Moving towards defining STRICT_R_HEADERS in Rcpp.h #1158

eddelbuettel · 2021-04-25T21:29:34Z

As previously discussed in the (preliminary, unmerged) pull requests #613 and #615 as well as in issues #612 and (at much greater length) in issue #898, it is desirable for compilations of R extensions to define STRICT_R_HEADERS so that terms like ERROR or MESSAGE do not clash due to a redefinition, or that PI remains undefined, and of course so that Calloc(), Realloc() or Free() are not defined.

However, as the use of the definition has always been an opt-in, some packages have been making use of the definitions that would otherwise have been defined away -- so that we now cannot simply define it as they would then error. The issue ticket #898 discusses two attempts at quantifying just how extended the damage at CRAN would be: about 58 packages in late Sep 2018, about 62 packages in Jul 2019, and and around 51 earlier this month. Based on the earlier discussions some packages did make changes, and that is greatly appreciated.

And after some more discussion in #898 today, the time seems right to try to address this, one-by-one, in the affected packages. There is no rush: if this takes us six or eight or ten months, so be it. It would be nice to get it done, so let's try to make a start.

What follows is a list by package. The list may be wrong, and if a package is included by accident or error in our process we will remove it. The list may be incomplete: if we find other packages we will add them. Otherwise it will list the names of packages that did come up as failing to pass R CMD check when STRICT_R_HEADERS was defined by us, and the error is almost always one of an immediate failure to compile. A simple re-definition of the affected symbols will be the solution, and we will aim to provide pull requests as we go along. Help in that process would be appreciated.

So give this list, the suggested plan is to submit PRs. And then to follow-up as PRs are folded in addressing the issue, and to 'tick off' each package and maybe mark the version of the package containing the fix and PR. Let's see how it goes, and discuss below what we learn.

The text was updated successfully, but these errors were encountered:

Enchufa2 · 2021-04-25T22:24:25Z

As a preliminary task, I could adapt the code in 222a17b to download an analyze all these packages to produce a comprehensive list of files and line numbers containing any of these macros.

eddelbuettel · 2021-04-25T22:28:53Z

You could, but it is a royal pain to set a box up with all the build dependencies (see my comments to Duncan on r-package-devel today) and I do have one set up... I can also build on that box, so I am three patch sets in so it is fairly quick (on simple packages). But should we discuss that elsewhere to not dilute this issue ticket?

SebKrantz · 2021-05-01T20:14:02Z

I merged your pull request Dirk, although I'm not sure why you chose those 2 files, from your comment I presume because I was using DBL_MIN?

eddelbuettel · 2021-05-01T20:26:57Z

Great, thank you!

And yes it breaks without the PR I sent as you can check easily if you want: use e.g. the CRAN sources, add #define STRICT_R_HEADERS and it will fail because switching to STRICT_R_HEADERS no longer includes float.h (or, if one prefers C++ headers) cmath. Which ... strikes me as a bug in R for no longer including it but anyway...

The modern higher-end variant (if one is willing to use C++11 or newer) would be to use std::numeric_limits<double>::min(), maybe even in a constexpr just as we all could just 'compute' the value of \pi at compile-time with constexpr double pi = std::acos(-1);.

The changes I have sent to maintainers so far really were almost always one of these two:

PI changes to M_PI (as it has been in C headers since possibly Kernighan and Ritchie themselves, or so it feels to me)
including float.h or cfloat so that DBL_MIN and DBL_EPSILON are known; sometime also conversion from DOUBLE_EPS
so it really is not earth-shattering, and we'll all be better off as ERROR and MESSAGE and other definitions will be gone.

chkiefer · 2021-05-02T18:54:58Z

I merged the pull request. Thanks for all your work!

gforge · 2021-05-03T06:48:10Z

Gmisc merged, thanks! This was incredibly smooth, awesome work!

somakd · 2021-07-04T15:22:58Z

Thanks! fad has been updated (but not yet on CRAN as more feature are going to be included).

