| Back to Long Tests report for BioC 3.21 |
This page was generated on 2025-03-22 23:55 -0400 (Sat, 22 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4547 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| 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 1.11.0 (landing page) Jean-Philippe Fortin
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | |||||||
| palomino7 | 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: 1.11.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no crisprScore_1.11.0.tar.gz |
| StartedAt: 2025-03-22 16:08:02 -0400 (Sat, 22 Mar 2025) |
| EndedAt: 2025-03-22 16:15:24 -0400 (Sat, 22 Mar 2025) |
| EllapsedTime: 442.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: crisprScore.Rcheck |
| Warnings: 0 |
crisprScore.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(crisprScore)
Loading required package: crisprScoreData
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
>
> test_check("crisprScore")
Channels:
- bioconda
- conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk
added / updated specs:
- python=2.7
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2025.1.31-hbcca054_0
certifi conda-forge/linux-64::certifi-2019.11.28-py27h8c360ce_1
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_4
libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
libgcc conda-forge/linux-64::libgcc-14.2.0-h767d61c_2
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_2
libgomp conda-forge/linux-64::libgomp-14.2.0-h767d61c_2
libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-h8f9b012_2
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_2
libzlib conda-forge/linux-64::libzlib-1.2.13-h4ab18f5_6
ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3
openssl conda-forge/linux-64::openssl-1.1.1w-hd590300_0
pip conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
python conda-forge/linux-64::python-2.7.15-h5a48372_1011_cpython
python_abi conda-forge/linux-64::python_abi-2.7-1_cp27mu
readline conda-forge/linux-64::readline-8.2-h8c095d6_2
setuptools conda-forge/linux-64::setuptools-44.0.0-py27_0
sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
zlib conda-forge/linux-64::zlib-1.2.13-h4ab18f5_6
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- bioconda
- conda-forge
Platform: linux-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: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- bioconda
- conda-forge
Platform: linux-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: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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
---------------------------|-----------------
atk-2.36.0 | ha770c72_4 12 KB conda-forge
atk-1.0-2.36.0 | haf93ef1_1 530 KB conda-forge
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 | py27h516909a_0 2.5 MB conda-forge
cairo-1.16.0 | h18b612c_1001 1.5 MB conda-forge
cycler-0.10.0 | py_2 9 KB conda-forge
dbus-1.13.6 | he372182_0 602 KB conda-forge
expat-2.6.4 | h5888daf_0 135 KB conda-forge
functools32-3.2.3.2 | py_3 15 KB conda-forge
futures-3.3.0 | py27h8c360ce_1 26 KB conda-forge
gdk-pixbuf-2.32.2 | 1 759 KB bioconda
gettext-0.23.1 | h5888daf_0 473 KB conda-forge
gettext-tools-0.23.1 | h5888daf_0 2.8 MB conda-forge
glib-2.58.3 |py27he9b9f4b_1003 3.3 MB conda-forge
gobject-introspection-1.56.1|py27h2da5eee_1002 1.3 MB conda-forge
gstreamer-1.14.5 | h36ae1b5_2 4.5 MB conda-forge
gtk2-2.24.32 | h90f3771_0 7.3 MB conda-forge
harfbuzz-2.4.0 | h37c48d4_1 1.5 MB conda-forge
icu-58.2 | hf484d3e_1000 22.6 MB conda-forge
kiwisolver-1.1.0 | py27h9e3301b_1 88 KB conda-forge
libasprintf-0.23.1 | h8e693c7_0 42 KB conda-forge
libasprintf-devel-0.23.1 | h8e693c7_0 33 KB conda-forge
libdeflate-1.14 | h166bdaf_0 81 KB conda-forge
libgettextpo-0.23.1 | h5888daf_0 163 KB conda-forge
libgettextpo-devel-0.23.1 | h5888daf_0 36 KB conda-forge
libgfortran-ng-7.5.0 | h14aa051_20 23 KB conda-forge
libgfortran4-7.5.0 | h14aa051_20 1.2 MB conda-forge
libtiff-4.4.0 | h82bc61c_5 473 KB conda-forge
libxcb-1.17.0 | h8a09558_0 387 KB conda-forge
libxml2-2.9.9 | h13577e0_2 1.3 MB conda-forge
matplotlib-2.2.3 | py27h8a2030e_1 7 KB conda-forge
matplotlib-base-2.2.3 | py27h60b886d_1 6.4 MB conda-forge
numpy-1.11.3 |py27he5ce36f_1207 3.6 MB conda-forge
openssl-1.0.2u | h516909a_0 3.2 MB conda-forge
pandas-0.23.4 |py27h637b7d7_1000 9.8 MB conda-forge
pango-1.42.4 | h7062337_4 521 KB conda-forge
pcre-8.45 | h9c3ff4c_0 253 KB conda-forge
pixman-0.38.0 | h516909a_1003 594 KB conda-forge
pyparsing-2.4.7 | pyh9f0ad1d_0 60 KB conda-forge
pyqt-5.6.0 |py27h13b7fb3_1008 5.2 MB conda-forge
python-2.7.15 | h938d71a_1006 11.9 MB conda-forge
python-dateutil-2.8.1 | py_0 220 KB conda-forge
pytz-2020.1 | pyh9f0ad1d_0 227 KB conda-forge
qt-5.6.2 | hce4f676_1013 44.6 MB conda-forge
readline-7.0 | hf8c457e_1001 391 KB conda-forge
scipy-1.2.1 | py27h09a28d5_1 18.1 MB conda-forge
singledispatch-3.6.1 | pyh44b312d_0 12 KB conda-forge
sip-4.18.1 |py27hf484d3e_1000 278 KB conda-forge
sqlite-3.28.0 | h8b20d00_0 1.9 MB conda-forge
subprocess32-3.5.4 | py27h516909a_0 46 KB conda-forge
tornado-5.1.1 |py27h14c3975_1000 642 KB conda-forge
xorg-libice-1.1.2 | hb9d3cd8_0 57 KB conda-forge
xorg-libsm-1.2.6 | he73a12e_0 27 KB conda-forge
xorg-libx11-1.8.12 | h4f16b4b_0 816 KB conda-forge
