##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scifer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scifer_1.7.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scifer.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘scifer’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/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
+ /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.17.0/0/bin/conda create --yes --prefix /Users/biocbuild/Library/Caches/org.R-project.R/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: /Users/biocbuild/Library/Caches/org.R-project.R/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/osx-arm64::bzip2-1.0.8-h93a5062_5
  ca-certificates    conda-forge/osx-arm64::ca-certificates-2024.7.4-hf0a4a13_0
  libffi             conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
  libsqlite          conda-forge/osx-arm64::libsqlite-3.46.0-hfb93653_0
  libzlib            conda-forge/osx-arm64::libzlib-1.3.1-hfb2fe0b_1
  ncurses            conda-forge/osx-arm64::ncurses-6.5-hb89a1cb_0
  openssl            conda-forge/osx-arm64::openssl-3.3.1-hfb2fe0b_1
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/osx-arm64::python-3.9.19-hd7ebdb9_0_cpython
  readline           conda-forge/osx-arm64::readline-8.2-h92ec313_1
  setuptools         conda-forge/noarch::setuptools-70.1.1-pyhd8ed1ab_0
  tk                 conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.17.0/0/bin/conda install --yes --prefix /Users/biocbuild/Library/Caches/org.R-project.R/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.

+ /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.17.0/0/bin/conda install --yes --prefix /Users/biocbuild/Library/Caches/org.R-project.R/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/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/scifer.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scifer
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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
2024-07-06 05:06:33.851 R[19064:83683289] XType: Using static font registry.
output file: HC_report.knit.md

/opt/homebrew/bin/pandoc +RTS -K512m -RTS HC_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp27EPeF/QC_report.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp27EPeF/rmarkdown-str4a785d9511f5.html 

Output created: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp27EPeF/QC_report.html
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 36 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 36 ]
> 
> proc.time()
   user  system elapsed 
 51.883   0.541  65.550