eddelbuettel · 2021-09-03T15:54:05Z

Same as above (as of 2021-09-03) but now sorted by state and name (case-insensitve) rather than chronologically:

activegp (1.0.5) -- not on GitHub, patch emailed 2021-04-25, ack from maintainer 2021-04-25, 'real soon', on CRAN 2021-11-30
basad (0.2.0) -- not on GitHub, patch emailed 2021-04-25; at qingdan/basad, pull request sent 2021-11-02, on CRAN 2021-11-17
bcf, not on GH, patch emailed 2021-06-10, on CRAN 2022-01-18
biglasso, at YaohuiZeng/biglasso, PR #40 filed 2021-06-10, merged 2022-01-06, removed from CRAN 2022-01-28
binnednp (0.4.0) -- not on GH, patch emailed 2021-04-27, removed from CRAN 2022-01-28
blockmodels, not on GH, patch emailed 2021-06-10, merged and on CRAN 2021-12-01, (and at jb-leger/blockmodels)
ClusPred, not at GH, patch emailed 2021-06-27, on CRAN 2021-12-02
compas (0.1) -- at wongswk/compass, PR #1 sent on 2021-04-29, merged 2022-01-08, on CRAN 2022-01-09
dfphase1 (1.1.3) -- not on GH, patch emailed 2021-04-29, on CRAN 2021-12-01
DGM, at schw4b/DGM, PR #14 filed 2021-06-10, merged and on CRAN 2021-12-05
emIRT (0.0.11) -- at kosukeimai/emIRT, PR #6 sent 2021-04-30. merged 2021-05-12, removed from CRAN 2022-01-28
EMVS, not on GH, patch emailed 2021-06-10, on CRAN 2021-10-13
eulerrr, at jolars/eulerr, PR #82 filed 2021-06-10, merged 2021-06-11
facilitation (0.5.2) -- at Lobz/facilitation and already fixed since 2018 (!!) via Lobz/facilitation@130ac76, removed from CRAN 2022-01-28
factorstochvol (1.0.0), at gregorkastner/factorstochvol, PR #10 files 2021-12-04. version 1.0.1 on CRAN 2021-12-06
fasteraster (1.1.1) -- not on GH, patch emailed 2021-05-01, removed from CRAN 2022-01-28
fctbases, at naolsen/fctbases, PR #1 filed 2021-06-10, merged 2021-08-13, removed from CRAN 2022-01-28
fddm, at rtdists/fddm, PR #2 filed 2021-08-11, heard back 2021-08-13, on CRAN 2021-12-13
FORTLS (1.0.2) -- at Molina-Valero/FORTLS, PR #2 filed 2021-05-01, applied to branch 2021-05-24, on CRAN 2021-09-03
frailtySurv (1.3.6) -- at vmonaco/frailtySurv, PR #8 filed 2021-05-01, merged 2021-05-04, on CRAN 2021-09-13
GAS, at LeopoldoCatania/GAS PR #14 filed 2021-06-11, removed from CRAN 2022-01-28
goffda, at egarpor/goffda, PR #5 filed 2021-06-12, merged 2021-06-26
GWmodel, not on GH, patch emailed 2021-06-13, heard back 2021-06-15: "asap", on CRAN 2021-10-09
HDTSA, at Linc2021/HDTSA, PR #1 filed 2021-06-13, merged 2021-06-28, on CRAN 2021-11-08
ideq, at eastonhuch/ideq, PR #1 filed 2021-06-13. merged 2021-11-23, removed from CRAN 2022-01-28
IFC (0.1.1) -- at gitdemont/IFC, PR #1 filed 2021-05-02, merged 2021-05-06, on CRAN 2021-10-13
ldsep, at dcgerard/ldsep, PR #5 filed 2021-06-13, merged 2021-06-14, on its way to CRAN 2021-08-10
MAINT.Data, not on GH, patch emailed 2021-08-11, on CRAN 2021-09-21
mcmcsae (0.6.0) -- not on GH, patch emailed 2021-05-03, heard back 2021-05-05, merged, on CRAN 2021-10-10
mcmcse, not on GH, patch emailed 2021-06-14
