| Back to Long Tests report for BioC 3.20 |
This page was generated on 2024-06-29 23:55 -0400 (Sat, 29 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4693 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4408 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
| 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 17/32 | Hostname | OS / Arch | CHECK | |||||||
| crisprScore 1.9.0 (landing page) Jean-Philippe Fortin
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | ||||||||
| 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: 1.9.0 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no crisprScore_1.9.0.tar.gz |
| StartedAt: 2024-06-29 16:11:40 -0400 (Sat, 29 Jun 2024) |
| EndedAt: 2024-06-29 16:32:45 -0400 (Sat, 29 Jun 2024) |
| EllapsedTime: 1264.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: crisprScore.Rcheck |
| Warnings: 0 |
crisprScore.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.17.0\crisprScore\1.9.0\azimuth_basilisk
added / updated specs:
- python=2.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
certifi-2019.11.28 | py27h8c360ce_1 149 KB conda-forge
pip-20.1.1 | pyh9f0ad1d_0 1.1 MB conda-forge
python-2.7.15 |h2880e7c_1011_cpython 20.3 MB conda-forge
python_abi-2.7 | 1_cp27m 4 KB conda-forge
setuptools-44.0.0 | py27_0 665 KB conda-forge
vc-9 | h2eaa2aa_6 5 KB
vs2008_runtime-9.0.30729.6161| 0 1.0 MB conda-forge
wheel-0.37.1 | pyhd8ed1ab_0 31 KB conda-forge
wincertstore-0.2 | pyhd8ed1ab_1009 11 KB conda-forge
------------------------------------------------------------
Total: 23.2 MB
The following NEW packages will be INSTALLED:
certifi conda-forge/win-64::certifi-2019.11.28-py27h8c360ce_1
pip conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
python conda-forge/win-64::python-2.7.15-h2880e7c_1011_cpython
python_abi conda-forge/win-64::python_abi-2.7-1_cp27m
setuptools conda-forge/win-64::setuptools-44.0.0-py27_0
vc pkgs/main/win-64::vc-9-h2eaa2aa_6
vs2008_runtime conda-forge/win-64::vs2008_runtime-9.0.30729.6161-0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
wincertstore conda-forge/noarch::wincertstore-0.2-pyhd8ed1ab_1009
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: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.17.0\crisprScore\1.9.0\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 | py27h0c8e037_0 2.5 MB conda-forge
cycler-0.10.0 | py_2 9 KB conda-forge
freetype-2.10.1 | h4d385ea_0 927 KB conda-forge
functools32-3.2.3.2 | py_3 15 KB conda-forge
futures-3.3.0 | py27h8c360ce_1 25 KB conda-forge
icc_rt-2022.1.0 | h6049295_2 6.5 MB
icu-58.2 | vc9_0 21.9 MB conda-forge
jpeg-9c | h0c8e037_1001 307 KB conda-forge
kiwisolver-1.1.0 | py27h6c69bd3_1 67 KB conda-forge
libblas-3.9.0 | 8_mkl 3.9 MB conda-forge
libcblas-3.9.0 | 8_mkl 3.9 MB conda-forge
liblapack-3.9.0 | 8_mkl 3.9 MB conda-forge
libpng-1.6.37 | h7a46e7a_0 489 KB conda-forge
libtiff-4.0.10 | h52ad3ab_1002 972 KB conda-forge
matplotlib-2.2.3 | py27h8a2030e_1 7 KB conda-forge
matplotlib-base-2.2.3 | py27hf194043_1 6.3 MB conda-forge
mkl-2020.4 | hb70f87d_311 172.4 MB conda-forge
