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gnu: r-snpstats: Patch for compatibility with R 4.6.0.

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* gnu/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch,
gnu/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch: New files.
* gnu/local.mk (dist_patch_DATA): Record them.
* gnu/packages/bioconductor.scm (r-snpstats)[source]: Register patches.

Change-Id: I911f5833199448a16a23f9e715903a8427b08233
This commit is contained in:
Ricardo Wurmus
2026-04-27 11:49:35 +02:00
parent 4a3633caf5
commit e72baf6d34
4 changed files with 568 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files
gnu/local.mk
+2
View File
@@ -2351,6 +2351,8 @@ dist_patch_DATA = \
%D%/packages/patches/rdkit-unbundle-external-dependencies.patch \
%D%/packages/patches/r-biostrings-r4.6.0-compat.patch \
%D%/packages/patches/r-httpuv-1.6.6-unvendor-libuv.patch \
%D%/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch \
%D%/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch \
%D%/packages/patches/r-sapa-lapack.patch \
%D%/packages/patches/ripperx-missing-file.patch \
%D%/packages/patches/rpcbind-CVE-2017-8779.patch \
gnu/packages/bioconductor.scm
+5 -1
View File
@@ -27335,7 +27335,11 @@ whole-genome and whole-exome variant data.")
(uri (bioconductor-uri "snpStats" version))
(sha256
(base32
"0fyh1qzhfkiqdksxcwpr76mmlk13c6mi0m27kcdr5frb77kv1sq9"))))
"0fyh1qzhfkiqdksxcwpr76mmlk13c6mi0m27kcdr5frb77kv1sq9"))
(patches
(search-patches
"r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch"
"r-snpstats-0002-fixed-IS_S4_OBJECT.patch"))))
(properties `((upstream-name . "snpStats")))
(build-system r-build-system)
(inputs (list zlib))
gnu/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch
+412
View File
@@ -0,0 +1,412 @@
From 803cda41994a22890e0a6e379e6588084d4bc91b Mon Sep 17 00:00:00 2001
From: vjcitn <stvjc@channing.harvard.edu>
Date: Fri, 13 Mar 2026 04:04:59 -0400
Subject: [PATCH 1/2] fixed non-API except for IS_S4_OBJECT
---
src/bind.c | 8 ++++----
src/glm_test_R.c | 20 ++++++++++----------
src/imputation.c | 8 ++++----
src/input.c | 2 +-
src/plink.c | 2 +-
src/read_uncertain.c | 4 ++--
src/readped.c | 2 +-
src/single_snp_tests.c | 8 ++++----
src/snp_summary.c | 8 ++++----
src/snpmpy.c | 8 ++++----
src/structure.c | 4 ++--
src/subset.c | 2 +-
src/switch.c | 2 +-
src/tdt.c | 8 ++++----
src/testBig.c | 2 +-
15 files changed, 44 insertions(+), 44 deletions(-)
diff --git a/src/bind.c b/src/bind.c
index 44b1536..fa87e7c 100644
--- a/src/bind.c
+++ b/src/bind.c
@@ -19,7 +19,7 @@ SEXP snp_rbind(SEXP args) {
const SEXP This = CAR(args);
Class = getAttrib(This, R_ClassSymbol);
if (TYPEOF(Class) != STRSXP) {
- Class = R_data_class(This, FALSE);
+ Class = R_class(This);
}
const char *cli = CHAR(STRING_ELT(Class, 0));
if(!IS_S4_OBJECT(This)) {
@@ -66,7 +66,7 @@ SEXP snp_rbind(SEXP args) {
SEXP Result, Rnames, Dnames, Diploid = R_NilValue;
PROTECT(Result = allocMatrix(RAWSXP, nr, nc));
classgets(Result, duplicate(Class));
- SET_S4_OBJECT(Result);
+ Rf_asS4(Result, TRUE, 0);
PROTECT(Rnames = allocVector(STRSXP, nr));
PROTECT(Dnames = allocVector(VECSXP, 2));
SET_VECTOR_ELT(Dnames, 0, Rnames);
@@ -148,7 +148,7 @@ SEXP snp_cbind(SEXP args) {
SEXP This = CAR(args);
Class = getAttrib(This, R_ClassSymbol);
if (TYPEOF(Class) != STRSXP) {
- Class = R_data_class(This, FALSE);
+ Class = R_class(This);
}