meshed, at mkln/meshed, PR #1 filed 2021-08-11, merged 2021-08-11, on CRAN 2021-10-05
MixMatrix, at gzt/MixMatrix, PR #1 filed 2021-08-11, merged 2021-09-25, on CRAN 2021-11-16
MNARclust, not at GH, patch emailed 2021-07-25, on CRAN 2021-12-02
MSGARCH, at keblu/MSGARCH, PR #71 filed 2021-08-12, merged 2021-08-16, on CRAN 2022-01-16
multdyn, at schw4bM/DGM, and same as above under DGM, package should be retired from CRAN; heard from maintainer 2021-12-05, off CRAN 2021-12-06
MultiFit, not on GH, patch emailed 2021-06-15, on CRAN 2022-01-18
oce (1.4-0) -- at dankelley/oce, PR #1822 filed 2021-05-04, merged 2021-05-05, on CRAN 2022-01-08
parglm, at boennecd/parglm, PR #11 filed 2021-06-15, merged and on CRAN 2021-10-14
partialAR, not on GH, patch emailed 2021-06-17, removed from CRAN 2022-01-28
partialCI (1.2.0) not on GH, patch emailed 2021-05-05, removed from CRAN 2022-01-28
PLFD, at gitee.com/xu-zc/PLFD, patch emailed 2021-08-19, on CRAN 2021-10-19
rcosmo (1.1.2) at frycast/rcosmo, PR #3 filed 2021-05-06, merged 2021-05-10, on CRAN 2021-12-01
sdetorus, at egarpor/sdetorus, PR #5 filed 2021-06-17, merged 2021-06-26
spaMM, not on GH, patch emailed 2021-08-12, replied 2021-08-13, "likely September", on CRAN 2021-09-13
spamtree, at mkln/spamtree, PR 1 filed 2021-08-12, merged 2021-08-12, version 0.2.2 on CRAN 2021-1207
supc (0.2.2) at wush978/supc, PR #33 filed 2021-05-08, on CRAN 2021-09-22
survival.svb (0.0.1) at mkomod/survival.svb, PR #1 filed 2022-01-04, meged 2022-01-05, on CRAN 2022-01-17
atakrig (0.9.7) -- ~~not on GitHub~~ at maoguihu/atakrig, patch emailed 2021-04-25, PR #1 send 2021-04-26 too, ack from maintainer 2021-04-26, 'soon', 0.9.8 on CRAN 2021-04-30
Benchmarking (0.29) -- not on GitHub, patch emailed 2021-04-26, ack from maintainer 2021-04-26, 'done locally', 'CRAN later...'
BGVAR (2.1.5) -- at mboeck11/BGVAR (2.2.0), PR #4 sent 2021-04-26, merged 2021-04-26
bigmemory (4.5.36) -- at kaneplusplus/bigmemory, PR #104 sent 2021-04-26, merged 2021-06-14
biwavelet (0.20.19) -- at tgouhier/biwavelet, PR #96 sent 2021-04-27; heard back via email 2021-05-24, merged, "upload soon", on CRAN 2021-05-26
blatent (0.1.1) -- at jonathantemplin/blatent, PR #1 sent 2021-04-27, heard via email 2021-05-24, "soon"
CARlasso, at YunyiShen/CAR-LASSO, PR #6 filed 2021-07-25, merged 2021-07-31, on CRAN in 0.1.2
cbinom (1.5) -- not on GH, patch emailed 2021-04-27, heard back 2021-04-27 "soon", on CRAN 2021-04-28
circumplex (0.3.6) -- at jmgirard/circumplex, PR #13 sent on 2021-04-28, merged 2021-04-28, on CRAN 2021-05-28
collapse (1.5.3) -- at SebKrantz/collapse, PR #149 sent on 2021-04-29; merged 2021-05-01
fad (0.3-3) -- at somakd/fad, PR #4 filed 2021-04-30, merged 2021-07-04
fixest (0.8.4) -- at lrberge/fixest, PR #138 filed 2021-05-01, merged 2021-05-01
fracture (0.1.2) -- at rossellhayes/fracture, PR #1 filed 2021-05-01, merged 2021-05-24
