* using log directory ‘/srv/hornik/tmp/CRAN_pretest/fibos.Rcheck’
* using R Under development (unstable) (2025-02-22 r87796)
* 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 ‘1.1.0’
* 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 ... OK
* 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 ... WARNING
Found the following file with non-ASCII characters:
  R/manage_os.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII
characters in files.
* 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] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 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/3s] 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
  <e4>
* checking PDF version of manual ... [3s/3s] 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, 2 WARNINGs, 2 NOTEs