Back to Long Tests report for BioC 3.19

This page was generated on 2024-07-13 23:55 -0400 (Sat, 13 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
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 3/33HostnameOS / ArchCHECK
basilisk 1.16.0  (landing page)
Aaron Lun
Snapshot Date: 2024-07-13 09:55 -0400 (Sat, 13 Jul 2024)
git_url: https://git.bioconductor.org/packages/basilisk
git_branch: RELEASE_3_19
git_last_commit: 0a27ae6
git_last_commit_date: 2024-04-30 11:20:50 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino7Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.4 Monterey / x86_64  OK  


CHECK results for basilisk on palomino7

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

raw results


Summary

Package: basilisk
Version: 1.16.0
Command: E:\biocbuild\bbs-3.19-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 basilisk_1.16.0.tar.gz
StartedAt: 2024-07-13 16:03:28 -0400 (Sat, 13 Jul 2024)
EndedAt: 2024-07-13 16:12:58 -0400 (Sat, 13 Jul 2024)
EllapsedTime: 569.3 seconds
RetCode: 0
Status:   OK  
CheckDir: basilisk.Rcheck
Warnings: 0

Tests output

basilisk.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(basilisk)
Loading required package: reticulate
> test_check("basilisk")
* installing *source* package 'son.of.basilisk' ...
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (son.of.basilisk)
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\1.16.0\son.of.basilisk\0.99.0\env1

  added / updated specs:
    - python=3.9.12


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    setuptools-70.3.0          |     pyhd8ed1ab_0         485 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         485 KB

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/win-64::bzip2-1.0.8-hcfcfb64_5
  ca-certificates    conda-forge/win-64::ca-certificates-2024.7.4-h56e8100_0
  libffi             conda-forge/win-64::libffi-3.4.2-h8ffe710_5
  libsqlite          conda-forge/win-64::libsqlite-3.46.0-h2466b09_0
  libzlib            conda-forge/win-64::libzlib-1.3.1-h2466b09_1
  openssl            conda-forge/win-64::openssl-3.3.1-h2466b09_1
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/win-64::python-3.9.12-hcf16a7b_1_cpython
  setuptools         conda-forge/noarch::setuptools-70.3.0-pyhd8ed1ab_0
  sqlite             conda-forge/win-64::sqlite-3.46.0-h2466b09_0
  tk                 conda-forge/win-64::tk-8.6.13-h5226925_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  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/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/win-64::xz-5.2.6-h8d14728_0


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


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

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

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


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

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.16.0\son.of.basilisk\0.99.0\env1

  added / updated specs:
    - pandas=1.4.3
    - python-dateutil=2.8.2
    - python=3.9.12
    - pytz=2022.2.1


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    numpy-1.26.4               |   py39hddb5d58_0         5.6 MB  conda-forge
    pandas-1.4.3               |   py39h2e25243_0        11.0 MB  conda-forge
    pytz-2022.2.1              |     pyhd8ed1ab_0         224 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        16.9 MB

The following NEW packages will be INSTALLED:

  intel-openmp       conda-forge/win-64::intel-openmp-2024.2.0-h57928b3_979
  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-2.11.1-default_h8125262_1000
  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-h0f24e4e_3
  mkl                conda-forge/win-64::mkl-2024.1.0-h66d3029_692
  numpy              conda-forge/win-64::numpy-1.26.4-py39hddb5d58_0
  pandas             conda-forge/win-64::pandas-1.4.3-py39h2e25243_0
  pthreads-win32     conda-forge/win-64::pthreads-win32-2.9.1-hfa6e2cd_3
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
  python_abi         conda-forge/win-64::python_abi-3.9-4_cp39
  pytz               conda-forge/noarch::pytz-2022.2.1-pyhd8ed1ab_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  tbb                conda-forge/win-64::tbb-2021.12.0-hc790b64_3



Downloading and Extracting Packages

numpy-1.26.4         | 5.6 MB    |            |   0% 
numpy-1.26.4         | 5.6 MB    |            |   0% 
numpy-1.26.4         | 5.6 MB    | ########## | 100% 
numpy-1.26.4         | 5.6 MB    | ########## | 100% 

pandas-1.4.3         | 11.0 MB   |            |   0% 
pandas-1.4.3         | 11.0 MB   | ###7       |  37% 
pandas-1.4.3         | 11.0 MB   | ########## | 100% 
pandas-1.4.3         | 11.0 MB   | ########## | 100% 

pytz-2022.2.1        | 224 KB    |            |   0% 
pytz-2022.2.1        | 224 KB    | ########## | 100% 
pytz-2022.2.1        | 224 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
sys:1: FutureWarning: pandas.Float64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
sys:1: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
sys:1: FutureWarning: pandas.UInt64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
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\1.16.0\son.of.basilisk\0.99.0\env2

  added / updated specs:
    - python=3.9.12


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/win-64::bzip2-1.0.8-hcfcfb64_5
  ca-certificates    conda-forge/win-64::ca-certificates-2024.7.4-h56e8100_0
  libffi             conda-forge/win-64::libffi-3.4.2-h8ffe710_5
  libsqlite          conda-forge/win-64::libsqlite-3.46.0-h2466b09_0
  libzlib            conda-forge/win-64::libzlib-1.3.1-h2466b09_1
  openssl            conda-forge/win-64::openssl-3.3.1-h2466b09_1
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/win-64::python-3.9.12-hcf16a7b_1_cpython
  setuptools         conda-forge/noarch::setuptools-70.3.0-pyhd8ed1ab_0
  sqlite             conda-forge/win-64::sqlite-3.46.0-h2466b09_0
  tk                 conda-forge/win-64::tk-8.6.13-h5226925_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  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/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/win-64::xz-5.2.6-h8d14728_0


