* using log directory ‘/srv/hornik/tmp/CRAN_pretest/fibos.Rcheck’
* using R Under development (unstable) (2025-02-26 r87830)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘fibos/DESCRIPTION’ ... OK
* this is package ‘fibos’ version ‘1.2.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Herson Hebert Mendes Soares <hersonhebert@hotmail.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  bioinformatics (9:32)
  fibos (8:18)

Found the following (possibly) invalid URLs:
  URL: https://github.com/insilico-unifei/fibos-R-case-study-supp.git (moved to https://github.com/insilico-unifei/fibos-R-case-study-supp)
    From: README.md
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.
* 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 executable files ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

CRAN-pack does not know about
  .github
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘fibos’ can be installed ... [13s/8s] OK
* used C compiler: ‘Debian clang version 19.1.7 (1+b1)’
* used Fortran compiler: ‘Debian flang-new version 19.1.7 (1+b1)’
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking use of S3 registration ... 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 ... [4s/4s] NOTE
osp_windows: no visible global function definition for
  ‘python_binary_path’
Undefined global functions or variables:
  python_binary_path
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'execute.Rd':
  ‘read_osp’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  execute.Rd: read_osp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'execute.Rd'
  ‘pdb’ ‘method’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... WARNING
File ‘fibos/libs/fibos.so’:
  Found ‘_FortranAStopStatement’, possibly from ‘stop’ (Fortran)
    Objects: ‘ds75.o’, ‘occsurf75.o’, ‘surfcal76.o’
  Found ‘_FortranAStopStatementText’, possibly from ‘stop’ (Fortran)
    Object: ‘ds75.o’
  Found ‘_FortranAioBeginClose’, possibly from ‘close’ (Fortran)
    Objects: ‘ds75.o’, ‘main75.o’, ‘renum75.o’, ‘respak75.o’,
      ‘surfcal76.o’
  Found ‘_FortranAioBeginOpenUnit’, possibly from ‘open’ (Fortran)
    Objects: ‘ds75.o’, ‘main75.o’, ‘occsurf75.o’, ‘renum75.o’,
      ‘respak75.o’, ‘surfcal76.o’
  Found ‘_FortranAioBeginRewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘ds75.o’, ‘main75.o’, ‘surfcal76.o’
  Found ‘_FortranAioInputAscii’, possibly from ‘read’ (Fortran)
    Objects: ‘ds75.o’, ‘main75.o’, ‘occsurf75.o’, ‘renum75.o’,
      ‘respak75.o’, ‘surfcal76.o’
  Found ‘_FortranAioInputInteger’, possibly from ‘read’ (Fortran)
    Objects: ‘ds75.o’, ‘main75.o’, ‘occsurf75.o’, ‘renum75.o’,
      ‘respak75.o’, ‘surfcal76.o’
  Found ‘_FortranAioInputReal32’, possibly from ‘read’ (Fortran)
    Objects: ‘main75.o’, ‘occsurf75.o’, ‘respak75.o’, ‘surfcal76.o’
  Found ‘_FortranAioInputReal64’, possibly from ‘read’ (Fortran)
    Object: ‘ds75.o’
  Found ‘_FortranAioOutputAscii’, possibly from ‘print’ (Fortran),
    ‘write’ (Fortran)
    Objects: ‘ds75.o’, ‘main75.o’, ‘occsurf75.o’, ‘renum75.o’,
      ‘respak75.o’, ‘surfcal76.o’
  Found ‘_FortranAioOutputInteger32’, possibly from ‘print’ (Fortran),
    ‘write’ (Fortran)
    Objects: ‘ds75.o’, ‘main75.o’, ‘occsurf75.o’, ‘renum75.o’,
      ‘respak75.o’, ‘surfcal76.o’
  Found ‘_FortranAioOutputReal32’, possibly from ‘print’ (Fortran),
    ‘write’ (Fortran)
    Objects: ‘main75.o’, ‘occsurf75.o’, ‘respak75.o’, ‘surfcal76.o’
  Found ‘_FortranAioOutputReal64’, possibly from ‘print’ (Fortran),
    ‘write’ (Fortran)
    Object: ‘ds75.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking usage of KIND in Fortran files ... OK
* checking examples ... [1s/2s] ERROR
Running examples in ‘fibos-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: occluded_surface
> ### Title: Occluded Surface (OS)
> ### Aliases: occluded_surface
> 
> ### ** Examples
> 
> library(fibos)
> 
> # Calculate FIBOS per atom and create .srf files in fibos_files folder
> pdb_fibos <- occluded_surface("8rxn", method = "FIBOS")
trying URL 'https://files.rcsb.org/download/8rxn.pdb'
downloaded 71 KB

Error in execute(1, iresl, meth, verbose) : 
  NA/NaN/Inf in foreign function call (arg 1)
Calls: occluded_surface -> <Anonymous> -> <Anonymous> -> force -> execute
Execution halted
  r'E
* checking PDF version of manual ... [2s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘fibos_files’
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 3 WARNINGs, 4 NOTEs