const char *cli = CHAR(STRING_ELT(Class, 0));
if(!IS_S4_OBJECT(This)) {
@@ -205,7 +205,7 @@ SEXP snp_cbind(SEXP args) {
SEXP Result, Cnames, Dnames;
PROTECT(Result = allocMatrix(RAWSXP, nr, nc));
classgets(Result, duplicate(Class));
- SET_S4_OBJECT(Result);
+ Rf_asS4(Result, TRUE, 0);
PROTECT(Dnames = allocVector(VECSXP, 2));
setAttrib(Result, R_DimNamesSymbol, Dnames);
PROTECT(Cnames = allocVector(STRSXP, nc));
diff --git a/src/glm_test_R.c b/src/glm_test_R.c
index d865182..dc8ebef 100644
--- a/src/glm_test_R.c
+++ b/src/glm_test_R.c
@@ -19,8 +19,8 @@ SEXP snp_lhs_score(const SEXP Y, const SEXP X, const SEXP Stratum,
/* Y should be a SnpMatrix or an XSnpMatrix */
const char *classY = NULL;
- if (TYPEOF(R_data_class(Y, FALSE)) == STRSXP) {
- classY = CHAR(STRING_ELT(R_data_class(Y, FALSE), 0));
+ if (TYPEOF(R_class(Y)) == STRSXP) {
+ classY = CHAR(STRING_ELT(R_class(Y), 0));
} else {
classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
}
@@ -431,8 +431,8 @@ SEXP snp_rhs_score(SEXP Y, SEXP family, SEXP link,
/* Z should be a SnpMatrix or an XSnpMatrix */
const char *classZ = NULL;
- if (TYPEOF(R_data_class(Z, FALSE)) == STRSXP) {
- classZ = CHAR(STRING_ELT(R_data_class(Z, FALSE), 0));
+ if (TYPEOF(R_class(Z)) == STRSXP) {
+ classZ = CHAR(STRING_ELT(R_class(Z), 0));
} else {
classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
}
@@ -1003,8 +1003,8 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
/* Y should be a SnpMatrix or an XSnpMatrix */
const char *classY = NULL;
- if (TYPEOF(R_data_class(Y, FALSE)) == STRSXP) {
- classY = CHAR(STRING_ELT(R_data_class(Y, FALSE), 0));
+ if (TYPEOF(R_class(Y)) == STRSXP) {
+ classY = CHAR(STRING_ELT(R_class(Y), 0));
} else {
classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
}
@@ -1286,7 +1286,7 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
LOGICAL(Lhs)[0] = 1;
setAttrib(Estimates, install("snpLHS"), Lhs);
UNPROTECT(6);
- SET_S4_OBJECT(Estimates);
+ Rf_asS4(Estimates, TRUE, 0);
return(Estimates);
}
@@ -1360,8 +1360,8 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
/* Z should be a SnpMatrix or an XSnpMatrix */
const char *classZ = NULL;
- if (TYPEOF(R_data_class(Z, FALSE)) == STRSXP) {
- classZ = CHAR(STRING_ELT(R_data_class(Z, FALSE), 0));
+ if (TYPEOF(R_class(Z)) == STRSXP) {
+ classZ = CHAR(STRING_ELT(R_class(Z), 0));
} else {
classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
}
@@ -1724,7 +1724,7 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
UNPROTECT(gen_names? 7: 6);
- SET_S4_OBJECT(Estimates);
+ Rf_asS4(Estimates, TRUE, 0);
return(Estimates);
}
diff --git a/src/imputation.c b/src/imputation.c
index ff9403b..d796c1b 100644
--- a/src/imputation.c
+++ b/src/imputation.c
@@ -77,7 +77,7 @@ SEXP snp_impute(const SEXP X, const SEXP Y, const SEXP Xord, const SEXP Yord,
int *diploid = NULL;
SEXP cl = GET_CLASS(X);
if (TYPEOF(cl) != STRSXP) {
- cl = R_data_class(X, FALSE); /* S4 way of getting class attribute */
+ cl = R_class(X); /* S4 way of getting class attribute */
}
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
SEXP Diploid = R_do_slot(X, mkString("diploid"));
@@ -395,7 +395,7 @@ SEXP snp_impute(const SEXP X, const SEXP Y, const SEXP Xord, const SEXP Yord,
PROTECT(Maxpred = allocVector(INTSXP, 1));
INTEGER(Maxpred)[0] = maxpred;
setAttrib(Result, install("Max.predictors"), Maxpred);
- SET_S4_OBJECT(Result);
+ Rf_asS4(Result, TRUE, 0);
