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USE_NO_REMAP
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@zhengxwen
zhengxwen committed Sep 29, 2024
1 parent 640748c commit 18c170d
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
Package: HIBAG
Type: Package
Title: HLA Genotype Imputation with Attribute Bagging
Version: 1.40.1
Date: 2024-05-07
Version: 1.41.2
Date: 2024-09-29
Depends: R (>= 3.2.0)
Imports: methods, RcppParallel
Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr,
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5 changes: 4 additions & 1 deletion NEWS
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
CHANGES IN VERSION 1.41.1
CHANGES IN VERSION 1.41.2
-------------------------

o the input of `hlaUniqueAllele()` can be a hlaAttrBagClass object or
Expand All @@ -7,6 +7,9 @@ CHANGES IN VERSION 1.41.1
o `hlaAlleleToVCF()` outputs 0 instead of NaN if the location of HLA gene
is unknown or unspecified

o update the C codes according to '_R_USE_STRICT_R_HEADERS_=true' &
'_R_CXX_USE_NO_REMAP_=true'


CHANGES IN VERSION 1.40.0
-------------------------
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54 changes: 27 additions & 27 deletions src/HIBAG.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -333,9 +333,9 @@ SEXP HIBAG_AlleleStrand(SEXP allele1, SEXP afreq1, SEXP I1,
out_flag[i] = switch_flag;
}

SET_ELEMENT(rv_ans, 1, ScalarInteger(out_n_stand_amb));
SET_ELEMENT(rv_ans, 2, ScalarInteger(out_n_mismatch));
SET_ELEMENT(rv_ans, 3, ScalarInteger(out_n_swap_stand));
SET_ELEMENT(rv_ans, 1, Rf_ScalarInteger(out_n_stand_amb));
SET_ELEMENT(rv_ans, 2, Rf_ScalarInteger(out_n_mismatch));
SET_ELEMENT(rv_ans, 3, Rf_ScalarInteger(out_n_swap_stand));
UNPROTECT(2);

CORE_CATCH
Expand All @@ -345,7 +345,7 @@ SEXP HIBAG_AlleleStrand(SEXP allele1, SEXP afreq1, SEXP I1,
SEXP HIBAG_AlleleStrand2(SEXP allele1, SEXP allele2)
{
if (XLENGTH(allele1) != XLENGTH(allele2))
error("'allele1' and 'allele2' should have the same length.");
Rf_error("'allele1' and 'allele2' should have the same length.");

CORE_TRY
// initialize: A-T pair, C-G pair
Expand Down Expand Up @@ -466,10 +466,10 @@ static void model_free(SEXP ptr_obj)

static SEXP new_model_id(int id, CAttrBag_Model *mod_ptr)
{
SEXP ans = PROTECT(ScalarInteger(id));
SEXP ans = PROTECT(Rf_ScalarInteger(id));
SEXP ptr = PROTECT(R_MakeExternalPtr(mod_ptr, R_NilValue, R_NilValue));
R_RegisterCFinalizerEx(ptr, model_free, (Rboolean)TRUE);
Rf_setAttrib(ans, install("handle_ptr"), ptr);
Rf_setAttrib(ans, Rf_install("handle_ptr"), ptr);
UNPROTECT(2);
return ans;
}
Expand All @@ -487,13 +487,13 @@ SEXP HIBAG_New(SEXP nSamp, SEXP nSNP, SEXP nHLA)
{
int n_samp = Rf_asInteger(nSamp);
if (n_samp <= 0)
error("Invalid number of samples: %d.", n_samp);
Rf_error("Invalid number of samples: %d.", n_samp);
int n_snp = Rf_asInteger(nSNP);
if (n_snp <= 0)
error("Invalid number of SNPs: %d.", n_snp);
Rf_error("Invalid number of SNPs: %d.", n_snp);
int n_hla = Rf_asInteger(nHLA);
if (n_hla <= 0)
error("Invalid number of unique HLA alleles: %d.", n_hla);
Rf_error("Invalid number of unique HLA alleles: %d.", n_hla);
CORE_TRY
int id = _Need_New_HIBAG_Model();
CAttrBag_Model *obj = _HIBAG_MODELS_[id] = new CAttrBag_Model;
Expand All @@ -519,13 +519,13 @@ SEXP HIBAG_Training(SEXP nSNP, SEXP nSamp, SEXP snp_geno, SEXP nHLA,
{
int n_samp = Rf_asInteger(nSamp);
if (n_samp <= 0)
error("Invalid number of samples: %d.", n_samp);
Rf_error("Invalid number of samples: %d.", n_samp);
int n_snp = Rf_asInteger(nSNP);
if (n_snp <= 0)
error("Invalid number of SNPs: %d.", n_snp);
Rf_error("Invalid number of SNPs: %d.", n_snp);
int n_hla = Rf_asInteger(nHLA);
if (n_hla <= 0)
error("Invalid number of unique HLA alleles: %d.", n_hla);
Rf_error("Invalid number of unique HLA alleles: %d.", n_hla);
CORE_TRY
int id = _Need_New_HIBAG_Model();
CAttrBag_Model *obj = _HIBAG_MODELS_[id] = new CAttrBag_Model;
Expand Down Expand Up @@ -820,9 +820,9 @@ SEXP HIBAG_NewClassifierHaplo(SEXP model, SEXP snpidx,
int midx = Rf_asInteger(model);
int nHaplo = Rf_length(freq);
if (nHaplo != Rf_length(hla))
error("Invalid length of 'hla'.");
Rf_error("Invalid length of 'hla'.");
if (nHaplo != Rf_length(haplo))
error("Invalid length of 'haplo'.");
Rf_error("Invalid length of 'haplo'.");
double Acc = Rf_isNull(acc) ? 0.0 : Rf_asReal(acc);