mmtf-python-1.1.2 | py_0 21 KB conda-forge
msgpack-python-1.0.0 | py27h6c69bd3_1 27 KB conda-forge
nose-1.3.7 |py27h8c360ce_1004 240 KB conda-forge
numpy-1.11.3 |py27hab51878_1207 3.3 MB conda-forge
olefile-0.46 | pyh9f0ad1d_1 32 KB conda-forge
openssl-1.0.2u | h0c8e037_0 4.7 MB conda-forge
pandas-0.23.4 |py27h39f3610_1000 8.8 MB conda-forge
pillow-6.2.1 | py27h1bb17ff_0 686 KB conda-forge
pyparsing-2.4.7 | pyh9f0ad1d_0 60 KB conda-forge
pyqt-5.6.0 |py27h4cbc711_1008 4.2 MB conda-forge
pytz-2020.1 | pyh9f0ad1d_0 227 KB conda-forge
qt-5.6.2 | vc9hc26998b_12 40.8 MB
reportlab-3.5.42 | py27h253739d_0 2.4 MB conda-forge
scipy-1.2.1 | py27h4c3ab11_0 11.0 MB
singledispatch-3.6.1 | pyh44b312d_0 12 KB conda-forge
sip-4.18.1 |py27hc56fc5f_1000 263 KB conda-forge
six-1.15.0 | pyh9f0ad1d_0 14 KB conda-forge
sqlite-3.30.1 | h0c8e037_0 1.1 MB conda-forge
subprocess32-3.5.4 | py27h0c8e037_0 37 KB conda-forge
tk-8.6.10 | h0c8e037_0 3.0 MB conda-forge
tornado-5.1.1 |py27h0c8e037_1000 640 KB conda-forge
wheel-0.36.2 | pyhd3deb0d_0 31 KB conda-forge
xz-5.2.4 | h3cc03e0_1001 296 KB conda-forge
zlib-1.2.11 | h3cc03e0_1006 117 KB conda-forge
zstd-1.3.3 | vc9_1 380 KB conda-forge
------------------------------------------------------------
Total: 306.3 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/win-64::biopython-1.74-py27h0c8e037_0
blas pkgs/main/win-64::blas-1.0-mkl
ca-certificates conda-forge/win-64::ca-certificates-2024.6.2-h56e8100_0
cycler conda-forge/noarch::cycler-0.10.0-py_2
freetype conda-forge/win-64::freetype-2.10.1-h4d385ea_0
functools32 conda-forge/noarch::functools32-3.2.3.2-py_3
futures conda-forge/win-64::futures-3.3.0-py27h8c360ce_1
icc_rt pkgs/main/win-64::icc_rt-2022.1.0-h6049295_2
icu conda-forge/win-64::icu-58.2-vc9_0
intel-openmp conda-forge/win-64::intel-openmp-2024.1.0-h57928b3_966
jpeg conda-forge/win-64::jpeg-9c-h0c8e037_1001
kiwisolver conda-forge/win-64::kiwisolver-1.1.0-py27h6c69bd3_1
libblas conda-forge/win-64::libblas-3.9.0-8_mkl
libcblas conda-forge/win-64::libcblas-3.9.0-8_mkl
liblapack conda-forge/win-64::liblapack-3.9.0-8_mkl
libpng conda-forge/win-64::libpng-1.6.37-h7a46e7a_0
libtiff conda-forge/win-64::libtiff-4.0.10-h52ad3ab_1002
matplotlib conda-forge/win-64::matplotlib-2.2.3-py27h8a2030e_1
matplotlib-base conda-forge/win-64::matplotlib-base-2.2.3-py27hf194043_1
mkl conda-forge/win-64::mkl-2020.4-hb70f87d_311
mmtf-python conda-forge/noarch::mmtf-python-1.1.2-py_0
msgpack-python conda-forge/win-64::msgpack-python-1.0.0-py27h6c69bd3_1
nose conda-forge/win-64::nose-1.3.7-py27h8c360ce_1004
numpy conda-forge/win-64::numpy-1.11.3-py27hab51878_1207
olefile conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1
openssl conda-forge/win-64::openssl-1.0.2u-h0c8e037_0
pandas conda-forge/win-64::pandas-0.23.4-py27h39f3610_1000
pillow conda-forge/win-64::pillow-6.2.1-py27h1bb17ff_0
pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
pyqt conda-forge/win-64::pyqt-5.6.0-py27h4cbc711_1008
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
