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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:garfield.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings garfield_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/garfield.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘garfield/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘garfield’ version ‘1.34.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘garfield’ can be installed ... WARNING
Found the following significant warnings:
  garfield_perm.cpp:306:29: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘long int’ [-Wformat=]
  garfield_perm.cpp:306:32: warning: format ‘%s’ expects argument of type ‘char*’, but argument 3 has type ‘int’ [-Wformat=]
  garfield_perm.cpp:306:38: warning: format ‘%s’ expects argument of type ‘char*’, but argument 4 has type ‘double’ [-Wformat=]
  garfield_perm.cpp:306:41: warning: unknown conversion type character ‘\x09’ in format [-Wformat=]
  garfield_perm.cpp:306:46: warning: format ‘%s’ expects argument of type ‘char*’, but argument 5 has type ‘int’ [-Wformat=]
  garfield_perm.cpp:306:83: warning: format ‘%s’ expects argument of type ‘char*’, but argument 6 has type ‘double’ [-Wformat=]
  garfield_perm.cpp:356:27: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘int’ [-Wformat=]
  garfield_prep.cpp:144:28: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  garfield_prep.cpp:225:37: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  garfield_prep.cpp:234:37: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  garfield_prep.cpp:245:38: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  garfield_prep.cpp:273:37: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/garfield.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... 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
garfield.plot: no visible global function definition for ‘read.table’
garfield.plot: no visible global function definition for
  ‘colorRampPalette’
garfield.plot: no visible global function definition for ‘pdf’
garfield.plot: no visible global function definition for ‘layout’
garfield.plot: no visible global function definition for ‘par’
garfield.plot: no visible global function definition for ‘title’
garfield.plot: no visible global function definition for ‘legend’
garfield.plot: no visible global function definition for ‘dev.off’
garfield.plot.fnx: no visible global function definition for ‘par’
garfield.plot.fnx: no visible global function definition for ‘polygon’
garfield.plot.fnx: no visible global function definition for ‘segments’
garfield.plot.fnx: no visible global function definition for ‘points’
garfield.plot.fnx: no visible global function definition for ‘lines’
garfield.plot.fnx: no visible global function definition for ‘median’
garfield.plot.fnx: no visible global function definition for ‘text’
Undefined global functions or variables:
  colorRampPalette dev.off layout legend lines median par pdf points
  polygon read.table segments text title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "layout", "legend", "lines", "par", "points",
             "polygon", "segments", "text", "title")
  importFrom("stats", "median")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/garfield/libs/garfield.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘srand’, possibly from ‘srand’ (C)

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 ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/garfield.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL garfield
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘garfield’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c garfield_init.c -o garfield_init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c garfield_perm.cpp -o garfield_perm.o
garfield_perm.cpp: In function ‘void batchfeep(std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, const std::vector<bin>&, const std::vector<double>&, int, int, bool, int, double, int, std::vector<bool>)’:
garfield_perm.cpp:306:29: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘long int’ [-Wformat=]
  306 |                 Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
      |                            ~^                                                          ~~~
      |                             |                                                           |
      |                             char*                                                       long int
      |                            %ld
garfield_perm.cpp:306:32: warning: format ‘%s’ expects argument of type ‘char*’, but argument 3 has type ‘int’ [-Wformat=]
  306 |                 Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
      |                               ~^                                                           ~~~~~~
      |                                |                                                           |
      |                                char*                                                       int
      |                               %d
garfield_perm.cpp:306:38: warning: format ‘%s’ expects argument of type ‘char*’, but argument 4 has type ‘double’ [-Wformat=]
  306 |                 Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
      |                                     ~^                                                             ~~~~~~~~~~~~~~~~~~~~~~
      |                                      |                                                                           |
      |                                      char*                                                                       double
      |                                     %f
garfield_perm.cpp:306:41: warning: unknown conversion type character ‘\x09’ in format [-Wformat=]
  306 |                 Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
      |                                         ^~
garfield_perm.cpp:306:46: warning: format ‘%s’ expects argument of type ‘char*’, but argument 5 has type ‘int’ [-Wformat=]
  306 |                 Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
      |                                             ~^                                                                             ~~~~~~
      |                                              |                                                                             |
      |                                              char*                                                                         int
      |                                             %d
garfield_perm.cpp:306:83: warning: format ‘%s’ expects argument of type ‘char*’, but argument 6 has type ‘double’ [-Wformat=]
  306 |                 Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
      |                                                                                  ~^                                               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                   |                                                                      |
      |                                                                                   char*                                                                  double
      |                                                                                  %f
garfield_perm.cpp: In function ‘int garfield_perm(char**, char**, char**, char**, char**, char**, char**, char**, char**, char**, char**, char**, char**)’:
garfield_perm.cpp:356:27: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘int’ [-Wformat=]
  356 |                 Rprintf("%s",nannot);
      |                          ~^  ~~~~~~
      |                           |  |
      |                           |  int
      |                           char*
      |                          %d
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c garfield_prep.cpp -o garfield_prep.o
garfield_prep.cpp:144:28: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  144 | struct Enumerator : public iterator<input_iterator_tag, typename Iterator::value_type>  {
      |                            ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from garfield_prep.cpp:19:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
garfield_prep.cpp:225:37: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  225 | struct TagsOutputIterator1 : public iterator<output_iterator_tag,void,void,void,void> {
      |                                     ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
garfield_prep.cpp:234:37: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  234 | struct TagsOutputIterator2 : public iterator<output_iterator_tag,void,void,void,void> {
      |                                     ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
garfield_prep.cpp:245:38: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  245 | struct TagRefOutputIterator : public iterator<output_iterator_tag,void,void,void,void> {
      |                                      ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
garfield_prep.cpp:273:37: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  273 | struct PrintOutputIterator : public iterator<output_iterator_tag,void,void,void,void> {
      |                                     ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o garfield.so garfield_init.o garfield_perm.o garfield_prep.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-garfield/00new/garfield/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (garfield)