Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 1847/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scifer 1.7.5 (landing page) Rodrigo Arcoverde Cerveira
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the scifer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scifer.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: scifer |
Version: 1.7.5 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scifer.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scifer_1.7.5.tar.gz |
StartedAt: 2024-07-16 03:48:02 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 04:02:13 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 851.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: scifer.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scifer.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scifer_1.7.5.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/scifer.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 option '--no-vignettes' * checking for file 'scifer/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'scifer' version '1.7.5' * 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 ... OK * checking whether package 'scifer' can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/scifer.Rcheck/00install.out' for details. * checking installed package size ... OK * checking package directory ... OK * checking 'build' 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 ... OK * 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' ... OK * checking examples ... ERROR Running examples in 'scifer-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: igblast > ### Title: Run IgDiscover for IgBlast using basilisk, which enables the > ### python environment for Igblast > ### Aliases: igblast > > ### ** Examples > > ## Example with test sequences > igblast( + database = system.file("/inst/extdata/test_fasta/KIMDB_rm", package = "scifer"), + + fasta = system.file("/inst/extdata/test_fasta/test_igblast.txt", package = "scifer"), + + threads = 1 + ) Warning in check_forbidden_install("Python packages") : cannot install Python packages during R CMD check Warning in check_forbidden_install("Conda Environments") : cannot install Conda Environments during R CMD check + "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/0/condabin/conda.bat" create --yes --prefix "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/scifer/1.7.5/igblast_wrap_basilisk" "python=3.9.19" --quiet -c bioconda -c conda-forge 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\scifer\1.7.5\igblast_wrap_basilisk added / updated specs: - python=3.9.19 The following NEW packages will be INSTALLED: bzip2 conda-forge/win-64::bzip2-1.0.8-h2466b09_7 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-3.9.19-h4de0772_0_cpython setuptools conda-forge/noarch::setuptools-70.3.0-pyhd8ed1ab_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 + "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/0/condabin/conda.bat" install --yes --prefix "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/scifer/1.7.5/igblast_wrap_basilisk" "python=3.9.19" -c bioconda -c conda-forge 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. + "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/0/condabin/conda.bat" install --yes --prefix "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/scifer/1.7.5/igblast_wrap_basilisk" -c bioconda -c conda-forge "python=3.9.19" "python=3.9.19" "dnaio=1.2.1" "igblast=1.22.0" 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... failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: - igblast=1.22.0 - dnaio=1.2.1 Current channels: - https://conda.anaconda.org/bioconda/win-64 - https://conda.anaconda.org/bioconda/noarch - https://conda.anaconda.org/conda-forge/win-64 - https://conda.anaconda.org/conda-forge/noarch - https://repo.anaconda.com/pkgs/main/win-64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/win-64 - https://repo.anaconda.com/pkgs/r/noarch - https://repo.anaconda.com/pkgs/msys2/win-64 - https://repo.anaconda.com/pkgs/msys2/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. Error: one or more Python packages failed to install [error code 1] Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: 12. └─reticulate:::stopf(fmt, result) ── Error ('test-igblast.R:49:5'): returns a data.frame object ────────────────── Error: one or more Python packages failed to install [error code 1] Backtrace: ▆ 1. └─scifer::igblast(...) at test-igblast.R:49:5 2. └─basilisk::basiliskStart(env) 3. └─basilisk::obtainEnvironmentPath(env) 4. └─basilisk::setupBasiliskEnv(...) 5. └─reticulate::conda_install(...) 6. └─reticulate:::stopf(fmt, result) [ FAIL 3 | WARN 13 | SKIP 0 | PASS 42 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/scifer.Rcheck/00check.log' for details.
scifer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL scifer ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'scifer' ... ** using non-staged installation via StagedInstall field ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (scifer)
scifer.Rcheck/tests/testthat.Rout.fail
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(scifer) > > test_check("scifer") + "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/0/condabin/conda.bat" create --yes --prefix "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/scifer/1.7.5/igblast_wrap_basilisk" "python=3.9.19" --quiet -c bioconda -c conda-forge 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\scifer\1.7.5\igblast_wrap_basilisk added / updated specs: - python=3.9.19 The following NEW packages will be INSTALLED: bzip2 conda-forge/win-64::bzip2-1.0.8-h2466b09_7 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-3.9.19-h4de0772_0_cpython setuptools conda-forge/noarch::setuptools-70.3.0-pyhd8ed1ab_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 + "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/0/condabin/conda.bat" install --yes --prefix "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/scifer/1.7.5/igblast_wrap_basilisk" "python=3.9.19" -c bioconda -c conda-forge 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. + "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/0/condabin/conda.bat" install --yes --prefix "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/scifer/1.7.5/igblast_wrap_basilisk" -c bioconda -c conda-forge "python=3.9.19" "python=3.9.19" "dnaio=1.2.1" "igblast=1.22.0" 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... failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: - dnaio=1.2.1 - igblast=1.22.0 Current channels: - https://conda.anaconda.org/bioconda/win-64 - https://conda.anaconda.org/bioconda/noarch - https://conda.anaconda.org/conda-forge/win-64 - https://conda.anaconda.org/conda-forge/noarch - https://repo.anaconda.com/pkgs/main/win-64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/win-64 - https://repo.anaconda.com/pkgs/r/noarch - https://repo.anaconda.com/pkgs/msys2/win-64 - https://repo.anaconda.com/pkgs/msys2/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. + "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/0/condabin/conda.bat" create --yes --prefix "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/scifer/1.7.5/igblast_wrap_basilisk" "python=3.9.19" --quiet -c bioconda -c conda-forge 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\scifer\1.7.5\igblast_wrap_basilisk added / updated specs: - python=3.9.19 The following NEW packages will be INSTALLED: bzip2 conda-forge/win-64::bzip2-1.0.8-h2466b09_7 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-3.9.19-h4de0772_0_cpython setuptools conda-forge/noarch::setuptools-70.3.0-pyhd8ed1ab_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 + "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/0/condabin/conda.bat" install --yes --prefix "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/scifer/1.7.5/igblast_wrap_basilisk" "python=3.9.19" -c bioconda -c conda-forge 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. + "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/0/condabin/conda.bat" install --yes --prefix "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/scifer/1.7.5/igblast_wrap_basilisk" -c bioconda -c conda-forge "python=3.9.19" "python=3.9.19" "dnaio=1.2.1" "igblast=1.22.0" 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... failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: - dnaio=1.2.1 - igblast=1.22.0 Current channels: - https://conda.anaconda.org/bioconda/win-64 - https://conda.anaconda.org/bioconda/noarch - https://conda.anaconda.org/conda-forge/win-64 - https://conda.anaconda.org/conda-forge/noarch - https://repo.anaconda.com/pkgs/main/win-64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/win-64 - https://repo.anaconda.com/pkgs/r/noarch - https://repo.anaconda.com/pkgs/msys2/win-64 - https://repo.anaconda.com/pkgs/msys2/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. + "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/0/condabin/conda.bat" create --yes --prefix "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/scifer/1.7.5/igblast_wrap_basilisk" "python=3.9.19" --quiet -c bioconda -c conda-forge 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\scifer\1.7.5\igblast_wrap_basilisk added / updated specs: - python=3.9.19 The following NEW packages will be INSTALLED: bzip2 conda-forge/win-64::bzip2-1.0.8-h2466b09_7 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-3.9.19-h4de0772_0_cpython setuptools conda-forge/noarch::setuptools-70.3.0-pyhd8ed1ab_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 + "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/0/condabin/conda.bat" install --yes --prefix "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/scifer/1.7.5/igblast_wrap_basilisk" "python=3.9.19" -c bioconda -c conda-forge 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. + "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/0/condabin/conda.bat" install --yes --prefix "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.17.0/scifer/1.7.5/igblast_wrap_basilisk" -c bioconda -c conda-forge "python=3.9.19" "python=3.9.19" "dnaio=1.2.1" "igblast=1.22.0" 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... failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: - igblast=1.22.0 - dnaio=1.2.1 Current channels: - https://conda.anaconda.org/bioconda/win-64 - https://conda.anaconda.org/bioconda/noarch - https://conda.anaconda.org/conda-forge/win-64 - https://conda.anaconda.org/conda-forge/noarch - https://repo.anaconda.com/pkgs/main/win-64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/win-64 - https://repo.anaconda.com/pkgs/r/noarch - https://repo.anaconda.com/pkgs/msys2/win-64 - https://repo.anaconda.com/pkgs/msys2/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. processing file: HC_report.Rmd output file: HC_report.knit.md "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS HC_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandocf16c43a47819.html --lua-filter "C:\Users\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --section-divs --template "C:\Users\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "C:\Users\biocbuild\bbs-3.20-bioc\tmpdir\Rtmpsd2JOd\rmarkdown-strf16c5bdb32dd.html" Output created: C:/Users/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpsd2JOd/QC_report.html [ FAIL 3 | WARN 13 | SKIP 0 | PASS 42 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-igblast.R:14:5'): the database directory does not exists SPACE ── Error: one or more Python packages failed to install [error code 1] Backtrace: ▆ 1. ├─testthat::expect_message(...) at test-igblast.R:14:5 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─scifer::igblast(...) 8. └─basilisk::basiliskStart(env) 9. └─basilisk::obtainEnvironmentPath(env) 10. └─basilisk::setupBasiliskEnv(...) 11. └─reticulate::conda_install(...) 12. └─reticulate:::stopf(fmt, result) ── Error ('test-igblast.R:37:5'): the file directory does not exists SPACE ───── Error: one or more Python packages failed to install [error code 1] Backtrace: ▆ 1. ├─testthat::expect_message(...) at test-igblast.R:37:5 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─scifer::igblast(...) 8. └─basilisk::basiliskStart(env) 9. └─basilisk::obtainEnvironmentPath(env) 10. └─basilisk::setupBasiliskEnv(...) 11. └─reticulate::conda_install(...) 12. └─reticulate:::stopf(fmt, result) ── Error ('test-igblast.R:49:5'): returns a data.frame object ────────────────── Error: one or more Python packages failed to install [error code 1] Backtrace: ▆ 1. └─scifer::igblast(...) at test-igblast.R:49:5 2. └─basilisk::basiliskStart(env) 3. └─basilisk::obtainEnvironmentPath(env) 4. └─basilisk::setupBasiliskEnv(...) 5. └─reticulate::conda_install(...) 6. └─reticulate:::stopf(fmt, result) [ FAIL 3 | WARN 13 | SKIP 0 | PASS 42 ] Error: Test failures Execution halted
scifer.Rcheck/scifer-Ex.timings
name | user | system | elapsed | |
df_to_fasta | 0.04 | 0.00 | 0.03 | |
fcs_plot | 0.25 | 0.07 | 0.31 | |
fcs_processing | 0.17 | 0.04 | 0.24 | |