pytz conda-forge/noarch::pytz-2020.1-pyh9f0ad1d_0
qt pkgs/main/win-64::qt-5.6.2-vc9hc26998b_12
reportlab conda-forge/win-64::reportlab-3.5.42-py27h253739d_0
scipy pkgs/main/win-64::scipy-1.2.1-py27h4c3ab11_0
singledispatch conda-forge/noarch::singledispatch-3.6.1-pyh44b312d_0
sip conda-forge/win-64::sip-4.18.1-py27hc56fc5f_1000
six conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
sqlite conda-forge/win-64::sqlite-3.30.1-h0c8e037_0
subprocess32 conda-forge/win-64::subprocess32-3.5.4-py27h0c8e037_0
tk conda-forge/win-64::tk-8.6.10-h0c8e037_0
tornado conda-forge/win-64::tornado-5.1.1-py27h0c8e037_1000
xz conda-forge/win-64::xz-5.2.4-h3cc03e0_1001
zlib conda-forge/win-64::zlib-1.2.11-h3cc03e0_1006
zstd conda-forge/win-64::zstd-1.3.3-vc9_1
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 | 3.3 MB | | 0%
numpy-1.11.3 | 3.3 MB | | 0%
numpy-1.11.3 | 3.3 MB | ########## | 100%
numpy-1.11.3 | 3.3 MB | ########## | 100%
matplotlib-base-2.2. | 6.3 MB | | 0%
matplotlib-base-2.2. | 6.3 MB | | 0%
matplotlib-base-2.2. | 6.3 MB | ######4 | 64%
matplotlib-base-2.2. | 6.3 MB | ########## | 100%
matplotlib-base-2.2. | 6.3 MB | ########## | 100%
freetype-2.10.1 | 927 KB | | 0%
freetype-2.10.1 | 927 KB | 1 | 2%
freetype-2.10.1 | 927 KB | ########## | 100%
freetype-2.10.1 | 927 KB | ########## | 100%
libcblas-3.9.0 | 3.9 MB | | 0%
libcblas-3.9.0 | 3.9 MB | ########## | 100%
libcblas-3.9.0 | 3.9 MB | ########## | 100%
pillow-6.2.1 | 686 KB | | 0%
pillow-6.2.1 | 686 KB | 2 | 2%
pillow-6.2.1 | 686 KB | ########## | 100%
pillow-6.2.1 | 686 KB | ########## | 100%
functools32-3.2.3.2 | 15 KB | | 0%
functools32-3.2.3.2 | 15 KB | ########## | 100%
functools32-3.2.3.2 | 15 KB | ########## | 100%
icu-58.2 | 21.9 MB | | 0%
icu-58.2 | 21.9 MB | 8 | 9%
icu-58.2 | 21.9 MB | ######9 | 70%
icu-58.2 | 21.9 MB | ########## | 100%
backports-1.0 | 6 KB | | 0%
backports-1.0 | 6 KB | ########## | 100%
backports-1.0 | 6 KB | ########## | 100%
nose-1.3.7 | 240 KB | | 0%
nose-1.3.7 | 240 KB | 6 | 7%
nose-1.3.7 | 240 KB | ########## | 100%
nose-1.3.7 | 240 KB | ########## | 100%
libpng-1.6.37 | 489 KB | | 0%
libpng-1.6.37 | 489 KB | 3 | 3%
libpng-1.6.37 | 489 KB | ########## | 100%
libpng-1.6.37 | 489 KB | ########## | 100%
jpeg-9c | 307 KB | | 0%
jpeg-9c | 307 KB | 5 | 5%
jpeg-9c | 307 KB | ########## | 100%
jpeg-9c | 307 KB | ########## | 100%
sqlite-3.30.1 | 1.1 MB | | 0%
sqlite-3.30.1 | 1.1 MB | 1 | 1%
sqlite-3.30.1 | 1.1 MB | ########## | 100%
sqlite-3.30.1 | 1.1 MB | ########## | 100%
tk-8.6.10 | 3.0 MB | | 0%
tk-8.6.10 | 3.0 MB | | 1%
tk-8.6.10 | 3.0 MB | ########## | 100%
tk-8.6.10 | 3.0 MB | ########## | 100%
pytz-2020.1 | 227 KB | | 0%
pytz-2020.1 | 227 KB | ########## | 100%
pytz-2020.1 | 227 KB | ########## | 100%
scipy-1.2.1 | 11.0 MB | | 0%
scipy-1.2.1 | 11.0 MB | | 0%
scipy-1.2.1 | 11.0 MB | ## | 21%
scipy-1.2.1 | 11.0 MB | ########## | 100%
scipy-1.2.1 | 11.0 MB | ########## | 100%
six-1.15.0 | 14 KB | | 0%
six-1.15.0 | 14 KB | ########## | 100%
six-1.15.0 | 14 KB | ########## | 100%
msgpack-python-1.0.0 | 27 KB | | 0%
