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HenrikBengtsson / affxparser

🔬 R package: This is the Bioconductor devel version of the affxparser package.
http://bioconductor.org/packages/devel/bioc/html/affxparser.html
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R CMD check WARNINGs: Compiler warnings (from `-Waddress-of-packed-member`) #45

Open HenrikBengtsson opened 1 year ago

HenrikBengtsson commented 1 year ago

R CMD check gives:

* checking whether package ‘affxparser’ can be installed ... [82s/82s] WARNING
Found the following significant warnings:
  fusion/file/CELFileData.cpp:2409:27: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2414:27: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2419:28: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2445:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2451:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2457:38: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2[50](https://github.com/HenrikBengtsson/affxparser/actions/runs/3215453329/jobs/5256558962#step:13:51)6:23: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2509:23: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2[51](https://github.com/HenrikBengtsson/affxparser/actions/runs/3215453329/jobs/5256558962#step:13:52)2:24: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2551:24: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:25[54](https://github.com/HenrikBengtsson/affxparser/actions/runs/3215453329/jobs/5256558962#step:13:55):24: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:3194:16: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:3199:16: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:3204:17: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:3251:17: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:32[55](https://github.com/HenrikBengtsson/affxparser/actions/runs/3215453329/jobs/5256558962#step:13:56):16: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:3294:28: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
See ‘/home/runner/work/affxparser/affxparser/check/affxparser.Rcheck/00install.out’ for details.

All warnings are for the same src/fusion/file/CELFileData.cpp. Example of the first few warnings:

https://github.com/HenrikBengtsson/affxparser/blob/b8b2bf474a1bcc6b32b3a7dc50392c69f277c3c4/src/fusion/file/CELFileData.cpp#L2406-L2420

kasperdanielhansen commented 1 year ago

I am just guessing, but this looks like it could be related to the memory mapping in affxparser (and to the fact that code breaks under optimization).

Best, Kasper

On Sun, Oct 9, 2022 at 4:37 PM Henrik Bengtsson @.***> wrote:

R CMD check gives:

  • checking whether package ‘affxparser’ can be installed ... [82s/82s] WARNING

Found the following significant warnings:

fusion/file/CELFileData.cpp:2409:27: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:2414:27: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:2419:28: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:2445:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:2451:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:2457:38: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:2506:23: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:2509:23: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:2512:24: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:2551:24: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:2554:24: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:3194:16: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:3199:16: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:3204:17: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:3251:17: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:3255:16: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

fusion/file/CELFileData.cpp:3294:28: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]

See ‘/home/runner/work/affxparser/affxparser/check/affxparser.Rcheck/00install.out’ for details.

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-- Best, Kasper