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omp.h before Rincludes.h #5122

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mattdowle opened this issue Aug 31, 2021 · 5 comments · Fixed by #5172
Closed

omp.h before Rincludes.h #5122

mattdowle opened this issue Aug 31, 2021 · 5 comments · Fixed by #5172
Milestone
1.14.2

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@mattdowle
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mattdowle commented Aug 31, 2021 •
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Received from Prof Brian Ripley today :

Subject: Packages including omp.h after Rincludes.h

That is

AMORE BNN BRISC OpenMPController RFCCA RFpredInterval RLT
RandomFields RandomFieldsUtils RandomForestsGLS RhpcBLASctl RxODE
STB TMB brnn coop data.table excursions float glinternet glmmTMB
gmGeostats graphscan hashr hutilscpp influenceR iq kit likeLTD
mRMRe magick meanShiftR meanr mnlogit poismf poppr praznik rFerns
randomForestSRC rasterKernelEstimates rehh simputation spBayes
spNNGP stringdist sylcount unfoldr

Compilation logs can be seen at
https://www.stats.ox.ac.uk/pub/bdr/clang13/ but beware these may only
show the first error.

The imminent clang 13.0.0 has an omp.h including

/* OpenMP 5.1 */
#if defined(_OPENMP) && _OPENMP >= 201811
  #pragma omp begin declare variant match(device={kind(host)})
  static inline int omp_is_initial_device(void) { return 1; }
  #pragma omp end declare variant
  #pragma omp begin declare variant match(device={kind(nohost)})
  static inline int omp_is_initial_device(void) { return 0; }
  #pragma omp end declare variant
#endif

whose use of match causes a compilation error if included after
Rinternals.h. 'Writing R Extensions' presents various workarounds, the
main one being the strong advice to include system headers before R headers.

Please correct before 2021-09-21 to safely retain your package on CRAN.
@mattdowle mattdowle added this to the 1.14.1 milestone Aug 31, 2021
@MichaelChirico
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I guess it's release time then? unless we plan to just patch this in quickly

@mattdowle
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yep, release time

@zkamvar zkamvar mentioned this issue Sep 4, 2021
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@MichaelChirico MichaelChirico mentioned this issue Sep 22, 2021
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@mattdowle
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Thanks to Prof Ripley he provided a patch :

I have attached the patch I used to get data.table to install with
clang-13. Hope it helps.

If I had compiled code as complicated as yours I would consider using
R_NO_REMAP and adding Rf_ prefixes in the code.

data.table.patch.txt

@mattdowle mattdowle mentioned this issue Sep 22, 2021
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@mattdowle mattdowle modified the milestones: 1.14.3, 1.14.1 Sep 22, 2021
@mattdowle
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mattdowle commented Sep 23, 2021 •
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From Prof Ripley :

This is still open for

AMORE BNN OpenMPController RandomFields RandomFieldsUtils data.table
graphscan influenceR likeLTD mnlogit spBayes unfoldr

This is a final reminder: the archival process will start on Sep 25.

@mattdowle
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mattdowle commented Sep 27, 2021 •
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Owing to the deadline, v1.14.2 is now on CRAN which is a manual minimal patch of v1.14.0. The change to as.character.hexmode() in R-devel 6 days ago was caught that day (thanks to GitLab CI) and fix included before submitting 5 days ago.

netbsd-srcmastr pushed a commit to NetBSD/pkgsrc that referenced this issue Jan 25, 2024
(textproc/R-data.table) Updated 1.14.0 to 1.14.10
248f5f4 
# data.table [v1.14.10](https://github.com/Rdatatable/data.table/milestone/20)

## NOTES

1. Maintainer of the package for CRAN releases is from now on Tyson
  Barrett (@TysonStanley),
  [#5710](Rdatatable/data.table#5710).

2. Updated internal code for breaking change of `is.atomic(NULL)` in
  R-devel,
  [#5691](Rdatatable/data.table#5691). Thanks to
  Martin Maechler for the patch.

3. Fix multiple test concerning coercion to missing complex numbers,
  [#5695](Rdatatable/data.table#5695) and
  [#5748](Rdatatable/data.table#5748). Thanks
  to @MichaelChirico and @ben-schwen for the patches.

4. Fix multiple format warnings (e.g., -Wformat)
  [#5712](Rdatatable/data.table#5712),
  [#5781](Rdatatable/data.table#5781),
  [#5880](Rdatatable/data.table#5800),
  [#5786](Rdatatable/data.table#5786). Thanks to
  @MichaelChirico and @jangorecki for the patches.



# data.table [v1.14.8](https://github.com/Rdatatable/data.table/milestone/28?closed=1)  (17 Feb 2023)

## NOTES

1. Test 1613.605 now passes changes to `as.data.frame()` in R-devel,
  [#5597](Rdatatable/data.table#5597). Thanks to
  Avraham Adler for reporting.

2. An out of bounds read when combining non-equi join with `by=.EACHI`
  has been found and fixed thanks to clang ASAN,
  [#5598](Rdatatable/data.table#5598). There
  was no bug or consequence because the read was followed (now preceded)
  by a bounds test.

3. `.rbind.data.table` (note the leading `.`) is no longer exported
  when `data.table` is installed in R>=4.0.0 (Apr 2020),
  [#5600](Rdatatable/data.table#5600). It was
  never documented which R-devel now detects and warns about. It is only
  needed by `data.table` internals to support R<4.0.0; see note 1 in
  v1.12.6 (Oct 2019) below in this file for more details.