msgpack-python-1.0.0 | 27 KB | #####8 | 59%
msgpack-python-1.0.0 | 27 KB | ########## | 100%
msgpack-python-1.0.0 | 27 KB | ########## | 100%
zlib-1.2.11 | 117 KB | | 0%
zlib-1.2.11 | 117 KB | ########## | 100%
zlib-1.2.11 | 117 KB | ########## | 100%
pyqt-5.6.0 | 4.2 MB | | 0%
pyqt-5.6.0 | 4.2 MB | | 0%
pyqt-5.6.0 | 4.2 MB | ########## | 100%
pyqt-5.6.0 | 4.2 MB | ########## | 100%
liblapack-3.9.0 | 3.9 MB | | 0%
liblapack-3.9.0 | 3.9 MB | ##6 | 27%
liblapack-3.9.0 | 3.9 MB | ########## | 100%
liblapack-3.9.0 | 3.9 MB | ########## | 100%
libblas-3.9.0 | 3.9 MB | | 0%
libblas-3.9.0 | 3.9 MB | ########## | 100%
libblas-3.9.0 | 3.9 MB | ########## | 100%
olefile-0.46 | 32 KB | | 0%
olefile-0.46 | 32 KB | ########## | 100%
olefile-0.46 | 32 KB | ########## | 100%
subprocess32-3.5.4 | 37 KB | | 0%
subprocess32-3.5.4 | 37 KB | ########## | 100%
subprocess32-3.5.4 | 37 KB | ########## | 100%
kiwisolver-1.1.0 | 67 KB | | 0%
kiwisolver-1.1.0 | 67 KB | ##3 | 24%
kiwisolver-1.1.0 | 67 KB | ########## | 100%
kiwisolver-1.1.0 | 67 KB | ########## | 100%
backports.functools_ | 8 KB | | 0%
backports.functools_ | 8 KB | ########## | 100%
backports.functools_ | 8 KB | ########## | 100%
qt-5.6.2 | 40.8 MB | | 0%
qt-5.6.2 | 40.8 MB | | 0%
qt-5.6.2 | 40.8 MB | 1 | 2%
qt-5.6.2 | 40.8 MB | ##1 | 21%
qt-5.6.2 | 40.8 MB | ######4 | 65%
qt-5.6.2 | 40.8 MB | ########## | 100%
qt-5.6.2 | 40.8 MB | ########## | 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%
xz-5.2.4 | 296 KB | | 0%
xz-5.2.4 | 296 KB | 5 | 5%
xz-5.2.4 | 296 KB | ########## | 100%
xz-5.2.4 | 296 KB | ########## | 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%
cycler-0.10.0 | 9 KB | | 0%
cycler-0.10.0 | 9 KB | ########## | 100%
pandas-0.23.4 | 8.8 MB | | 0%
pandas-0.23.4 | 8.8 MB | | 0%
pandas-0.23.4 | 8.8 MB | ########1 | 81%
pandas-0.23.4 | 8.8 MB | ########## | 100%
openssl-1.0.2u | 4.7 MB | | 0%
openssl-1.0.2u | 4.7 MB | #########3 | 94%
openssl-1.0.2u | 4.7 MB | ########## | 100%
sip-4.18.1 | 263 KB | | 0%
sip-4.18.1 | 263 KB | 6 | 6%
sip-4.18.1 | 263 KB | ########## | 100%
sip-4.18.1 | 263 KB | ########## | 100%
mkl-2020.4 | 172.4 MB | | 0%
mkl-2020.4 | 172.4 MB | #1 | 11%
mkl-2020.4 | 172.4 MB | ##5 | 25%
mkl-2020.4 | 172.4 MB | ###6 | 37%
mkl-2020.4 | 172.4 MB | ####7 | 47%
mkl-2020.4 | 172.4 MB | #####8 | 58%
mkl-2020.4 | 172.4 MB | ######8 | 68%
mkl-2020.4 | 172.4 MB | #######9 | 79%
mkl-2020.4 | 172.4 MB | ######### | 91%
mkl-2020.4 | 172.4 MB | ########## | 100%
singledispatch-3.6.1 | 12 KB | | 0%
singledispatch-3.6.1 | 12 KB | ########## | 100%
singledispatch-3.6.1 | 12 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%
pyparsing-2.4.7 | 60 KB | | 0%
pyparsing-2.4.7 | 60 KB | ########## | 100%
pyparsing-2.4.7 | 60 KB | ########## | 100%
icc_rt-2022.1.0 | 6.5 MB | | 0%
icc_rt-2022.1.0 | 6.5 MB | ########## | 100%
icc_rt-2022.1.0 | 6.5 MB | ########## | 100%
backports_abc-0.5 | 5 KB | | 0%
backports_abc-0.5 | 5 KB | ########## | 100%
backports_abc-0.5 | 5 KB | ########## | 100%
wheel-0.36.2 | 31 KB | | 0%
wheel-0.36.2 | 31 KB | ########## | 100%