xorg-libxau-1.0.12 | hb9d3cd8_0 14 KB conda-forge
xorg-libxext-1.3.6 | hb9d3cd8_0 49 KB conda-forge
xorg-libxrender-0.9.12 | hb9d3cd8_0 32 KB conda-forge
xorg-libxt-1.3.1 | hb9d3cd8_0 371 KB conda-forge
------------------------------------------------------------
Total: 162.8 MB
The following NEW packages will be INSTALLED:
atk conda-forge/linux-64::atk-2.36.0-ha770c72_4
atk-1.0 conda-forge/linux-64::atk-1.0-2.36.0-haf93ef1_1
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/linux-64::biopython-1.74-py27h516909a_0
cairo conda-forge/linux-64::cairo-1.16.0-h18b612c_1001
cycler conda-forge/noarch::cycler-0.10.0-py_2
dbus conda-forge/linux-64::dbus-1.13.6-he372182_0
expat conda-forge/linux-64::expat-2.6.4-h5888daf_0
fontconfig conda-forge/linux-64::fontconfig-2.14.2-h14ed4e7_0
freetype conda-forge/linux-64::freetype-2.12.1-h267a509_2
fribidi conda-forge/linux-64::fribidi-1.0.10-h36c2ea0_0
functools32 conda-forge/noarch::functools32-3.2.3.2-py_3
futures conda-forge/linux-64::futures-3.3.0-py27h8c360ce_1
gdk-pixbuf bioconda/linux-64::gdk-pixbuf-2.32.2-1
gettext conda-forge/linux-64::gettext-0.23.1-h5888daf_0
gettext-tools conda-forge/linux-64::gettext-tools-0.23.1-h5888daf_0
glib conda-forge/linux-64::glib-2.58.3-py27he9b9f4b_1003
gobject-introspec~ conda-forge/linux-64::gobject-introspection-1.56.1-py27h2da5eee_1002
graphite2 conda-forge/linux-64::graphite2-1.3.13-h59595ed_1003
gstreamer conda-forge/linux-64::gstreamer-1.14.5-h36ae1b5_2
gtk2 conda-forge/linux-64::gtk2-2.24.32-h90f3771_0
harfbuzz conda-forge/linux-64::harfbuzz-2.4.0-h37c48d4_1
icu conda-forge/linux-64::icu-58.2-hf484d3e_1000
jpeg conda-forge/linux-64::jpeg-9e-h0b41bf4_3
kiwisolver conda-forge/linux-64::kiwisolver-1.1.0-py27h9e3301b_1
lerc conda-forge/linux-64::lerc-4.0.0-h27087fc_0
libasprintf conda-forge/linux-64::libasprintf-0.23.1-h8e693c7_0
libasprintf-devel conda-forge/linux-64::libasprintf-devel-0.23.1-h8e693c7_0
libblas conda-forge/linux-64::libblas-3.9.0-20_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-20_linux64_openblas
libdeflate conda-forge/linux-64::libdeflate-1.14-h166bdaf_0
libexpat conda-forge/linux-64::libexpat-2.6.4-h5888daf_0
libgettextpo conda-forge/linux-64::libgettextpo-0.23.1-h5888daf_0
libgettextpo-devel conda-forge/linux-64::libgettextpo-devel-0.23.1-h5888daf_0
libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.5.0-h14aa051_20
libgfortran4 conda-forge/linux-64::libgfortran4-7.5.0-h14aa051_20
libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hf1ad2bd_2
libiconv conda-forge/linux-64::libiconv-1.18-h4ce23a2_1
liblapack conda-forge/linux-64::liblapack-3.9.0-20_linux64_openblas
liblzma conda-forge/linux-64::liblzma-5.6.4-hb9d3cd8_0
liblzma-devel conda-forge/linux-64::liblzma-devel-5.6.4-hb9d3cd8_0
libopenblas conda-forge/linux-64::libopenblas-0.3.25-pthreads_h413a1c8_0
libpng conda-forge/linux-64::libpng-1.6.43-h2797004_0
libtiff conda-forge/linux-64::libtiff-4.4.0-h82bc61c_5
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libwebp-base conda-forge/linux-64::libwebp-base-1.5.0-h851e524_0
libxcb conda-forge/linux-64::libxcb-1.17.0-h8a09558_0
libxml2 conda-forge/linux-64::libxml2-2.9.9-h13577e0_2
matplotlib conda-forge/linux-64::matplotlib-2.2.3-py27h8a2030e_1
matplotlib-base conda-forge/linux-64::matplotlib-base-2.2.3-py27h60b886d_1
numpy conda-forge/linux-64::numpy-1.11.3-py27he5ce36f_1207
pandas conda-forge/linux-64::pandas-0.23.4-py27h637b7d7_1000
pango conda-forge/linux-64::pango-1.42.4-h7062337_4
pcre conda-forge/linux-64::pcre-8.45-h9c3ff4c_0
pixman conda-forge/linux-64::pixman-0.38.0-h516909a_1003
pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-hb9d3cd8_1002
pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
pyqt conda-forge/linux-64::pyqt-5.6.0-py27h13b7fb3_1008
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
pytz conda-forge/noarch::pytz-2020.1-pyh9f0ad1d_0
qt conda-forge/linux-64::qt-5.6.2-hce4f676_1013
scipy conda-forge/linux-64::scipy-1.2.1-py27h09a28d5_1
singledispatch conda-forge/noarch::singledispatch-3.6.1-pyh44b312d_0
sip conda-forge/linux-64::sip-4.18.1-py27hf484d3e_1000
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
subprocess32 conda-forge/linux-64::subprocess32-3.5.4-py27h516909a_0
tornado conda-forge/linux-64::tornado-5.1.1-py27h14c3975_1000
xorg-libice conda-forge/linux-64::xorg-libice-1.1.2-hb9d3cd8_0
xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.6-he73a12e_0
xorg-libx11 conda-forge/linux-64::xorg-libx11-1.8.12-h4f16b4b_0
xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.12-hb9d3cd8_0
xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.5-hb9d3cd8_0
xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.6-hb9d3cd8_0
xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.12-hb9d3cd8_0
xorg-libxt conda-forge/linux-64::xorg-libxt-1.3.1-hb9d3cd8_0
xz conda-forge/linux-64::xz-5.6.4-hbcc6ac9_0
xz-gpl-tools conda-forge/linux-64::xz-gpl-tools-5.6.4-hbcc6ac9_0
xz-tools conda-forge/linux-64::xz-tools-5.6.4-hb9d3cd8_0
zstd conda-forge/linux-64::zstd-1.5.6-ha6fb4c9_0
The following packages will be DOWNGRADED:
openssl 1.1.1w-hd590300_0 --> 1.0.2u-h516909a_0
python 2.7.15-h5a48372_1011_cpython --> 2.7.15-h938d71a_1006
readline 8.2-h8c095d6_2 --> 7.0-hf8c457e_1001
sqlite 3.46.0-h6d4b2fc_0 --> 3.28.0-h8b20d00_0
Downloading and Extracting Packages: ...working...