/* Tidy up */
@@ -701,7 +701,7 @@ SEXP impute_snps(const SEXP Rules, const SEXP Snps, const SEXP Subset,
int *diploid_in=NULL, *diploid=NULL;
SEXP cl = GET_CLASS(Snps);
if (TYPEOF(cl) != STRSXP) {
- cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
+ cl = R_class(Snps); /* S4 way of getting class attribute */
}
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
@@ -753,7 +753,7 @@ SEXP impute_snps(const SEXP Rules, const SEXP Snps, const SEXP Subset,
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
setAttrib(Class, install("package"), Package);
classgets(Result, Class);
- SET_S4_OBJECT(Result);
+ Rf_asS4(Result, TRUE, 0);
}
PROTECT(Dimnames = allocVector(VECSXP, 2));
SET_VECTOR_ELT(Dimnames, 0, VECTOR_ELT(names, 0));
diff --git a/src/input.c b/src/input.c
index 1d2a95b..60cdad8 100644
--- a/src/input.c
+++ b/src/input.c
@@ -330,7 +330,7 @@ SEXP insnp_new(const SEXP Filenames, const SEXP Sample_id, const SEXP Snp_id,
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
setAttrib(Class, install("package"), Package);
classgets(Result, Class);
- SET_S4_OBJECT(Result);
+ Rf_asS4(Result, TRUE, 0);
unsigned char *result = RAW(Result);
memset(result, 0x00, Nsample*Nsnp);
diff --git a/src/plink.c b/src/plink.c
index a413440..9095c2d 100644
--- a/src/plink.c
+++ b/src/plink.c
@@ -59,7 +59,7 @@ SEXP readbed(SEXP Bed, SEXP Id, SEXP Snps, SEXP Rsel, SEXP Csel) {
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
setAttrib(Class, install("package"), Package);
classgets(Result, Class);
- SET_S4_OBJECT(Result);
+ Rf_asS4(Result, TRUE, 0);
unsigned char *result = RAW(Result);
R_xlen_t ncell = (R_xlen_t)nrow*(R_xlen_t)ncol;
diff --git a/src/read_uncertain.c b/src/read_uncertain.c
index 2e3b901..fd82617 100644
--- a/src/read_uncertain.c
+++ b/src/read_uncertain.c
@@ -137,7 +137,7 @@ SEXP read_mach(const SEXP Filename, const SEXP Colnames, const SEXP Nsubject) {
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
setAttrib(Class, install("package"), Package);
classgets(Result, Class);
- SET_S4_OBJECT(Result);
+ Rf_asS4(Result, TRUE, 0);
UNPROTECT(2);
/* Read in data */
@@ -278,7 +278,7 @@ SEXP read_impute(const SEXP Filename, const SEXP Rownames, const SEXP Nsnp,
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
setAttrib(Class, install("package"), Package);
classgets(Result, Class);
- SET_S4_OBJECT(Result);
+ Rf_asS4(Result, TRUE, 0);
UNPROTECT(2);
char buffer[BUFFERSIZE];
diff --git a/src/readped.c b/src/readped.c
index 4e8563e..020d05f 100644
--- a/src/readped.c
+++ b/src/readped.c
@@ -327,7 +327,7 @@ SEXP readped(SEXP filename, SEXP snp_names, SEXP missing, SEXP X, SEXP sep) {
else
SET_STRING_ELT(SMClass, 0, mkChar("SnpMatrix"));
classgets(Smat, SMClass);
- SET_S4_OBJECT(Smat);
+ Rf_asS4(Smat, TRUE, 0);
PROTECT(DimNames = allocVector(VECSXP, 2));
SET_VECTOR_ELT(DimNames, 0, duplicate(Rnames));
protected += 2;
diff --git a/src/single_snp_tests.c b/src/single_snp_tests.c
index a242e17..08bd098 100644
--- a/src/single_snp_tests.c
+++ b/src/single_snp_tests.c
@@ -53,8 +53,8 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
/* SNPs ---- should be a SnpMatrix or an XSnpMatrix */
const char *classS = NULL;
- if (TYPEOF(R_data_class(Snps, FALSE)) == STRSXP) {
- classS = CHAR(STRING_ELT(R_data_class(Snps, FALSE), 0));
+ if (TYPEOF(R_class(Snps)) == STRSXP) {
+ classS = CHAR(STRING_ELT(R_class(Snps), 0));
} else {
