[Rcpp-devel] Moving towards STRICT_R_HEADERS by default
Dirk Eddelbuettel
edd at debian.org
Tue Sep 18 02:40:11 CEST 2018
# Moving towards STRICT_R_HEADERS by default
## Summary
tl;dr: STRICT_R_HEADERS are a worthwhile change, and we want to make that
change in one year. If your package is affected, you should get
another email and we ask that you make the change within 12 months.
More details below.
## What is this about?
Recently Romain opened ticket #898 on Github about possibly adding the define
for STRICT_R_HEADERS by default. Please see the URL at
https://github.com/RcppCore/Rcpp/issues/898
for more discussion. In general, we are all in favour but there are some side
effects. Hence this email.
## Background
What does the change do? As a brief summary, this only hits two R include
files and, if set, omits the definitions from two header files in R_ext/,
namely RS.h and Constants.h. The definitions are (indented by two spaces)
#ifndef STRICT_R_HEADERS
#define R_PROBLEM_BUFSIZE 4096
/* Parentheses added for FC4 with gcc4 and -D_FORTIFY_SOURCE=2 */
#define PROBLEM {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf,
#define MESSAGE {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf,
#define ERROR ),error(R_problem_buf);}
#define RECOVER(x) ),error(R_problem_buf);}
#define WARNING(x) ),warning(R_problem_buf);}
#define LOCAL_EVALUATOR /**/
#define NULL_ENTRY /**/
#define WARN WARNING(NULL)
#endif
and
#ifndef STRICT_R_HEADERS
/* S-PLUS 3.x but not 5.x NULLs the pointer in the following */
#define Calloc(n, t) (t *) R_chk_calloc( (R_SIZE_T) (n), sizeof(t) )
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (R_SIZE_T)((n) * sizeof(t)) )
#define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL)
#endif
and
#ifndef STRICT_R_HEADERS
#define PI M_PI
#include <float.h> /* Defines the rest, at least in C99 */
#define SINGLE_EPS FLT_EPSILON
#define SINGLE_BASE FLT_RADIX
#define SINGLE_XMIN FLT_MIN
#define SINGLE_XMAX FLT_MAX
#define DOUBLE_DIGITS DBL_MANT_DIG
#define DOUBLE_EPS DBL_EPSILON
#define DOUBLE_XMAX DBL_MAX
#define DOUBLE_XMIN DBL_MIN
#endif
The second sets is easiest. Just replace Calloc / Realloc / Free (if you
really need it!) with R_Calloc / R_Realloc / R_Free. The third is easy too:
instead of PI use M_PI and so on. The first set is problematic and where I
have most often seen clashes (requiring change in include order, or `#undef
ERROR`, or, ...). But R itself has Rf_error, Rf_warning, ... And Rcpp itself
has Rcpp::stop() and Rcpp::warning() and more.
## What is the effect?
We ran full reverse depends check last weekend and found 62 packages failed
to compiled (but almost 1300 passes, 62 were skipped for various reasons).
The failing packages are list at the #898 issue ticket and below.
## What changes are needed?
The *really good news* is that the changes should be trivial:
- replace PI with M_PI
- replace DBL_EPSILON with DOUBLE_EPS
- replace Calloc with R_Calloc
and so on.
If you really cannot / do not want to make the change, define
#RCPP_NO_STRICT_HEADERS
before #include <Rcpp.h> and things will be as before. Otherwise we plan to
make this a new default in twelve months.
## How can you test things?
In your package, please just add the line `#define STRICT_R_HEADERS` before
including Rcpp.h, ie use (ignore the twp space indent)
#define STRICT_R_HEADERS
#include <Rcpp.h>
or, even simpler, set -DSTRICT_R_HEADERS in eg CXXFLAGS in ~/.R/Makevars.
## How can you override things?
Define RCPP_NO_STRICT_R_HEADERS and things will remain as they are.
You can do that locally in you compiler-flags for now, and in your package in
either its compiler flags (ie src/Makevars and src/Makevars.win) or your
headers if you do not want to change your code to work with STRICT_R_HEADERS.
However, we feel working with STRICT_R_HEADERS is an improvement so we
suggest you set it now and work out the (likely few and simple) compilation
errors.
## Details logs
Below is a collated grep run finding the first (and hence NOT EXHAUSTIVE)
failure per package.