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


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

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

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


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

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.16.0\son.of.basilisk\0.99.0\env2

  added / updated specs:
    - python-dateutil=2.8.1
    - python=3.9.12
    - pytz=2022.1
    - scikit-learn=1.1.1


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    python-dateutil-2.8.1      |             py_0         220 KB  conda-forge
    pytz-2022.1                |     pyhd8ed1ab_0         242 KB  conda-forge
    scikit-learn-1.1.1         |   py39he931e04_0         7.5 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         8.0 MB

The following NEW packages will be INSTALLED:

  intel-openmp       conda-forge/win-64::intel-openmp-2024.2.0-h57928b3_979
  joblib             conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0
  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-2.11.1-default_h8125262_1000
  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-h0f24e4e_3
  mkl                conda-forge/win-64::mkl-2024.1.0-h66d3029_692
  numpy              conda-forge/win-64::numpy-1.26.4-py39hddb5d58_0
  pthreads-win32     conda-forge/win-64::pthreads-win32-2.9.1-hfa6e2cd_3
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  python_abi         conda-forge/win-64::python_abi-3.9-4_cp39
  pytz               conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
  scikit-learn       conda-forge/win-64::scikit-learn-1.1.1-py39he931e04_0
  scipy              conda-forge/win-64::scipy-1.13.1-py39h1a10956_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  tbb                conda-forge/win-64::tbb-2021.12.0-hc790b64_3
  threadpoolctl      conda-forge/noarch::threadpoolctl-3.5.0-pyhc1e730c_0



Downloading and Extracting Packages

python-dateutil-2.8. | 220 KB    |            |   0% 
python-dateutil-2.8. | 220 KB    | 7          |   7% 
python-dateutil-2.8. | 220 KB    | ########## | 100% 

pytz-2022.1          | 242 KB    |            |   0% 
pytz-2022.1          | 242 KB    | ########## | 100% 
pytz-2022.1          | 242 KB    | ########## | 100% 

scikit-learn-1.1.1   | 7.5 MB    |            |   0% 
scikit-learn-1.1.1   | 7.5 MB    |            |   0% 
scikit-learn-1.1.1   | 7.5 MB    | ########## | 100% 
scikit-learn-1.1.1   | 7.5 MB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
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\1.16.0\son.of.basilisk\0.99.0\env3

  added / updated specs:
    - python=3.9.12


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/win-64::bzip2-1.0.8-hcfcfb64_5
  ca-certificates    conda-forge/win-64::ca-certificates-2024.7.4-h56e8100_0
  libffi             conda-forge/win-64::libffi-3.4.2-h8ffe710_5
  libsqlite          conda-forge/win-64::libsqlite-3.46.0-h2466b09_0
  libzlib            conda-forge/win-64::libzlib-1.3.1-h2466b09_1
  openssl            conda-forge/win-64::openssl-3.3.1-h2466b09_1
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/win-64::python-3.9.12-hcf16a7b_1_cpython
  setuptools         conda-forge/noarch::setuptools-70.3.0-pyhd8ed1ab_0
  sqlite             conda-forge/win-64::sqlite-3.46.0-h2466b09_0
  tk                 conda-forge/win-64::tk-8.6.13-h5226925_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  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/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/win-64::xz-5.2.6-h8d14728_0


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


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

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... 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.

Processing e:\biocbuild\bbs-3.19-bioc-longtests\tmpdir\rtmpebi2aw\rlib.53586554138e\son.of.basilisk\test_dummy
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: test_dummy
  Building wheel for test_dummy (setup.py): started
  Building wheel for test_dummy (setup.py): finished with status 'done'
  Created wheel for test_dummy: filename=test_dummy-0.1-py3-none-any.whl size=1287 sha256=5a2710c85f4eccbd0cd338a857fa3f655328cf7a8c23c84173b77280acedbb74
  Stored in directory: E:\biocbuild\bbs-3.19-bioc-longtests\tmpdir\pip-ephem-wheel-cache-olm2wg9c\wheels\d0\2c\b9\75c75635b99515c89a025e5ab19296d96c867a3b3c961ba04e
Successfully built test_dummy
Installing collected packages: test_dummy
Successfully installed test_dummy-0.1
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
   1.84    1.01  528.84 

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.19-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 basilisk_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.19-bioc-longtests/meat/basilisk.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 'basilisk/DESCRIPTION' ... OK
* this is package 'basilisk' version '1.16.0'
* 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 ... NOTE
Found the following hidden files and directories:
  inst/example/.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'basilisk' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'E:/biocbuild/bbs-3.19-bioc-longtests/meat/basilisk.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 dependencies in R code ... OK
* 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 line endings in shell scripts ... 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: 2 NOTEs
See
  'E:/biocbuild/bbs-3.19-bioc-longtests/meat/basilisk.Rcheck/00check.log'
for details.


Installation output

basilisk.Rcheck/00install.out

* installing *source* package 'basilisk' ...
** using non-staged installation via StagedInstall field
** R
** 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 (basilisk)