/deephf_basilisk/lib/python3.6/site-packages (from paramz>=0.9.0->GPy>=1.8->GPyOpt->DeepHF==1.0) (4.4.2) 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
############################################################################## ############################################################################## ### ### 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.
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)