wheel-0.36.2 | 31 KB | ########## | 100%
libtiff-4.0.10 | 972 KB | | 0%
libtiff-4.0.10 | 972 KB | 1 | 2%
libtiff-4.0.10 | 972 KB | ########## | 100%
libtiff-4.0.10 | 972 KB | ########## | 100%
matplotlib-2.2.3 | 7 KB | | 0%
matplotlib-2.2.3 | 7 KB | ########## | 100%
matplotlib-2.2.3 | 7 KB | ########## | 100%
zstd-1.3.3 | 380 KB | | 0%
zstd-1.3.3 | 380 KB | 4 | 4%
zstd-1.3.3 | 380 KB | ########## | 100%
zstd-1.3.3 | 380 KB | ########## | 100%
tornado-5.1.1 | 640 KB | | 0%
tornado-5.1.1 | 640 KB | 2 | 3%
tornado-5.1.1 | 640 KB | ########## | 100%
tornado-5.1.1 | 640 KB | ########## | 100%
futures-3.3.0 | 25 KB | | 0%
futures-3.3.0 | 25 KB | ######2 | 63%
futures-3.3.0 | 25 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
Downloading scikit_learn-0.17.1-cp27-cp27m-win_amd64.whl (3.4 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 c:\users\biocbuild\bbs-3.20-bioc-longtests\meat\crisprscore.rcheck\crisprscore\python\azimuth
Requirement already satisfied: scipy<=1.2.1 in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\site-packages (from Azimuth==2.0) (1.2.1)
Requirement already satisfied: numpy<=1.14 in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\site-packages (from Azimuth==2.0) (1.11.3)
Requirement already satisfied: matplotlib in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\site-packages (from Azimuth==2.0) (2.2.3)
Requirement already satisfied: nose in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\site-packages (from Azimuth==2.0) (1.3.7)
Requirement already satisfied: scikit-learn<0.18,>=0.17.1 in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\site-packages (from Azimuth==2.0) (0.17.1)
Requirement already satisfied: pandas in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\site-packages (from Azimuth==2.0) (0.23.4)
Requirement already satisfied: biopython<=1.76 in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\site-packages (from Azimuth==2.0) (1.74)
Requirement already satisfied: cycler>=0.10 in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\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 c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\site-packages (from matplotlib->Azimuth==2.0) (2.4.7)
Requirement already satisfied: python-dateutil>=2.1 in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\site-packages (from matplotlib->Azimuth==2.0) (2.8.1)
Requirement already satisfied: pytz in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\site-packages (from matplotlib->Azimuth==2.0) (2020.1)
Requirement already satisfied: six>=1.10 in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\site-packages (from matplotlib->Azimuth==2.0) (1.15.0)
Requirement already satisfied: kiwisolver>=1.0.1 in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\site-packages (from matplotlib->Azimuth==2.0) (1.1.0)
Requirement already satisfied: backports.functools_lru_cache in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\site-packages (from matplotlib->Azimuth==2.0) (1.6.1)