qt-5.6.2 | 44.6 MB | | 0%
icu-58.2 | 22.6 MB | | 0% [A
scipy-1.2.1 | 18.1 MB | | 0% [A[A
python-2.7.15 | 11.9 MB | | 0% [A[A[A
pandas-0.23.4 | 9.8 MB | | 0% [A[A[A[A
gtk2-2.24.32 | 7.3 MB | | 0% [A[A[A[A[A
matplotlib-base-2.2. | 6.4 MB | | 0% [A[A[A[A[A[A
pyqt-5.6.0 | 5.2 MB | | 0% [A[A[A[A[A[A[A
gstreamer-1.14.5 | 4.5 MB | | 0% [A[A[A[A[A[A[A[A
numpy-1.11.3 | 3.6 MB | | 0% [A[A[A[A[A[A[A[A[A
glib-2.58.3 | 3.3 MB | | 0% [A[A[A[A[A[A[A[A[A[A
openssl-1.0.2u | 3.2 MB | | 0% [A[A[A[A[A[A[A[A[A[A[A
gettext-tools-0.23.1 | 2.8 MB | | 0% [A[A[A[A[A[A[A[A[A[A[A[A
biopython-1.74 | 2.5 MB | | 0% [A[A[A[A[A[A[A[A[A[A[A[A[A
sqlite-3.28.0 | 1.9 MB | | 0% [A[A[A[A[A[A[A[A[A[A[A[A[A[A
cairo-1.16.0 | 1.5 MB | | 0% [A[A[A[A[A[A[A[A[A[A[A[A[A[A[A
harfbuzz-2.4.0 | 1.5 MB | | 0% [A[A[A[A[A[A[A[A[A[A[A[A[A[A[A[A
libxml2-2.9.9 | 1.3 MB | | 0% [A[A[A[A[A[A[A[A[A[A[A[A[A[A[A[A[A
gobject-introspectio | 1.3 MB | | 0% [A[A[A[A[A[A[A[A[A[A[A[A[A[A[A[A[A[A
... (more hidden) ...[A[A[A[A[A[A[A[A[A[A[A[A[A[A[A[A[A[A[A
qt-5.6.2 | 44.6 MB | | 0%
icu-58.2 | 22.6 MB | | 0% [A
python-2.7.15 | 11.9 MB | | 1% [A[A[A
scipy-1.2.1 | 18.1 MB | | 0% [A[A
pandas-0.23.4 | 9.8 MB | | 0% [A[A[A[A
qt-5.6.2 | 44.6 MB | 9 | 10%
icu-58.2 | 22.6 MB | #9 | 20% [A
python-2.7.15 | 11.9 MB | ###7 | 38% [A[A[A
scipy-1.2.1 | 18.1 MB | #5 | 15% [A[A
pandas-0.23.4 | 9.8 MB | #### | 41% [A[A[A[A
qt-5.6.2 | 44.6 MB | ## | 20%
icu-58.2 | 22.6 MB | ####1 | 42% [A
python-2.7.15 | 11.9 MB | #######5 | 75% [A[A[A
scipy-1.2.1 | 18.1 MB | ###9 | 40% [A[A
pandas-0.23.4 | 9.8 MB | ########5 | 85% [A[A[A[A
qt-5.6.2 | 44.6 MB | ###2 | 32%
icu-58.2 | 22.6 MB | ######5 | 66% [A
scipy-1.2.1 | 18.1 MB | ######9 | 69% [A[A
pandas-0.23.4 | 9.8 MB | ########## | 100% [A[A[A[A
qt-5.6.2 | 44.6 MB | ####5 | 45%
icu-58.2 | 22.6 MB | #########3 | 94% [A
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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-cp27mu-manylinux1_x86_64.whl (17.6 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 /home/biocbuild/bbs-3.21-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/azimuth
Requirement already satisfied: scipy<=1.2.1 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.2.1)
Requirement already satisfied: numpy<=1.14 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.11.3)
Requirement already satisfied: matplotlib in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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 /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (0.17.1)
Requirement already satisfied: pandas in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (0.23.4)
Requirement already satisfied: biopython<=1.76 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.74)
Requirement already satisfied: cycler>=0.10 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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 /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (2.4.7)
Requirement already satisfied: python-dateutil>=2.1 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (2.8.1)
Requirement already satisfied: pytz in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (2020.1)
Requirement already satisfied: six>=1.10 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (1.16.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (1.1.0)
Requirement already satisfied: backports.functools_lru_cache in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (1.6.1)
Requirement already satisfied: subprocess32 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (3.5.4)
Requirement already satisfied: setuptools in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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=e6fe3e34112272d5fe9226ce623e7554dfa8b764ff62b166d7c3d6d6013cc051
Stored in directory: /tmp/pip-ephem-wheel-cache-zljE3j/wheels/82/ba/30/e521897350fe64fc211b3796a7ff33442db02f0d76ab624316
Successfully built Azimuth
Installing collected packages: nose, Azimuth
Successfully installed Azimuth-2.0 nose-1.3.7
Channels:
- conda-forge
- bioconda
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/deepcpf1_basilisk
added / updated specs:
- python=2.7
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2025.1.31-hbcca054_0
certifi conda-forge/linux-64::certifi-2019.11.28-py27h8c360ce_1
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_4
libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
libgcc conda-forge/linux-64::libgcc-14.2.0-h767d61c_2
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_2
libgomp conda-forge/linux-64::libgomp-14.2.0-h767d61c_2
libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-h8f9b012_2
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_2
libzlib conda-forge/linux-64::libzlib-1.2.13-h4ab18f5_6
ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3
openssl conda-forge/linux-64::openssl-1.1.1w-hd590300_0
pip conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
python conda-forge/linux-64::python-2.7.15-h5a48372_1011_cpython
python_abi conda-forge/linux-64::python_abi-2.7-1_cp27mu
readline conda-forge/linux-64::readline-8.2-h8c095d6_2
setuptools conda-forge/linux-64::setuptools-44.0.0-py27_0
sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
zlib conda-forge/linux-64::zlib-1.2.13-h4ab18f5_6
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
- bioconda
Platform: linux-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: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
- bioconda
Platform: linux-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: 25.1.1
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-cp27mu-manylinux1_x86_64.whl (2.8 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-cp27mu-manylinux1_x86_64.whl (17.0 MB)
Collecting scipy==1.2.1
Using cached scipy-1.2.1-cp27-cp27mu-manylinux1_x86_64.whl (24.8 MB)
Collecting tensorflow==1.0.0