** CorReg :
BicLoc_cpp.cpp:70:53: error: ‘PI’ was not declared in this scope
** CoxPlus :
coxReg.cpp:333:84: error: ‘DBL_MAX’ was not declared in this scope
coxReg.cpp:415:16: error: ‘DBL_MAX’ was not declared in this scope
coxReg.cpp:426:16: error: ‘DBL_MAX’ was not declared in this scope
coxReg.cpp:943:16: error: ‘DBL_MAX’ was not declared in this scope
** DGM :
dlmlpl.cpp:106:64: error: ‘PI’ was not declared in this scope
** EMVS :
functions.cpp:20:30: error: ‘PI’ was not declared in this scope
functions.cpp:27:37: error: ‘PI’ was not declared in this scope
functions.cpp:142:23: error: ‘PI’ was not declared in this scope
** ETAS :
fitMP.cpp:2107:28: error: ‘DBL_MAX’ was not declared in this scope
** GAS :
snorm.cpp:14:45: error: ‘PI’ was not declared in this scope
snorm.cpp:26:23: error: ‘PI’ was not declared in this scope
snorm.cpp:37:28: error: ‘PI’ was not declared in this scope
snorm.cpp:52:26: error: ‘PI’ was not declared in this scope
snorm.cpp:64:26: error: ‘PI’ was not declared in this scope
snorm.cpp:146:28: error: ‘PI’ was not declared in this scope
** Gmisc :
Gmisc_lines.cpp:107:20: error: ‘FLT_EPSILON’ was not declared in this scope
** HardyWeinberg :
SNPHWEX.cpp:84:21: error: ‘DBL_MAX’ was not declared in this scope
SNPHWEX.cpp:130:21: error: ‘DBL_MAX’ was not declared in this scope
SNPHWEX.cpp:360:21: error: ‘DBL_MAX’ was not declared in this scope
SNPHWEX.cpp:421:21: error: ‘DBL_MAX’ was not declared in this scope
SNPHWEX.cpp:587:21: error: ‘DBL_MAX’ was not declared in this scope
** MAINT.Data :
msnCP_dev.h:8:26: error: ‘PI’ was not declared in this scope
msnCP_dev.cpp:8:29: error: ‘PI’ was not declared in this scope
msnCP_dev.cpp:41:36: error: ‘PI’ was not declared in this scope
msnCP_dev_grad.cpp:7:26: error: ‘PI’ was not declared in this scope
** MSGARCH :
Utils.h:8:28: error: ‘DBL_MIN’ was not declared in this scope
** MultiFit :
singleFisher.cpp:25:19: error: ‘DBL_MIN’ was not declared in this scope
singleFisher.cpp:30:37: error: ‘DBL_MIN’ was not declared in this scope
** PAFit :
Cpp_code.cpp:751:41: error: ‘DBL_EPSILON’ was not declared in this scope
Cpp_code.cpp:969:17: error: ‘LDBL_EPSILON’ was not declared in this scope
** ReIns :
SpliceEM_Mstep.cpp:192:13: error: ‘DBL_MAX’ was not declared in this scope
SpliceEM_Mstep.cpp:200:17: error: ‘DBL_MAX’ was not declared in this scope
SpliceEM_Mstep.cpp:270:11: error: ‘DBL_MAX’ was not declared in this scope
SpliceEM_Mstep.cpp:278:15: error: ‘DBL_MAX’ was not declared in this scope
** basad :
utiliti.cpp:36:17: error: ‘PI’ was not declared in this scope
** bayesImageS :
smcPotts.cpp:343:17: error: ‘DBL_EPSILON’ was not declared in this scope
** bcp :
MCMC.h:119:16: error: ‘DBL_MAX’ was not declared in this scope
MCMC.h:135:16: error: ‘DBL_MAX’ was not declared in this scope
Cbcp.cpp:134:15: error: ‘DBL_MAX’ was not declared in this scope
** bfa :
bfa_common.cpp:25:15: error: ‘DBL_MAX’ was not declared in this scope
** bigReg :
map_reg.cpp:53:16: error: ‘DBL_EPSILON’ was not declared in this scope
** biglasso :
binomial_hsr.cpp:6:9: error: ‘Free’ was not declared in this scope
binomial_hsr.cpp:162:31: error: ‘Calloc’ was not declared in this scope
** bigmemory :
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:34:18: error: ‘FLT_MIN’ was not declared in this scope
../inst/include/bigmemory/bigmemoryDefines.h:35:20: error: ‘FLT_MAX’ was not declared in this scope
** binnednp :
gaussian_mise_201708_trsf.cpp:40:46: error: ‘PI’ was not declared in this scope
** biwavelet :
rcpp_wt_bases_morlet.cpp:4:28: error: ‘PI’ was not declared in this scope
** blockmodels :
models/gaussian.h:292:71: error: ‘PI’ was not declared in this scope
models/gaussian.h:366:67: error: ‘PI’ was not declared in this scope
models/gaussian_multivariate.h:302:93: error: ‘PI’ was not declared in this scope
models/gaussian_multivariate.h:390:91: error: ‘PI’ was not declared in this scope