gcKrig, not on GH, patch emailed 2021-06-11, heard back 2021-06-14: "soon"
gfilmm, at stla/gfilmm, PR #1 filed 2021-06-12, merged 2021-06-25
Gmisc (2.0.1) -- at gforge/Gmisc, PR #55 filed 2021-05-02, merged 2021-05-03, on CRAN 2021-05-04
huge (1.3.4.1) -- at HMJiangGatech/huge, PR #14 filed 2021-05-02, merged 2021-05-24, CRAN "soon"
jackalope, at lucasnell/jackalope, PR #15 filed 2021-06-13, merged 2021-06-14
lavacreg (0.1-1) -- at chkiefer/lavacreg, PR #1 filed 2021-05-02, merged 2021-05-02, on CRAN 2021-08-19
lme4, at lme4/lme4, PR #633 filed 2021-06-16, merged 2021-06-16
lpme, not on GH, patch emailed 2021-06-14
matrixprofiler (0.1.4) -- at matrix-profile-foundation/matrixprofiler, PR #15 filed 2021-05-03; email back 2021-05-23 'merge and CRAN soon', on CRAN 2021-05-26
medfate (1.1.0) -- ~~not on GH~~ at vegmod/medfate, patch emailed 2021-05-03, heard back 2021-05-04, merged
metapack at daeyounglim/metapack, PR #1 files 2021-06-14, merged 2021-06-16
minerva at rsamantha/minerva, PR #11 filed 2021-06-15
multivariance (2.4.0) -- not on GH, patch emailed 2021-05-03, on CRAN 2021-10-06
mwaved (1.1.7) -- at jrwishart/mwaved, PR #2 filed 2021-05-03, merged 2021-05-07
nnlib2Rcpp (0.1.6) -- at VNNikolaidis/nnlib2Rcpp, PR #11 file 2021-05-04, merged 2021-05-05, on CRAN 2021-05-05
npsf (0.8.0) -- not on GH, patch emailed 2021-05-10, heard back in email 2021-05-24: 'soon'
OpenMx (2.19.5) at OpenMx/OpenMx, PR #319 filed 2021-05-04, merged 2021-05-04
PAFit (1.0.1.8) at thongphamthe/PAFit, PR #3 filed 2021-05-05, merged 2021-05-11, on CRAN 2021-05-12
PoissonBinomial (1.2.3) not on GH, patch emailed 2021-05-05, heard back 2021-05-05, "soon"
precrec (0.12.5) at evalclass/precrec, PR #17 filed 2021-05-05, merged 2021-05-25
rayrender (0.21.2) at tylermorganwall/rayrender, PR #25 filed 2021-05-06, merged 2021-06-25
read.gt3x (1.0.2) at THLfi/read.gt3x, PR #39 filed 2021-05-06, merged 2021-11-16
recmap (1.0.7) at cpanse/recmap, PR #20 filed 2021-05-06, merged 2021-05-07, on CRAN 2021-05-10
RobustGaSP, not on GH, patch emailed 2021-06-15, heard back 2021-08-19, on CRAN 2021-09-02
robustlmm (2.4-3) at kollerma/robustlmm, PR #7 filed 2021-05-07, heard back via GH on 2021-05-24, merged, "soon to CRAN"
rpf (1.0.5) at jpritikin/rpf, PR #15 filed 2021-05-07, merged 2021-05-07, on CRAN 2021-08-11
rstpm2 (1.5.2) at mclements/rstpm2, PR #20 filed 2021-05-07, merged 2021-05-07
rtdists (0.11-2) at rtdists/rtdists, PR #14 filed 2021-05-07, merged 2021-05-12
RxODE, at nlmixrdevelopment/RxODE, PR #437 files 2021-06-20, merged 2021-06-21, on CRAN 2021-08-06
s2 (1.0.5) -- at r-spatial/s2, PR #118 filed 2021-06-02, merged 2021-06-02
serrsBayes, at mooresm/serrsBayes, PR #1 files 2021-06-15, merged 2021-06-18
shrinkTVP (2.0.1) not on GH, patch emailed 2021-05-08, on CRAN 2021-05-13
smam (0.5.4) at ChaoranHu/smam, PR #1 filed 2021-05-08, merged 2021-05-24
unmarked (1.0.1) -- at rbchan/unmarked, fixed by maintainer in PR #202