Using cached tensorflow-1.0.0-cp27-cp27mu-manylinux1_x86_64.whl (44.1 MB)
Processing /home/biocbuild/.cache/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-cp27mu-manylinux1_x86_64.whl (574 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-cp27mu-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.0 MB)
Requirement already satisfied: wheel in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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: six, numpy, h5py, pyyaml, scipy, 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 /home/biocbuild/bbs-3.21-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=d78be3143194ae10fa7d65918421fed081c4dfa4b512e689b70d119cabe00daa
Stored in directory: /tmp/pip-ephem-wheel-cache-ULTt2B/wheels/cb/cd/d1/2e5ac42ff54fe56a6c5132f232075a8bd1c7e0c27be5987d85
Successfully built DeepCpf1
Installing collected packages: DeepCpf1
Successfully installed DeepCpf1-1.0
Channels:
- conda-forge
- bioconda
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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 |hb7a2778_0_cpython 38.4 MB conda-forge
python_abi-3.6 | 2_cp36m 4 KB conda-forge
setuptools-58.0.4 | py36h5fab9bb_2 966 KB conda-forge
------------------------------------------------------------
Total: 40.5 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2025.1.31-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_4
libffi conda-forge/linux-64::libffi-3.4.6-h2dba641_0
libgcc conda-forge/linux-64::libgcc-14.2.0-h767d61c_2
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_2
libgomp conda-forge/linux-64::libgomp-14.2.0-h767d61c_2
liblzma conda-forge/linux-64::liblzma-5.6.4-hb9d3cd8_0
liblzma-devel conda-forge/linux-64::liblzma-devel-5.6.4-hb9d3cd8_0
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.49.1-hee588c1_2
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-h8f9b012_2
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_2
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3
openssl conda-forge/linux-64::openssl-1.1.1w-hd590300_0
pip conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.6.15-hb7a2778_0_cpython
python_abi conda-forge/linux-64::python_abi-3.6-2_cp36m
readline conda-forge/linux-64::readline-8.2-h8c095d6_2
setuptools conda-forge/linux-64::setuptools-58.0.4-py36h5fab9bb_2
sqlite conda-forge/linux-64::sqlite-3.49.1-h9eae976_2
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.6.4-hbcc6ac9_0
xz-gpl-tools conda-forge/linux-64::xz-gpl-tools-5.6.4-hbcc6ac9_0
xz-tools conda-forge/linux-64::xz-tools-5.6.4-hb9d3cd8_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
- bioconda
Platform: linux-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: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
- bioconda
Platform: linux-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: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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 | py36h8f6f2f9_2 2.7 MB conda-forge
certifi-2021.5.30 | py36h5fab9bb_0 141 KB conda-forge
h5py-2.10.0 |nompi_py36h4510012_106 1.1 MB conda-forge
joblib-1.2.0 | pyhd8ed1ab_0 205 KB conda-forge
numpy-1.19.5 | py36hfc0c790_2 5.3 MB conda-forge
pandas-1.1.5 | py36h284efc9_0 11.3 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 | py36hcdab131_1 6.7 MB conda-forge
scipy-1.5.3 | py36h81d768a_1 19.1 MB conda-forge
setuptools-49.6.0 | py36h5fab9bb_3 936 KB conda-forge
six-1.15.0 | pyh9f0ad1d_0 14 KB conda-forge
------------------------------------------------------------
Total: 48.7 MB
The following NEW packages will be INSTALLED:
biopython conda-forge/linux-64::biopython-1.78-py36h8f6f2f9_2
c-ares conda-forge/linux-64::c-ares-1.34.4-hb9d3cd8_0
certifi conda-forge/linux-64::certifi-2021.5.30-py36h5fab9bb_0
h5py conda-forge/linux-64::h5py-2.10.0-nompi_py36h4510012_106
hdf5 conda-forge/linux-64::hdf5-1.10.6-nompi_h6a2412b_1114
joblib conda-forge/noarch::joblib-1.2.0-pyhd8ed1ab_0
keras-preprocessi~ conda-forge/noarch::keras-preprocessing-1.1.2-pyhd8ed1ab_0
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
krb5 conda-forge/linux-64::krb5-1.20.1-hf9c8cef_0
libblas conda-forge/linux-64::libblas-3.9.0-20_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-20_linux64_openblas
libcurl conda-forge/linux-64::libcurl-7.87.0-h6312ad2_0
libedit conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0
libev conda-forge/linux-64::libev-4.33-hd590300_2
libgfortran conda-forge/linux-64::libgfortran-14.2.0-h69a702a_2
libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.2.0-h69a702a_2
libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hf1ad2bd_2
liblapack conda-forge/linux-64::liblapack-3.9.0-20_linux64_openblas
libnghttp2 conda-forge/linux-64::libnghttp2-1.51.0-hdcd2b5c_0
libopenblas conda-forge/linux-64::libopenblas-0.3.25-pthreads_h413a1c8_0
libssh2 conda-forge/linux-64::libssh2-1.10.0-haa6b8db_3
numpy conda-forge/linux-64::numpy-1.19.5-py36hfc0c790_2
pandas conda-forge/linux-64::pandas-1.1.5-py36h284efc9_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/linux-64::scikit-learn-0.21.2-py36hcdab131_1
scipy conda-forge/linux-64::scipy-1.5.3-py36h81d768a_1
six conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
zlib conda-forge/linux-64::zlib-1.2.13-h4ab18f5_6
The following packages will be DOWNGRADED:
libsqlite 3.49.1-hee588c1_2 --> 3.46.0-hde9e2c9_0
libzlib 1.3.1-hb9d3cd8_2 --> 1.2.13-h4ab18f5_6
pip 21.3.1-pyhd8ed1ab_0 --> 21.0.1-pyhd8ed1ab_0
setuptools 58.0.4-py36h5fab9bb_2 --> 49.6.0-py36h5fab9bb_3
sqlite 3.49.1-h9eae976_2 --> 3.46.0-h6d4b2fc_0
Downloading and Extracting Packages: ...working...
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joblib-1.2.0 | 205 KB | | 0% [A[A[A[A[A[A[A[A
pytz-2023.3.post1 | 183 KB | | 0% [A[A[A[A[A[A[A[A[A
certifi-2021.5.30 | 141 KB | | 0% [A[A[A[A[A[A[A[A[A[A
six-1.15.0 | 14 KB | | 0% [A[A[A[A[A[A[A[A[A[A[A