models/gaussian_multivariate_independent.h:300:79: error: ‘PI’ was not declared in this scope
models/gaussian_multivariate_independent.h:381:79: error: ‘PI’ was not declared in this scope
models/gaussian_multivariate_independent_homoscedastic.h:293:88: error: ‘PI’ was not declared in this scope
models/gaussian_multivariate_independent_homoscedastic.h:373:86: error: ‘PI’ was not declared in this scope
models/gaussian_covariates.h:383:71: error: ‘PI’ was not declared in this scope
models/gaussian_covariates.h:431:71: error: ‘PI’ was not declared in this scope
models/gaussian_covariates.h:478:69: error: ‘PI’ was not declared in this scope
** castor :
phylogenetics_cpp_routines.cpp:1559:67: error: ‘PI’ was not declared in this scope
** cbinom :
cbinom.cpp:5:20: error: ‘DBL_EPSILON’ was not declared in this scope
** circumplex :
circular.cpp:18:11: error: ‘DBL_EPSILON’ was not declared in this scope
circular.cpp:31:20: error: ‘PI’ was not declared in this scope
circular.cpp:34:12: error: ‘PI’ was not declared in this scope
circular.cpp:43:20: error: ‘PI’ was not declared in this scope
circular.cpp:48:37: error: ‘DBL_EPSILON’ was not declared in this scope
circular.cpp:66:21: error: ‘PI’ was not declared in this scope
** emIRT :
calcLB.cpp:86:46: error: ‘PI’ was not declared in this scope
** extraDistr :
wald-distribution.cpp:40:27: error: ‘PI’ was not declared in this scope
** fDMA :
tvpcpp.cpp:31:54: error: ‘PI’ was not declared in this scope
** facilitation :
Random.cpp:29:25: error: ‘PI’ was not declared in this scope
** fastGHQuad :
lib.cpp:331:49: error: ‘PI’ was not declared in this scope
lib.cpp:358:21: error: ‘PI’ was not declared in this scope
** fasteraster :
raster2vector.cpp:25:17: error: ‘DBL_MAX’ was not declared in this scope
raster2vector.cpp:25:17: error: ‘DBL_MAX’ was not declared in this scope
raster2vector.cpp:350:17: error: ‘PI’ was not declared in this scope
raster2vector.cpp:352:17: error: ‘PI’ was not declared in this scope
raster2vector.cpp:25:17: error: ‘DBL_MAX’ was not declared in this scope
raster2vector.cpp:25:17: error: ‘DBL_MAX’ was not declared in this scope
** frailtySurv :
distributions.cpp:217:38: error: ‘PI’ was not declared in this scope
distributions.cpp:225:35: error: ‘PI’ was not declared in this scope
distributions.cpp:234:61: error: ‘PI’ was not declared in this scope
distributions.cpp:335:25: error: ‘PI’ was not declared in this scope
distributions.cpp:342:35: error: ‘PI’ was not declared in this scope
distributions.cpp:354:11: error: ‘PI’ was not declared in this scope
distributions.cpp:459:24: error: ‘PI’ was not declared in this scope
** gcKrig :
gcgcFun.cpp:34:14: error: ‘DOUBLE_EPS’ was not declared in this scope
gcgcFun.cpp:40:47: error: ‘EPS1’ was not declared in this scope
gcgcFun.cpp:85:14: error: ‘DOUBLE_EPS’ was not declared in this scope
gcgcFun.cpp:100:45: error: ‘EPS1’ was not declared in this scope
gcgcFun.cpp:163:56: error: ‘EPS1’ was not declared in this scope
** geogrid :
minimal-assignment.cpp:407:21: error: ‘DBL_MAX’ was not declared in this scope
** glmBfp :
./types.h:53:32: error: ‘DOUBLE_EPS’ was not declared in this scope
./functionWraps.h:176:17: error: ‘DBL_MAX’ was not declared in this scope
** icenReg :
icenReg_files/basicUtilities.cpp:149:37: error: ‘PI’ was not declared in this scope
** lidR :
C_grid_canopy.cpp:58:31: error: ‘PI’ was not declared in this scope
** lpme :
lpme_common.cpp:45:30: error: ‘PI’ was not declared in this scope
lpme_common.cpp:111:51: error: ‘PI’ was not declared in this scope
lpme_common.cpp:150:51: error: ‘PI’ was not declared in this scope
** mcmcse :
msvec.cpp:16:21: error: ‘PI’ was not declared in this scope
** medfate :
PenmanMonteith.cpp:21:41: error: ‘PI’ was not declared in this scope
** meteoland :
radiation.cpp:56:40: error: ‘PI’ was not declared in this scope
