ENH: Handle error strings in a way that doesn't produce compile warnings #2205
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dave3d
approved these changes
Oct 12, 2024
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Please rebase the changes onto the release branch. Also can we get more detains about the compatibility of these functions. We should be able to list compatibility with R versions of the R Rprintf and the new REprintf methods. |
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Hi @richardbeare, Please provide more details in the commit message. Specifically, what build warning and at what version of R was it changed to an error. We want to be able to test these things on the development machines. Also, I believe this change replaces printing to std::out with printing to std:err. The change makes sense in that the original code was printing to the wrong location, is this both a build fix and bug fix at the same time? |
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Will get onto the rebasing - apologies, I always forget where to begin the modifications. Further details that will get included in the new PR. There are two changes - string formatting and use of REprintf. @zivy zivy Do you prefer them to be separate commits in the next PR, or is documentation sufficient? /tmp/RtmpSL0fo1/R.INSTALL1a911b1dcfc5df/SimpleITK/SITK/SimpleITK/Wrapping/R/sitkRArray.cxx: In function ‘SEXPREC* ImAsArray(itk::simple::Image)’:
/tmp/RtmpSL0fo1/R.INSTALL1a911b1dcfc5df/SimpleITK/SITK/SimpleITK/Wrapping/R/sitkRArray.cxx:54:15: error: format not a string literal and no format arguments [-Werror=format-security]
54 | Rprintf(error_msg);
| ^~~~~~~~~
/tmp/RtmpSL0fo1/R.INSTALL1a911b1dcfc5df/SimpleITK/SITK/SimpleITK/Wrapping/R/sitkRArray.cxx:207:15: error: format not a string literal and no format arguments [-Werror=format-security]
207 | Rprintf(error_msg);
| ^~~~~~~~~
/tmp/RtmpSL0fo1/R.INSTALL1a911b1dcfc5df/SimpleITK/SITK/SimpleITK/Wrapping/R/sitkRArray.cxx: In function ‘itk::simple::Image ArrayAsIm(SEXP, std::vector<unsigned int>, std::vector<double>, std::vector<double>, unsigned int)’:
/tmp/RtmpSL0fo1/R.INSTALL1a911b1dcfc5df/SimpleITK/SITK/SimpleITK/Wrapping/R/sitkRArray.cxx:237:13: error: format not a string literal and no format arguments [-Werror=format-security]
237 | Rprintf(error_msg);
| ^~~~~~~~~
cc1plus: some warnings being treated as errors
make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/build.make:460: Wrapping/R/CMakeFiles/SimpleITK_R.dir/sitkRArray.cxx.o] Error 1
make[4]: *** [CMakeFiles/Makefile2:1855: Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
make[3]: *** [Makefile:156: all] Error 2
make[2]: *** [CMakeFiles/SimpleITK-build.dir/build.make:76: SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
make[1]: *** [CMakeFiles/Makefile2:289: CMakeFiles/SimpleITK-build.dir/all] Error 2
make: *** [Makefile:91: all] Error 2
ERROR: configuration failed for package ‘SimpleITK’
* removing ‘/home/richard.beare/R/x86_64-pc-linux-gnu-library/4.4/SimpleITK’
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See PR - #2207 |
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Any idea on compatibility of this change? With what version of R is it required? With what versions of R is it compatible? Will it break any older versions of R? |
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I don't anticipate problems with older versions of R. I have only
encountered the elevation of warnings with 4.4.1.
…On Tue, Oct 22, 2024 at 12:40 AM Bradley Lowekamp ***@***.***> wrote:
Will get onto the rebasing - apologies, I always forget where to begin the
modifications.
Further details that will get included in the new PR. Warnings/errors
raised below, on ubuntu 22, R 4.4.1. The warnings are elevated to errors by
R when installation via SimpleITKRInstaller is attempted.
There are two changes - string formatting and use of REprintf. @zivy
<https://github.com/zivy> zivy Do you prefer them to be separate commits
in the next PR, or is documentation sufficient?
/tmp/RtmpSL0fo1/R.INSTALL1a911b1dcfc5df/SimpleITK/SITK/SimpleITK/Wrapping/R/sitkRArray.cxx: In function ‘SEXPREC* ImAsArray(itk::simple::Image)’:
/tmp/RtmpSL0fo1/R.INSTALL1a911b1dcfc5df/SimpleITK/SITK/SimpleITK/Wrapping/R/sitkRArray.cxx:54:15: error: format not a string literal and no format arguments [-Werror=format-security]
54 | Rprintf(error_msg);
| ^~~~~~~~~
/tmp/RtmpSL0fo1/R.INSTALL1a911b1dcfc5df/SimpleITK/SITK/SimpleITK/Wrapping/R/sitkRArray.cxx:207:15: error: format not a string literal and no format arguments [-Werror=format-security]
207 | Rprintf(error_msg);
| ^~~~~~~~~
/tmp/RtmpSL0fo1/R.INSTALL1a911b1dcfc5df/SimpleITK/SITK/SimpleITK/Wrapping/R/sitkRArray.cxx: In function ‘itk::simple::Image ArrayAsIm(SEXP, std::vector<unsigned int>, std::vector<double>, std::vector<double>, unsigned int)’:
/tmp/RtmpSL0fo1/R.INSTALL1a911b1dcfc5df/SimpleITK/SITK/SimpleITK/Wrapping/R/sitkRArray.cxx:237:13: error: format not a string literal and no format arguments [-Werror=format-security]
237 | Rprintf(error_msg);
| ^~~~~~~~~
cc1plus: some warnings being treated as errors
make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/build.make:460: Wrapping/R/CMakeFiles/SimpleITK_R.dir/sitkRArray.cxx.o] Error 1
make[4]: *** [CMakeFiles/Makefile2:1855: Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
make[3]: *** [Makefile:156: all] Error 2
make[2]: *** [CMakeFiles/SimpleITK-build.dir/build.make:76: SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
make[1]: *** [CMakeFiles/Makefile2:289: CMakeFiles/SimpleITK-build.dir/all] Error 2
make: *** [Makefile:91: all] Error 2
ERROR: configuration failed for package ‘SimpleITK’* removing ‘/home/richard.beare/R/x86_64-pc-linux-gnu-library/4.4/SimpleITK’
Any idea on compatibility of this change? With what version of R is it
required? With what versions of R is it compatible? Will it break any older
versions of R?
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Compiler warnings are being elevated to errors when encountered by SimpelITKRInstaller - presumably a change of defaults in the package build process in more recent versions of R.
The various prints are all errors, so the calls have also been changed to REprintf