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scikit-learn-0.21.2 | 6.7 MB | 6 | 6% [A[A
pandas-1.1.5 | 11.3 MB | | 1% [A
numpy-1.19.5 | 5.3 MB | 3 | 4% [A[A[A
biopython-1.78 | 2.7 MB | #7 | 17% [A[A[A[A
scipy-1.5.3 | 19.1 MB | ##5 | 26%
scikit-learn-0.21.2 | 6.7 MB | ####### | 71% [A[A
pandas-1.1.5 | 11.3 MB | ###3 | 33% [A
numpy-1.19.5 | 5.3 MB | ########1 | 81% [A[A[A
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scipy-1.5.3 | 19.1 MB | #####5 | 56%
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scikit-learn-0.21.2 | 6.7 MB | ########## | 100% [A[A
scipy-1.5.3 | 19.1 MB | ########7 | 87%
setuptools-49.6.0 | 936 KB | 1 | 2% [A[A[A[A[A[A[A
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pytz-2023.3.post1 | 183 KB | ########## | 100% [A[A[A[A[A[A[A[A[A
scipy-1.5.3 | 19.1 MB | ########## | 100%
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h5py-2.10.0 | 1.1 MB | ########## | 100% [A[A[A[A[A
biopython-1.78 | 2.7 MB | ########## | 100% [A[A[A[A
pip-21.0.1 | 1.1 MB | ########## | 100% [A[A[A[A[A[A
pip-21.0.1 | 1.1 MB | ########## | 100% [A[A[A[A[A[A
joblib-1.2.0 | 205 KB | ########## | 100% [A[A[A[A[A[A[A[A
joblib-1.2.0 | 205 KB | ########## | 100% [A[A[A[A[A[A[A[A
numpy-1.19.5 | 5.3 MB | ########## | 100% [A[A[A
six-1.15.0 | 14 KB | ########## | 100% [A[A[A[A[A[A[A[A[A[A[A
certifi-2021.5.30 | 141 KB | ########## | 100% [A[A[A[A[A[A[A[A[A[A
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scikit-learn-0.21.2 | 6.7 MB | ########## | 100% [A[A
pandas-1.1.5 | 11.3 MB | ########## | 100% [A
scipy-1.5.3 | 19.1 MB | ########## | 100%
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Collecting tensorflow==2.4.1
Using cached tensorflow-2.4.1-cp36-cp36m-manylinux2010_x86_64.whl (394.3 MB)
Collecting tensorboard~=2.4
Using cached tensorboard-2.10.1-py3-none-any.whl (5.9 MB)
Collecting google-pasta~=0.2
Using cached google_pasta-0.2.0-py3-none-any.whl (57 kB)
Collecting grpcio~=1.32.0
Using cached grpcio-1.32.0-cp36-cp36m-manylinux2014_x86_64.whl (3.8 MB)
Collecting flatbuffers~=1.12.0
Using cached flatbuffers-1.12-py2.py3-none-any.whl (15 kB)
Requirement already satisfied: wheel~=0.35 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow==2.4.1) (0.37.1)
Collecting typing-extensions~=3.7.4
Using cached typing_extensions-3.7.4.3-py3-none-any.whl (22 kB)
Collecting gast==0.3.3
Using cached gast-0.3.3-py2.py3-none-any.whl (9.7 kB)
Collecting astunparse~=1.6.3
Using cached astunparse-1.6.3-py2.py3-none-any.whl (12 kB)
Collecting protobuf>=3.9.2
Using cached protobuf-3.19.6-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
Collecting termcolor~=1.1.0
Using cached termcolor-1.1.0-py3-none-any.whl
Collecting tensorflow-estimator<2.5.0,>=2.4.0
Using cached tensorflow_estimator-2.4.0-py2.py3-none-any.whl (462 kB)
Requirement already satisfied: keras-preprocessing~=1.1.2 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow==2.4.1) (1.1.2)
Collecting absl-py~=0.10
Using cached absl_py-0.15.0-py3-none-any.whl (132 kB)
Requirement already satisfied: six~=1.15.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow==2.4.1) (1.15.0)
Collecting wrapt~=1.12.1
Using cached wrapt-1.12.1-cp36-cp36m-linux_x86_64.whl
Collecting opt-einsum~=3.3.0
Using cached opt_einsum-3.3.0-py3-none-any.whl (65 kB)
Requirement already satisfied: numpy~=1.19.2 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow==2.4.1) (1.19.5)
Requirement already satisfied: h5py~=2.10.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow==2.4.1) (2.10.0)
Collecting requests<3,>=2.21.0
Using cached requests-2.27.1-py2.py3-none-any.whl (63 kB)
Collecting google-auth<3,>=1.6.3
Using cached google_auth-2.22.0-py2.py3-none-any.whl (181 kB)
Collecting werkzeug>=1.0.1
Using cached Werkzeug-2.0.3-py3-none-any.whl (289 kB)
Collecting markdown>=2.6.8
Using cached Markdown-3.3.7-py3-none-any.whl (97 kB)
Requirement already satisfied: setuptools>=41.0.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow==2.4.1) (49.6.0.post20210108)
Collecting google-auth-oauthlib<0.5,>=0.4.1
Using cached google_auth_oauthlib-0.4.6-py2.py3-none-any.whl (18 kB)
Collecting tensorboard-data-server<0.7.0,>=0.6.0
Using cached tensorboard_data_server-0.6.1-py3-none-manylinux2010_x86_64.whl (4.9 MB)
Collecting tensorboard-plugin-wit>=1.6.0
Using cached tensorboard_plugin_wit-1.8.1-py3-none-any.whl (781 kB)
Collecting urllib3<2.0
Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
Collecting cachetools<6.0,>=2.0.0
Using cached cachetools-4.2.4-py3-none-any.whl (10 kB)
Collecting pyasn1-modules>=0.2.1
Using cached pyasn1_modules-0.3.0-py2.py3-none-any.whl (181 kB)
Collecting rsa<5,>=3.1.4
Using cached rsa-4.9-py3-none-any.whl (34 kB)
Collecting requests-oauthlib>=0.7.0
Using cached requests_oauthlib-2.0.0-py2.py3-none-any.whl (24 kB)
Collecting importlib-metadata>=4.4
Using cached importlib_metadata-4.8.3-py3-none-any.whl (17 kB)
Collecting zipp>=0.5
Using cached zipp-3.6.0-py3-none-any.whl (5.3 kB)
Collecting pyasn1<0.6.0,>=0.4.6
Using cached pyasn1-0.5.1-py2.py3-none-any.whl (84 kB)
Requirement already satisfied: certifi>=2017.4.17 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from requests<3,>=2.21.0->tensorboard~=2.4->tensorflow==2.4.1) (2021.5.30)
Collecting idna<4,>=2.5
Using cached idna-3.10-py3-none-any.whl (70 kB)
Collecting charset-normalizer~=2.0.0
Using cached charset_normalizer-2.0.12-py3-none-any.whl (39 kB)
Collecting oauthlib>=3.0.0
Using cached oauthlib-3.2.2-py3-none-any.whl (151 kB)
Collecting dataclasses
Using cached dataclasses-0.8-py3-none-any.whl (19 kB)
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 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 /home/biocbuild/bbs-3.21-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/enpamgb
Requirement already satisfied: biopython>=1.74 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (1.78)