# data.table [v1.14.6](https://github.com/Rdatatable/data.table/milestone/27?closed=1)  (16 Nov 2022)

## BUG FIXES

1. `fread()` could leak memory,
  [#3292](Rdatatable/data.table#3292). Thanks
  to @patrickhowerter for reporting, and Jim Hester for the fix. The fix
  requires R 3.4.0 or later. Loading `data.table` in earlier versions
  now highlights this issue on startup, asks users to upgrade R, and
  warns that we intend to upgrade `data.table`'s dependency from 8 year
  old R 3.1.0 (April 2014) to 5 year old R 3.4.0 (April 2017).

## NOTES

1. Test 1962.098 has been modified to pass latest changes to `POSIXt`
  in R-devel.

2. `test.data.table()` no longer creates `DT` in `.GlobalEnv`, a CRAN
  policy violation,
  [#5514](Rdatatable/data.table#5514). No
  other writes occurred to `.GlobalEnv` and release procedures have been
  improved to prevent this happening again.

3. The memory usage of the test suite has been halved,
  [#5507](Rdatatable/data.table#5507).


# data.table [v1.14.4](https://github.com/Rdatatable/data.table/milestone/26?closed=1)  (17 Oct 2022)

## NOTES

1. gcc 12.1 (May 2022) now detects and warns about an always-false
  condition (`-Waddress`) in `fread` which caused a small efficiency
  saving never to be invoked,
  [#5476](Rdatatable/data.table#5476). Thanks to
  CRAN for testing latest versions of compilers.

2. `update.dev.pkg()` has been renamed `update_dev_pkg()` to get out
  of the way of the `stats::update` generic function,
  [#5421](Rdatatable/data.table#5421). This is a
  utility function which upgrades the version of `data.table` to the
  latest commit in development which has passed all tests. As such we
  don't expect any backwards compatibility concerns. Its manual page was
  causing an intermittent hang/crash from `R CMD check` on Windows-only
  on CRAN which we hope will be worked around by changing its name.

3. Internal C code now passes `-Wstrict-prototypes` to satisfy the
  warnings now displayed on CRAN,
  [#5477](Rdatatable/data.table#5477).

4. `write.csv` in R-devel no longer responds to
  `getOption("digits.secs")` for `POSIXct`,
  [#5478](Rdatatable/data.table#5478). This
  caused our tests of `fwrite(, dateTimeAs="write.csv")` to fail on
  CRAN's daily checks using latest daily R-devel. While R-devel
  discussion continues, and currently it seems like the change is
  intended with further changes possible, this `data.table` release
  massages our tests to pass on latest R-devel. The idea is to try to
  get out of the way of R-devel changes in this regard until the new
  behavior of `write.csv` is released and confirmed. Package updates are
  not accepted on CRAN if they do not pass the latest daily version of
  R-devel, even if R-devel changes after the package update is
  submitted. If the change to `write.csv()` stands, then a future
  release of `data.table` will be needed to make `fwrite(,
  dateTimeAs="write.csv")` match `write.csv()` output again in that
  future version of R onwards. If you use an older version of
  `data.table` than said future one in the said future version of R,
  then `fwrite(, dateTimeAs="write.csv")` may not match `write.csv()` if
  you are using `getOption("digits.secs")` too. However, you can always
  check that your installation of `data.table` works in your version of
  R on your platform by simply running `test.data.table()`
  yourself. Doing so would detect such a situation for you: test 1741
  would fail in this case. `test.data.table()` runs the entire suite of
  tests and is always available to you locally. This way you do not need
  to rely on our statements about which combinations of versions of R
  and `data.table` on which platforms we have tested and support; just
  run `test.data.table()` yourself. Having said that, because test 1741
  has been relaxed in this release in order to be accepted on CRAN to
  pass latest R-devel, this won't be true for this particular release in
  regard to this particular test.

    ```R
    $ R --vanilla
    R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
    > DF = data.frame(A=as.POSIXct("2022-10-01 01:23:45.012"))
    > options(digits.secs=0)
    > write.csv(DF)
    "","A"
    "1",2022-10-01 01:23:45
    > options(digits.secs=3)
    > write.csv(DF)
    "","A"
    "1",2022-10-01 01:23:45.012

    $ Rdevel --vanilla
    R Under development (unstable) (2022-10-06 r83040) -- "Unsuffered Consequences"
    > DF = data.frame(A=as.POSIXct("2022-10-01 01:23:45.012"))
    > options(digits.secs=0)
    > write.csv(DF)
    "","A"
    "1",2022-10-01 01:23:45.012
    ```

5. Many thanks to Kurt Hornik for investigating potential impact of a
  possible future change to `base::intersect()` on empty input,
  providing a patch so that `data.table` won't break if the change is
  made to R, and giving us plenty of notice,
  [#5183](Rdatatable/data.table#5183).

6. `datatable.[dll|so]` has changed name to `data_table.[dll|so]`,
  [#4442](Rdatatable/data.table#4442). Thanks to
  Jan Gorecki for the PR. We had previously removed the `.` since `.` is
  not allowed by the following paragraph in the Writing-R-Extensions
  manual. Replacing `.` with `_` instead now seems more consistent with
  the last sentence.

    > ... the basename of the DLL needs to be both a valid file name
      and valid as part of a C entry point (e.g. it cannot contain
      ‘.’): for portable code it is best to confine DLL names to be
      ASCII alphanumeric plus underscore. If entry point R_init_lib is
      not found it is also looked for with ‘.’ replaced by ‘_’.


# data.table [v1.14.2](https://github.com/Rdatatable/data.table/milestone/24?closed=1)  (27 Sep 2021)

## NOTES

1. clang 13.0.0 (Sep 2021) requires the system header `omp.h` to be
  included before R's headers,
  [#5122](Rdatatable/data.table#5122). Many
  thanks to Prof Ripley for testing and providing a patch file.
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clang 13 omp Rdatatable/data.table
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@mattdowle @MichaelChirico