Requirement already satisfied: setuptools in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\azimut~1\lib\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=163897 sha256=626fdf1d3584b5964eb4ffca9fba6ebbd46054aa4399c2c748503770f741d454
Stored in directory: c:\users\biocbuild\bbs-3.20-bioc-longtests\tmpdir\pip-ephem-wheel-cache-ucwefl\wheels\e5\0b\d9\e6adad9962c3d4073be6982b5be98bdb9cd9e547700253c3f2
Successfully built Azimuth
Installing collected packages: Azimuth
Successfully installed Azimuth-2.0
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.17.0\crisprScore\1.9.0\lindel_basilisk
added / updated specs:
- python=3.6
The following packages will be downloaded:
package | build
---------------------------|-----------------
certifi-2020.6.20 | pyhd3eb1b0_3 155 KB
pip-20.0.2 | py36_1 1.9 MB conda-forge
python-3.6.15 |h39d44d4_0_cpython 18.9 MB conda-forge
python_abi-3.6 | 2_cp36m 4 KB conda-forge
setuptools-49.6.0 | py36ha15d459_3 921 KB conda-forge
wheel-0.34.2 | py36_0 60 KB conda-forge
------------------------------------------------------------
Total: 22.0 MB
The following NEW packages will be INSTALLED:
certifi pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
pip conda-forge/win-64::pip-20.0.2-py36_1
python conda-forge/win-64::python-3.6.15-h39d44d4_0_cpython
python_abi conda-forge/win-64::python_abi-3.6-2_cp36m
setuptools conda-forge/win-64::setuptools-49.6.0-py36ha15d459_3
ucrt conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_0
vc conda-forge/win-64::vc-14.3-h8a93ad2_20
vc14_runtime conda-forge/win-64::vc14_runtime-14.40.33810-ha82c5b3_20
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.40.33810-h3bf8584_20
wheel conda-forge/win-64::wheel-0.34.2-py36_0
wincertstore conda-forge/noarch::wincertstore-0.2-pyhd8ed1ab_1009
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: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.17.0\crisprScore\1.9.0\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 packages will be downloaded:
package | build
---------------------------|-----------------
certifi-2020.12.5 | py36ha15d459_1 144 KB conda-forge
numpy-1.19.5 | py36h4b40d73_2 4.9 MB conda-forge
pip-21.0.1 | pyhd8ed1ab_0 1.1 MB conda-forge
scipy-1.5.3 | py36h27d303f_1 21.9 MB conda-forge
------------------------------------------------------------
Total: 27.9 MB
The following NEW packages will be INSTALLED:
intel-openmp conda-forge/win-64::intel-openmp-2024.1.0-h57928b3_966
libblas conda-forge/win-64::libblas-3.9.0-22_win64_mkl
libcblas conda-forge/win-64::libcblas-3.9.0-22_win64_mkl
libhwloc conda-forge/win-64::libhwloc-2.10.0-default_h8125262_1001
libiconv conda-forge/win-64::libiconv-1.17-hcfcfb64_2
liblapack conda-forge/win-64::liblapack-3.9.0-22_win64_mkl
libxml2 conda-forge/win-64::libxml2-2.12.7-h283a6d9_1
libzlib conda-forge/win-64::libzlib-1.3.1-h2466b09_1
m2w64-gcc-libgfor~ conda-forge/win-64::m2w64-gcc-libgfortran-5.3.0-6
m2w64-gcc-libs conda-forge/win-64::m2w64-gcc-libs-5.3.0-7
m2w64-gcc-libs-co~ conda-forge/win-64::m2w64-gcc-libs-core-5.3.0-7
m2w64-gmp conda-forge/win-64::m2w64-gmp-6.1.0-2