Requirement already satisfied: joblib>=0.13.2 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (1.2.0)
Requirement already satisfied: numpy>=1.16.4 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (1.19.5)
Requirement already satisfied: pandas>=0.24.2 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (1.1.5)
Requirement already satisfied: scikit-learn==0.21.2 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (0.21.2)
Requirement already satisfied: scipy>=1.3.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (1.5.3)
Requirement already satisfied: tensorflow>=1.14.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from sgrna-modeler==0.1.0) (2.4.1)
Requirement already satisfied: python-dateutil>=2.7.3 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from pandas>=0.24.2->sgrna-modeler==0.1.0) (2.8.2)
Requirement already satisfied: pytz>=2017.2 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from pandas>=0.24.2->sgrna-modeler==0.1.0) (2023.3.post1)
Requirement already satisfied: six>=1.5 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from python-dateutil>=2.7.3->pandas>=0.24.2->sgrna-modeler==0.1.0) (1.15.0)
Requirement already satisfied: termcolor~=1.1.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.1.0)
Requirement already satisfied: h5py~=2.10.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.10.0)
Requirement already satisfied: opt-einsum~=3.3.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (3.3.0)
Requirement already satisfied: google-pasta~=0.2 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.2.0)
Requirement already satisfied: protobuf>=3.9.2 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (3.19.6)
Requirement already satisfied: wrapt~=1.12.1 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.12.1)
Requirement already satisfied: gast==0.3.3 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.3.3)
Requirement already satisfied: grpcio~=1.32.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.32.0)
Requirement already satisfied: keras-preprocessing~=1.1.2 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.1.2)
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Requirement already satisfied: tensorflow-estimator<2.5.0,>=2.4.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.4.0)
Requirement already satisfied: astunparse~=1.6.3 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.6.3)
Requirement already satisfied: tensorboard~=2.4 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.10.1)
Requirement already satisfied: flatbuffers~=1.12.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (1.12)
Requirement already satisfied: absl-py~=0.10 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.15.0)
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Requirement already satisfied: tensorboard-plugin-wit>=1.6.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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: werkzeug>=1.0.1 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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-oauthlib<0.5,>=0.4.1 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (0.4.6)
Requirement already satisfied: requests<3,>=2.21.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib/python3.6/site-packages (from tensorboard~=2.4->tensorflow>=1.14.0->sgrna-modeler==0.1.0) (2.27.1)
Requirement already satisfied: setuptools>=41.0.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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: google-auth<3,>=1.6.3 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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: tensorboard-data-server<0.7.0,>=0.6.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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: rsa<5,>=3.1.4 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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)
Requirement already satisfied: pyasn1-modules>=0.2.1 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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: urllib3<2.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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: cachetools<6.0,>=2.0.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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: requests-oauthlib>=0.7.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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 /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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 /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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 /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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: certifi>=2017.4.17 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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: charset-normalizer~=2.0.0 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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: idna<4,>=2.5 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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 /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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 /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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=44fe2fe535170b58b46f1ac7e8b59fe8751fbf0776962139a680a8fa1ffe634b
Stored in directory: /tmp/pip-ephem-wheel-cache-4_pe7k1g/wheels/af/20/c8/b48277feea7d7a21a87fa2f4c510240c7b5751e6ae8a0f5cc9
Successfully built sgrna-modeler
Installing collected packages: sgrna-modeler
Successfully installed sgrna-modeler-0.1.0