radiation.cpp:76:19: error: ‘PI’ was not declared in this scope
radiation.cpp:98:46: error: ‘PI’ was not declared in this scope
radiation.cpp:136:19: error: ‘PI’ was not declared in this scope
radiation.cpp:187:40: error: ‘PI’ was not declared in this scope
radiation.cpp:228:40: error: ‘PI’ was not declared in this scope
radiation.cpp:291:63: error: ‘PI’ was not declared in this scope
radiation.cpp:344:16: error: ‘PI’ was not declared in this scope
** minimaxdesign :
kmeanspso.cpp:89:23: error: ‘DBL_MAX’ was not declared in this scope
kmeanspso.cpp:267:24: error: ‘DBL_MAX’ was not declared in this scope
** multdyn :
dlmlpl.cpp:106:64: error: ‘PI’ was not declared in this scope
** mwaved :
mwaved.cpp:2736:49: error: ‘DBL_EPSILON’ was not declared in this scope
** netdiffuseR :
plot.cpp:403:90: error: ‘PI’ was not declared in this scope
plot.cpp:481:20: error: ‘PI’ was not declared in this scope
** nngeo :
distance.cpp:15:22: error: ‘PI’ was not declared in this scope
** npsf :
nllpk/simplexMethod.cpp:260:21: error: ‘DBL_MAX’ was not declared in this scope
nllpk/simplexMethod.cpp:564:18: error: ‘DBL_MAX’ was not declared in this scope
** packcircles :
pmenzel_circle_pack.cpp:182:28: error: ‘FLT_MAX’ was not declared in this scope
** partialCI :
cfit.cc:179:41: error: ‘PI’ was not declared in this scope
cfit.cc:211:66: error: ‘PI’ was not declared in this scope
** pense :
InitialEstimator.cpp:185:21: error: ‘DBL_MAX’ was not declared in this scope
** precrec :
calc_uauc.cpp:26:14: error: ‘DBL_MIN’ was not declared in this scope
calc_uauc.cpp:28:14: error: ‘DBL_MAX’ was not declared in this scope
** recmap :
../inst/include/recmap.h:114:35: error: ‘PI’ was not declared in this scope
../inst/include/recmap.h:126:35: error: ‘PI’ was not declared in this scope
../inst/include/recmap.h:138:43: error: ‘PI’ was not declared in this scope
../inst/include/recmap.h:150:39: error: ‘PI’ was not declared in this scope
../inst/include/recmap.h:384:38: error: ‘PI’ was not declared in this scope
** rmgarch :
ica.cpp:38:45: error: ‘PI’ was not declared in this scope
** robustlmm :
fastGHQuad.cpp:356:49: error: ‘PI’ was not declared in this scope
fastGHQuad.cpp:383:21: error: ‘PI’ was not declared in this scope
** rococo :
rcor_exacttest.cpp:142:29: error: ‘DBL_EPSILON’ was not declared in this scope
** rotations :
CppBayesFunctions.cpp:37:28: error: ‘PI’ was not declared in this scope
CppBayesFunctions.cpp:52:30: error: ‘PI’ was not declared in this scope
CppBayesFunctions.cpp:76:33: error: ‘PI’ was not declared in this scope
CppBayesFunctions.cpp:110:17: error: ‘PI’ was not declared in this scope
CppBayesFunctions.cpp:129:30: error: ‘PI’ was not declared in this scope
CppBayesFunctions.cpp:153:33: error: ‘PI’ was not declared in this scope
CppBayesFunctions.cpp:199:15: error: ‘PI’ was not declared in this scope
CppBayesFunctions.cpp:360:26: error: ‘PI’ was not declared in this scope
** rtdists :
CDF_st0_variability.h:126:20: error: ‘DBL_MAX’ was not declared in this scope
** serrsBayes :
mixVoigt.cpp:34:18: error: ‘PI’ was not declared in this scope
mixVoigt.cpp:44:25: error: ‘PI’ was not declared in this scope
mixVoigt.cpp:73:85: error: ‘PI’ was not declared in this scope
mixVoigt.cpp:99:50: error: ‘PI’ was not declared in this scope
mixVoigt.cpp:136:165: error: ‘PI’ was not declared in this scope
mixVoigt.cpp:252:37: error: ‘PI’ was not declared in this scope
** unmarked :
nll_distsamp.cpp:25:22: error: ‘DOUBLE_XMIN’ was not declared in this scope
** updog :
betabinom.cpp:5:21: error: ‘DBL_EPSILON’ was not declared in this scope
** vegclust :
trajectories.cpp:94:38: error: ‘PI’ was not declared in this scope
In case of question please discuss on the rcpp-devel list.
Thanks,
Dirk
on behalf of the RcppCore team
--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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