CORE_TRY
Expand Down Expand Up @@ -867,7 +867,7 @@ SEXP HIBAG_GetNumClassifiers(SEXP model)
int midx = Rf_asInteger(model);
CORE_TRY
_Check_HIBAG_Model(midx);
rv_ans = ScalarInteger(_HIBAG_MODELS_[midx]->ClassifierList().size());
rv_ans = Rf_ScalarInteger(_HIBAG_MODELS_[midx]->ClassifierList().size());
CORE_CATCH
}

Expand Down Expand Up @@ -930,7 +930,7 @@ SEXP HIBAG_GetClassifierList(SEXP model, SEXP hla_str)
for (size_t i=0; i < nHaplo; i++)
{
SET_STRING_ELT(haplo, i,
mkChar(Haplo.List[i].HaploToStr(nsnp).c_str()));
Rf_mkChar(Haplo.List[i].HaploToStr(nsnp).c_str()));
}

// convert to data.frame
Expand All @@ -949,7 +949,7 @@ SEXP HIBAG_GetClassifierList(SEXP model, SEXP hla_str)
for (size_t i=0; i < I.size(); i++) p[i] = I[i] + 1;
}
{ // outofbag.acc
SET_ELEMENT(lst, 3, ScalarReal(M.OutOfBag_Accuracy()));
SET_ELEMENT(lst, 3, Rf_ScalarReal(M.OutOfBag_Accuracy()));
}
}
UNPROTECT(1);
Expand Down Expand Up @@ -1076,7 +1076,7 @@ SEXP HIBAG_BEDFlag(SEXP bedfn)
file.read(prefix, 3);
if ((prefix[0] != 0x6C) || (prefix[1] != 0x1B))
throw ErrHLA("Invalid prefix in the PLINK BED file.");
rv_ans = ScalarInteger((unsigned char)prefix[2]);
rv_ans = Rf_ScalarInteger((unsigned char)prefix[2]);
CORE_CATCH
}

Expand Down Expand Up @@ -1200,7 +1200,7 @@ SEXP HIBAG_SeqMerge(SEXP seq)
{
const int len = XLENGTH(seq);
if (len <= 0)
error("Internal error in 'HIBAG_SeqMerge()'.");
Rf_error("Internal error in 'HIBAG_SeqMerge()'.");
// get the maximum length
int nmax = -1;
for (int i=0; i < len; i++)
Expand All @@ -1226,7 +1226,7 @@ SEXP HIBAG_SeqMerge(SEXP seq)
for (; j < nmax; j++) ss[j] = '*';
}
// output
return mkString(ss.c_str());
return Rf_mkString(ss.c_str());
} else
return Rf_ScalarString(NA_STRING);
}
Expand Down Expand Up @@ -1267,10 +1267,10 @@ SEXP HIBAG_SeqRmDot(SEXP ref, SEXP seq)
if (*s != '.')
ss.push_back(*p);
}
SET_STRING_ELT(seq, i, mkChar(ss.c_str()));
SET_STRING_ELT(seq, i, Rf_mkChar(ss.c_str()));
}
// set
SET_STRING_ELT(ref, 0, mkChar(ref_str.c_str()));
SET_STRING_ELT(ref, 0, Rf_mkChar(ref_str.c_str()));
UNPROTECT(2);
}

Expand Down Expand Up @@ -1364,7 +1364,7 @@ SEXP HIBAG_Kernel_Version()
// CPU information
SEXP info = NEW_CHARACTER(3);
SET_ELEMENT(ans, 1, info);
SET_STRING_ELT(info, 0, mkChar(CPU_Info()));
SET_STRING_ELT(info, 0, Rf_mkChar(CPU_Info()));
// compiler information
#ifdef __VERSION__
string version = __VERSION__;
Expand Down Expand Up @@ -1395,7 +1395,7 @@ SEXP HIBAG_Kernel_Version()
else
s = "Unknown compiler";
}
SET_STRING_ELT(info, 1, mkChar(s.c_str()));
SET_STRING_ELT(info, 1, Rf_mkChar(s.c_str()));
// supported implementation
s = "Algorithm SIMD:";
target_add(s, "SSE2", HIBAG_ALGORITHM_SSE2);
Expand All @@ -1405,7 +1405,7 @@ SEXP HIBAG_Kernel_Version()
target_add(s, "AVX512F", HIBAG_ALGORITHM_AVX512F);
target_add(s, "AVX512BW", HIBAG_ALGORITHM_AVX512BW);
target_add(s, "AVX512VPOPCNTDQ", HIBAG_ALGORITHM_AVX512VPOPCNTDQ);
SET_STRING_ELT(info, 2, mkChar(s.c_str()));
SET_STRING_ELT(info, 2, Rf_mkChar(s.c_str()));

// using Intel TBB or not
#if RCPP_PARALLEL_USE_TBB
Expand All @@ -1414,9 +1414,9 @@ SEXP HIBAG_Kernel_Version()
#else
int ntot = tbb::this_task_arena::max_concurrency();
#endif
SET_ELEMENT(ans, 2, ScalarInteger(ntot));
SET_ELEMENT(ans, 2, Rf_ScalarInteger(ntot));
#else
SET_ELEMENT(ans, 2, ScalarInteger(NA_INTEGER));
SET_ELEMENT(ans, 2, Rf_ScalarInteger(NA_INTEGER));
#endif
// output
UNPROTECT(1);
Expand Down

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