Multiple platform build/check report for BioC 3.20 - INSTALL results for garfield on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

INSTALL results for garfield on palomino8

To the developers/maintainers of the garfield package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/garfield.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: garfield

Version: 1.34.0

Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL garfield

StartedAt: 2024-12-19 15:24:34 -0500 (Thu, 19 Dec 2024)

EndedAt: 2024-12-19 15:24:55 -0500 (Thu, 19 Dec 2024)

EllapsedTime: 21.4 seconds

RetCode: 0

Status: OK

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL garfield
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'garfield' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c garfield_init.c -o garfield_init.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_algobase.h:65,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\algorithm:60,
                 from garfield_prep.cpp:19:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\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> {
      |                                     ^~~~~~~~
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\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> {
      |                                     ^~~~~~~~
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\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> {
      |                                      ^~~~~~~~
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\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> {
      |                                     ^~~~~~~~
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o garfield.dll tmp.def garfield_init.o garfield_perm.o garfield_prep.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-garfield/00new/garfield/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (garfield)