2025-03-22 16:12:41.749029: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib:/home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/enpamgb_basilisk/lib:/home/biocbuild/bbs-3.21-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.21-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.21-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.21-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.21-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.21-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server
2025-03-22 16:12:41.749181: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
Channels:
- conda-forge
- bioconda
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/lindel_basilisk
added / updated specs:
- python=3.6
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2025.1.31-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_4
libffi conda-forge/linux-64::libffi-3.4.6-h2dba641_0
libgcc conda-forge/linux-64::libgcc-14.2.0-h767d61c_2
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_2
libgomp conda-forge/linux-64::libgomp-14.2.0-h767d61c_2
liblzma conda-forge/linux-64::liblzma-5.6.4-hb9d3cd8_0
liblzma-devel conda-forge/linux-64::liblzma-devel-5.6.4-hb9d3cd8_0
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.49.1-hee588c1_2
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-h8f9b012_2
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_2
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3
openssl conda-forge/linux-64::openssl-1.1.1w-hd590300_0
pip conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.6.15-hb7a2778_0_cpython
python_abi conda-forge/linux-64::python_abi-3.6-2_cp36m
readline conda-forge/linux-64::readline-8.2-h8c095d6_2
setuptools conda-forge/linux-64::setuptools-58.0.4-py36h5fab9bb_2
sqlite conda-forge/linux-64::sqlite-3.49.1-h9eae976_2
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.6.4-hbcc6ac9_0
xz-gpl-tools conda-forge/linux-64::xz-gpl-tools-5.6.4-hbcc6ac9_0
xz-tools conda-forge/linux-64::xz-tools-5.6.4-hb9d3cd8_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
- bioconda
Platform: linux-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: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
- bioconda
Platform: linux-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: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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/linux-64::libblas-3.9.0-20_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-20_linux64_openblas
libgfortran conda-forge/linux-64::libgfortran-14.2.0-h69a702a_2
libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.2.0-h69a702a_2
libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hf1ad2bd_2
liblapack conda-forge/linux-64::liblapack-3.9.0-20_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.25-pthreads_h413a1c8_0
numpy conda-forge/linux-64::numpy-1.19.5-py36hfc0c790_2
scipy conda-forge/linux-64::scipy-1.5.3-py36h81d768a_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 /home/biocbuild/bbs-3.21-bioc-longtests/meat/crisprScore.Rcheck/crisprScore/python/lindel
Requirement already satisfied: numpy in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/lindel_basilisk/lib/python3.6/site-packages (from Lindel==1.0) (1.19.5)
Requirement already satisfied: scipy in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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=31cba0a8425f96aed1ea4ea5e25c725fe716928bc3099a0c29d8fc10bc9146e5
Stored in directory: /tmp/pip-ephem-wheel-cache-pu_ja03j/wheels/6d/86/95/2cfe200f4b7839154dc5965c503126d531f91d3179d420caa6
Successfully built Lindel
Installing collected packages: Lindel
Successfully installed Lindel-1.0
Channels:
- conda-forge
- bioconda
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/deephf_basilisk
added / updated specs:
- python=3.6
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2025.1.31-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_4
libffi conda-forge/linux-64::libffi-3.4.6-h2dba641_0
libgcc conda-forge/linux-64::libgcc-14.2.0-h767d61c_2
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_2
libgomp conda-forge/linux-64::libgomp-14.2.0-h767d61c_2
liblzma conda-forge/linux-64::liblzma-5.6.4-hb9d3cd8_0
liblzma-devel conda-forge/linux-64::liblzma-devel-5.6.4-hb9d3cd8_0
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.49.1-hee588c1_2
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-h8f9b012_2
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_2
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3
openssl conda-forge/linux-64::openssl-1.1.1w-hd590300_0
pip conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.6.15-hb7a2778_0_cpython
python_abi conda-forge/linux-64::python_abi-3.6-2_cp36m
readline conda-forge/linux-64::readline-8.2-h8c095d6_2
setuptools conda-forge/linux-64::setuptools-58.0.4-py36h5fab9bb_2
sqlite conda-forge/linux-64::sqlite-3.49.1-h9eae976_2
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.6.4-hbcc6ac9_0
xz-gpl-tools conda-forge/linux-64::xz-gpl-tools-5.6.4-hbcc6ac9_0
xz-tools conda-forge/linux-64::xz-tools-5.6.4-hb9d3cd8_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
- bioconda
Platform: linux-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: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
- bioconda
Platform: linux-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: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/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 | py36hd28b015_2 9.7 MB bioconda
------------------------------------------------------------
Total: 9.7 MB
The following NEW packages will be INSTALLED:
viennarna bioconda/linux-64::viennarna-2.4.5-py36hd28b015_2
zlib conda-forge/linux-64::zlib-1.2.13-h4ab18f5_6
The following packages will be DOWNGRADED:
libsqlite 3.49.1-hee588c1_2 --> 3.46.0-hde9e2c9_0
libzlib 1.3.1-hb9d3cd8_2 --> 1.2.13-h4ab18f5_6
sqlite 3.49.1-h9eae976_2 --> 3.46.0-h6d4b2fc_0
Downloading and Extracting Packages: ...working...