m2w64-libwinpthre~ conda-forge/win-64::m2w64-libwinpthread-git-5.0.0.4634.697f757-2
mkl conda-forge/win-64::mkl-2024.1.0-h66d3029_692
msys2-conda-epoch conda-forge/win-64::msys2-conda-epoch-20160418-1
numpy conda-forge/win-64::numpy-1.19.5-py36h4b40d73_2
pthreads-win32 conda-forge/win-64::pthreads-win32-2.9.1-hfa6e2cd_3
scipy conda-forge/win-64::scipy-1.5.3-py36h27d303f_1
tbb conda-forge/win-64::tbb-2021.12.0-hc790b64_1
The following packages will be UPDATED:
certifi pkgs/main/noarch::certifi-2020.6.20-p~ --> conda-forge/win-64::certifi-2020.12.5-py36ha15d459_1
pip conda-forge/win-64::pip-20.0.2-py36_1 --> conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0
wheel conda-forge/win-64::wheel-0.34.2-py36~ --> conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
Downloading and Extracting Packages
certifi-2020.12.5 | 144 KB | | 0%
certifi-2020.12.5 | 144 KB | #1 | 11%
certifi-2020.12.5 | 144 KB | ########## | 100%
certifi-2020.12.5 | 144 KB | ########## | 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%
scipy-1.5.3 | 21.9 MB | | 0%
scipy-1.5.3 | 21.9 MB | 7 | 7%
scipy-1.5.3 | 21.9 MB | ####4 | 45%
scipy-1.5.3 | 21.9 MB | ########## | 100%
scipy-1.5.3 | 21.9 MB | ########## | 100%
numpy-1.19.5 | 4.9 MB | | 0%
numpy-1.19.5 | 4.9 MB | ########## | 100%
numpy-1.19.5 | 4.9 MB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Processing c:\users\biocbuild\bbs-3.20-bioc-longtests\meat\crisprscore.rcheck\crisprscore\python\lindel
Requirement already satisfied: numpy in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\lindel~1\lib\site-packages (from Lindel==1.0) (1.19.5)
Requirement already satisfied: scipy in c:\users\biocbu~1\appdata\local\r\cache\r\basilisk\117~1.0\crispr~1\196380~1.0\lindel~1\lib\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=6221d51e2416464c0aad3a105839b992ce3d2538e755ac2e7c1ce8dbaf493d61
Stored in directory: C:\Users\biocbuild\bbs-3.20-bioc-longtests\tmpdir\pip-ephem-wheel-cache-g2k507uo\wheels\b4\4f\5a\80829ae84eb3a6dd1432a46e6918f8e7ad553ff44b84d43905
Successfully built Lindel
Installing collected packages: Lindel
Successfully installed Lindel-1.0
[ FAIL 0 | WARN 4 | SKIP 3 | PASS 2 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On Windows (3): 'test-ontargets.R:23:5', 'test-ontargets.R:28:5',
'test-ontargets.R:37:5'
[ FAIL 0 | WARN 4 | SKIP 3 | PASS 2 ]
>
> proc.time()
user system elapsed
5.21 0.65 1152.15
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no crisprScore_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc-longtests/meat/crisprScore.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 '1.9.0'
* 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 whether package 'crisprScore' can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See 'C:/Users/biocbuild/bbs-3.20-bioc-longtests/meat/crisprScore.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 7.0Mb
sub-directories of 1Mb or more:
python 5.8Mb
* 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
'C:/Users/biocbuild/bbs-3.20-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)