* using log directory 'd:/RCompile/CRANincoming/R-devel/fibos.Rcheck'
* using R Under development (unstable) (2025-01-27 r87654 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'fibos/DESCRIPTION' ... OK
* this is package 'fibos' version '1.0.0.9'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Herson Hebert Mendes Soares <hersonhebert@hotmail.com>'

New submission

Possibly misspelled words in DESCRIPTION:
  Biomolecules (3:9)
  bioinformatics (9:32)
  fibos (8:18)
* 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 serialization versions ... OK
* checking whether package 'fibos' can be installed ... WARNING
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: Obsolescent feature: Old-style character length at (1)
  Warning: GNU Extension: Nonstandard type declaration INTEGER*4 at (1)
  Warning: GNU Extension: Nonstandard type declaration LOGICAL*1 at (1)
  Warning: GNU Extension: Nonstandard type declaration INTEGER*2 at (1)
  Warning: GNU Extension: Old-style initialization at (1)
  Warning: GNU Extension: Nonstandard type declaration REAL*4 at (1)
  Warning: Obsolescent feature: DATA statement at (1) after the first executable statement
  Warning: GNU Extension: $ descriptor at (1)
  Warning: Legacy Extension: Label at (1) is not in the same block as the GOTO statement at (2)
See 'd:/RCompile/CRANincoming/R-devel/fibos.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used Fortran compiler: 'GNU Fortran (GCC) 13.3.0'
* checking installed package size ... OK
* 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 ... 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 loading without being on the library search path ... 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 ... OK
* checking Rd files ... 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/x64/fibos.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Objects: 'ds75.o', 'main75.o', 'renum75.o', 'respak75.o',
      'surfcal76.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Objects: 'ds75.o', 'main75.o', 'occsurf75.o', 'renum75.o',
      'respak75.o', 'surfcal76.o'
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
    Objects: 'ds75.o', 'occsurf75.o', 'surfcal76.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 ... [300s] ERROR
Running examples in 'fibos-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: osp
> ### Title: Occluded Surface Packing (OSP)
> ### Aliases: osp
> 
> ### ** Examples
> 
> 
> library(fibos)
> 
> # Calculate FIBOS per atom and create .srf files in fibos_files folder
> pdb_fibos <- occluded_surface("1fib", method = "FIBOS")
trying URL 'https://files.rcsb.org/download/1fib.pdb'
downloaded 203 KB

  @
Examples with CPU (user + system) or elapsed time > 10s
                  user system elapsed
occluded_surface 155.9   2.54   159.4
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 1 NOTE