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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FLAMES.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings FLAMES_1.5.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/FLAMES.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'FLAMES/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FLAMES' version '1.5.1'
* 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 'FLAMES' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
  installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
* 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 R 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 ... NOTE
combine_sce: no visible global function definition for 'is'
generate_sc_sce: no visible binding for global variable 'FSM_match'
sc_DTU_analysis: no visible global function definition for 'is'
sc_DTU_analysis: no visible binding for global variable 'FSM_match'
sc_DTU_analysis: no visible binding for global variable 'gene_name'
sc_DTU_analysis: no visible binding for global variable 'cell_id'
sc_DTU_analysis: no visible binding for global variable 'cnt'
sc_DTU_analysis: no visible binding for global variable 'tr_id'
sc_DTU_analysis : get_rm: no visible binding for global variable
  'gene_name'
sc_DTU_analysis : get_rm: no visible binding for global variable 'l'
sc_annotate_plots: no visible binding for global variable 'gene_id'
sc_annotate_plots: no visible binding for global variable 'x'
sc_annotate_plots: no visible binding for global variable 'y'
sc_annotate_plots : plot_idx: no visible binding for global variable
  'x'
sc_annotate_plots : plot_idx: no visible binding for global variable
  'y'
sc_annotate_plots : plot_idx_impute: no visible binding for global
  variable 'x'
sc_annotate_plots : plot_idx_impute: no visible binding for global
  variable 'y'
Undefined global functions or variables:
  FSM_match cell_id cnt gene_id gene_name is l tr_id x y
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/FLAMES/libs/x64/FLAMES.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'FLAMES-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: parse_gff_tree
> ### Title: Parse Gff3 file
> ### Aliases: parse_gff_tree
> 
> ### ** Examples
> 
> temp_path <- tempfile()
> bfc <- BiocFileCache::BiocFileCache(temp_path, ask = FALSE)
> file_url <-
+     "https://raw.githubusercontent.com/OliverVoogd/FLAMESData/master/data"
> gff <- bfc[[names(BiocFileCache::bfcadd(bfc, "GFF", paste(file_url, "SIRV_isoforms_multi-fasta-annotation_C_170612a.gtf", sep = "/")))]]
> parsed_gff <- parse_gff_tree(gff)
Warning in check_forbidden_install("Python packages") :
  cannot install Python packages during R CMD check
+ "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.11.2/0/condabin/conda.bat" "create" "--yes" "--prefix" "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.11.2/FLAMES/1.5.1/flames_env" "python=3.7" "--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\1.11.2\FLAMES\1.5.1\flames_env

  added / updated specs:
    - python=3.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/win-64::ca-certificates-2022.12.7-h5b45459_0
  libsqlite          conda-forge/win-64::libsqlite-3.40.0-hcfcfb64_0
  openssl            conda-forge/win-64::openssl-3.0.7-hcfcfb64_1
  pip                conda-forge/noarch::pip-22.3.1-pyhd8ed1ab_0
  python             conda-forge/win-64::python-3.7.12-h900ac77_100_cpython
  setuptools         conda-forge/noarch::setuptools-65.6.3-pyhd8ed1ab_0
  sqlite             conda-forge/win-64::sqlite-3.40.0-hcfcfb64_0
  ucrt               conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.3-h3d8a991_9
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.32.31332-h1d6e394_9
  wheel              conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.11.2/0/condabin/conda.bat" "install" "--yes" "--prefix" "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.11.2/FLAMES/1.5.1/flames_env" "python=3.7"
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\1.11.2\FLAMES\1.5.1\flames_env

  added / updated specs:
    - python=3.7


The following packages will be UPDATED:

  python             conda-forge::python-3.7.12-h900ac77_1~ --> pkgs/main::python-3.7.15-h6244533_1

The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2022.10.11-haa95532_0
  openssl             conda-forge::openssl-3.0.7-hcfcfb64_1 --> pkgs/main::openssl-1.1.1s-h2bbff1b_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 22.11.1

Please update conda by running

    $ conda update -n base -c defaults conda


+ "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.11.2/0/condabin/conda.bat" "install" "--yes" "--prefix" "C:/Users/biocbuild/AppData/Local/R/cache/R/basilisk/1.11.2/FLAMES/1.5.1/flames_env" "-c" "bioconda" "-c" "conda-forge" "python=3.7" "python=3.7" "numpy=1.16.5" "editdistance=0.5.3" "scipy=1.2.0" "pysam=0.18.0"
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:

  - pysam=0.18.0

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 in 'inst/doc' ... 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, 4 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/FLAMES.Rcheck/00check.log'
for details.