eddelbuettel · 2022-01-13T22:15:59Z

Rcpp 1.0.8 is now on CRAN with STRICT_R_HEADERS enabled (unless an override is set to prevent it and restore prior behaviour).

A sincere Thank You So Much! to everybody who updated their package with the patches or PR we supplied, and shipped an updated version to CRAN. Your help is truly appreciated.

eddelbuettel · 2022-01-29T02:33:15Z

The remaining un-updated packages were remove from CRAN by the CRAN maintainers earlier today.

The tranition is now complete -- nine months after we started. A big, big, Thank You! to everybody for helping along!

This was referenced Apr 28, 2021

STRICT_R_HEADERS rbchan/unmarked#201

Closed

Define STRICT_R_HEADERS and fix resulting problems rbchan/unmarked#202

Merged

eddelbuettel mentioned this issue Apr 28, 2021

define STRICT_R_HEADERS, include float.h, adjust dbl eps constant jmgirard/circumplex#13

Merged

RobinHankin referenced this issue in RobinHankin/clifford Apr 28, 2021

strict_r_headers

33fbb13

RobinHankin referenced this issue in RobinHankin/spray Apr 28, 2021

strict_r_headers

7426ea1

RobinHankin referenced this issue in RobinHankin/freealg Apr 28, 2021

strict_r_headers

c7a2277

RobinHankin referenced this issue in RobinHankin/mvp Apr 28, 2021

strict_r_headers

f13ac18

eddelbuettel mentioned this issue Jun 20, 2021

Support STRICT_R_HEADERS via R_{Calloc,Free} and DBL_EPSILON nlmixrdevelopment/RxODE#437

Merged

eddelbuettel mentioned this issue Jul 25, 2021

use DBL_EPSILON instead of DOUBLE_EPS to support STRICT_R_HEADERS YunyiShen/CAR-LASSO#6

Merged

This was referenced Oct 27, 2021

Eigen 3.4.0 RcppCore/RcppEigen#102

Merged

RcppEigen 0.3.4.0.0 preparations RcppCore/RcppEigen#103

Closed

eddelbuettel mentioned this issue Nov 7, 2021

Fix dim problem with arma::field inputs RcppCore/RcppArmadillo#352

Merged

eddelbuettel mentioned this issue Dec 4, 2021

Use DBL_EPSILON instead of DOUBLE_EPS to allow STRICT_R_HEADERS gregorkastner/factorstochvol#10

Merged

eddelbuettel mentioned this issue Dec 14, 2021

Use std::isnormal(), remove LazyData stla/gfilogisreg#1

Merged

eddelbuettel mentioned this issue Jan 5, 2022

use M_PI instead of PI to support STRICT_R_HEADERS mkomod/survival.svb#1

Merged

eddelbuettel mentioned this issue Jan 14, 2022

define STRICT_R_HEADERS to avoid definition of Free, ... #898

Closed

xihaoli mentioned this issue Jan 24, 2022

Compilation error xihaoli/STAAR#9

Closed

eddelbuettel closed this as completed Jan 29, 2022

tlangfor mentioned this issue Mar 17, 2022

Rcpp STRICT_R_HEADERS breaks installation yandorazhang/GENESISasian#1

Open

amcdavid mentioned this issue May 9, 2022

I did not install HurdleNormal in R 4.2.0 amcdavid/HurdleNormal#8

Closed

eddelbuettel mentioned this issue Jul 23, 2022

Enable unwind protection by default #1225

Merged

4 tasks

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Moving towards defining STRICT_R_HEADERS in Rcpp.h #1158

Moving towards defining STRICT_R_HEADERS in Rcpp.h #1158

eddelbuettel commented Apr 25, 2021 •

edited

Loading

Enchufa2 commented Apr 25, 2021

eddelbuettel commented Apr 25, 2021

SebKrantz commented May 1, 2021

eddelbuettel commented May 1, 2021

chkiefer commented May 2, 2021

gforge commented May 3, 2021

somakd commented Jul 4, 2021

eddelbuettel commented Sep 3, 2021 •

edited

Loading

eddelbuettel commented Jan 13, 2022

eddelbuettel commented Jan 29, 2022

Moving towards defining STRICT_R_HEADERS in Rcpp.h #1158

Moving towards defining STRICT_R_HEADERS in Rcpp.h #1158

Comments

eddelbuettel commented Apr 25, 2021 • edited Loading

Enchufa2 commented Apr 25, 2021

eddelbuettel commented Apr 25, 2021

SebKrantz commented May 1, 2021

eddelbuettel commented May 1, 2021

chkiefer commented May 2, 2021

gforge commented May 3, 2021

somakd commented Jul 4, 2021

eddelbuettel commented Sep 3, 2021 • edited Loading

eddelbuettel commented Jan 13, 2022

eddelbuettel commented Jan 29, 2022

eddelbuettel commented Apr 25, 2021 •

edited

Loading

eddelbuettel commented Sep 3, 2021 •

edited

Loading