viennarna-2.4.5 | 9.7 MB | | 0%
viennarna-2.4.5 | 9.7 MB | | 0%
viennarna-2.4.5 | 9.7 MB | #########7 | 97%
viennarna-2.4.5 | 9.7 MB | ########## | 100%
viennarna-2.4.5 | 9.7 MB | ########## | 100%
done
Preparing transaction: - done
Verifying transaction: | / done
Executing transaction: \ done
Collecting biopython==1.71
Using cached biopython-1.71-cp36-cp36m-manylinux1_x86_64.whl (2.0 MB)
Collecting h5py==2.9.0
Using cached h5py-2.9.0-cp36-cp36m-manylinux1_x86_64.whl (2.8 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-manylinux1_x86_64.whl (17.2 MB)
Collecting scipy==1.1.0
Using cached scipy-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (31.2 MB)
Collecting pandas==0.25.3
Using cached pandas-0.25.3-cp36-cp36m-manylinux1_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-py3-none-any.whl
Collecting scikit-learn==0.19.1
Using cached scikit_learn-0.19.1-cp36-cp36m-manylinux1_x86_64.whl (12.4 MB)
Collecting matplotlib==3.1.1
Using cached matplotlib-3.1.1-cp36-cp36m-manylinux1_x86_64.whl (13.1 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-manylinux1_x86_64.whl (49.1 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-2025.1-py2.py3-none-any.whl (507 kB)
Collecting pyyaml
Using cached PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (677 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 kiwisolver>=1.0.1
Using cached kiwisolver-1.3.1-cp36-cp36m-manylinux1_x86_64.whl (1.1 MB)
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 html5lib==0.9999999
Using cached html5lib-0.9999999-py3-none-any.whl
Collecting werkzeug>=0.11.10
Using cached Werkzeug-2.0.3-py3-none-any.whl (289 kB)
Collecting markdown>=2.6.8
Using cached Markdown-3.3.7-py3-none-any.whl (97 kB)
Collecting bleach==1.5.0
Using cached bleach-1.5.0-py2.py3-none-any.whl (17 kB)
Collecting protobuf>=3.4.0
Using cached protobuf-3.19.6-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
Requirement already satisfied: wheel>=0.26 in /home/biocbuild/.cache/R/basilisk/1.19.3/crisprScore/1.11.0/deephf_basilisk/lib/python3.6/site-packages (from tensorboard==1.8.0) (0.37.1)
Collecting gast>=0.2.0
Using cached gast-0.6.0-py3-none-any.whl (21 kB)
Collecting grpcio>=1.8.6
Using cached grpcio-1.48.2-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
Collecting absl-py>=0.1.6
Using cached absl_py-1.4.0-py3-none-any.whl (126 kB)
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 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 zipp>=0.5
Using cached zipp-3.6.0-py3-none-any.whl (5.3 kB)
Collecting typing-extensions>=3.6.4
Using cached typing_extensions-4.1.1-py3-none-any.whl (26 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-2025.1 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 /home/biocbuild/bbs-3.21-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=69a570a1b0227e3f20835b4188fc179e003560091641c66a94de673edad26234
Stored in directory: /tmp/pip-ephem-wheel-cache-shfrv2th/wheels/57/15/c9/1d6d09fcfa4d1779d4339f321e83a7a5a6395783ea27f804b8
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
238.848 45.327 339.088
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no crisprScore_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/crisprScore.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘crisprScore/DESCRIPTION’ ... OK
* this is package ‘crisprScore’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file paths:
crisprScore/inst/python/deepspcas9/DeepCas9_Final/PreTrain-Final-False-3-5-7-100-70-40-0.001-550-True-80-60.data-00000-of-00001
crisprScore/inst/python/deepspcas9/DeepCas9_Final/PreTrain-Final-False-3-5-7-100-70-40-0.001-550-True-80-60.index
crisprScore/inst/python/deepspcas9/DeepCas9_Final/PreTrain-Final-False-3-5-7-100-70-40-0.001-550-True-80-60.meta
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘crisprScore’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/crisprScore.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
installed size is 5.6Mb
sub-directories of 1Mb or more:
python 4.2Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... 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
‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/crisprScore.Rcheck/00check.log’
for details.
crisprScore.Rcheck/00install.out
* installing *source* package ‘crisprScore’ ... ** this is package ‘crisprScore’ version ‘1.11.0’ ** 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)