##############################################################################
##############################################################################
###
### 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_1.7.3.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 '1.7.3'
* 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/1.7.3/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\1.7.3\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-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-3.9.19-h4de0772_0_cpython
  setuptools         conda-forge/noarch::setuptools-70.1.1-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/1.7.3/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/1.7.3/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.


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'
 OK
* 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: 1 ERROR, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/scifer.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### 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)

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")


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 pandoc16f203e7a17d3.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\Rtmp8kQkwi\rmarkdown-str16f20741377a3.html" 

Output created: C:/Users/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp8kQkwi/QC_report.html
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 36 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 36 ]
> 
> proc.time()
   user  system elapsed 
 114.67    2.46  118.70