classS = CHAR(STRING_ELT(getAttrib(Snps, R_ClassSymbol), 0));
}
@@ -108,8 +108,8 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
index_db name_index;
if (!isNull(Rules)) {
const char *classR = NULL;
- if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
- classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
+ if (TYPEOF(R_class(Rules)) == STRSXP) {
+ classR = CHAR(STRING_ELT(R_class(Rules), 0));
} else {
classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
}
diff --git a/src/snp_summary.c b/src/snp_summary.c
index 9b53693..6f181c9 100644
--- a/src/snp_summary.c
+++ b/src/snp_summary.c
@@ -47,8 +47,8 @@ SEXP X_snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
SEXP ruleNames = R_NilValue;
if (!isNull(Rules)) {
const char *classR = NULL;
- if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
- classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
+ if (TYPEOF(R_class(Rules)) == STRSXP) {
+ classR = CHAR(STRING_ELT(R_class(Rules), 0));
} else {
classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
}
@@ -321,8 +321,8 @@ SEXP snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
SEXP ruleNames = R_NilValue;
if (!isNull(Rules)) {
const char *classR = NULL;
- if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
- classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
+ if (TYPEOF(R_class(Rules)) == STRSXP) {
+ classR = CHAR(STRING_ELT(R_class(Rules), 0));
} else {
classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
}
diff --git a/src/snpmpy.c b/src/snpmpy.c
index 2447048..56b84d9 100644
--- a/src/snpmpy.c
+++ b/src/snpmpy.c
@@ -34,7 +34,7 @@ SEXP snp_pre(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
int *ifdiploid = NULL;
SEXP cl = GET_CLASS(Snps);
if (TYPEOF(cl) != STRSXP) {
- cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
+ cl = R_class(Snps); /* S4 way of getting class attribute */
}
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
SEXP diploid = R_do_slot(Snps, mkString("diploid"));
@@ -55,7 +55,7 @@ SEXP snp_pre(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
cl = GET_CLASS(Mat);
if (TYPEOF(cl) != STRSXP) {
- cl = R_data_class(Mat, FALSE); /* S4 way of getting class attribute */
+ cl = R_class(Mat); /* S4 way of getting class attribute */
}
if (strcmp(CHAR(STRING_ELT(cl, 0)), "matrix"))
error("Argument error - Mat wrong type");
@@ -161,7 +161,7 @@ SEXP snp_post(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
int *ifdiploid = NULL;
SEXP cl = GET_CLASS(Snps);
if (TYPEOF(cl) != STRSXP) {
- cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
+ cl = R_class(Snps); /* S4 way of getting class attribute */
}
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
SEXP diploid = R_do_slot(Snps, mkString("diploid"));
@@ -182,7 +182,7 @@ SEXP snp_post(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
cl = GET_CLASS(Mat);
if (TYPEOF(cl) != STRSXP) {
- cl = R_data_class(Mat, FALSE); /* S4 way of getting class attribute */
+ cl = R_class(Mat); /* S4 way of getting class attribute */
}
if (strcmp(CHAR(STRING_ELT(cl, 0)), "matrix"))
error("Argument error - Mat wrong type");
diff --git a/src/structure.c b/src/structure.c
index 2a05635..1f9b62e 100644
--- a/src/structure.c
+++ b/src/structure.c
@@ -66,7 +66,7 @@ SEXP xxt(const SEXP Snps, const SEXP Strata, const SEXP Correct_for_missing,
int *ifDiploid = NULL;
SEXP cl = GET_CLASS(Snps);
if (TYPEOF(cl) != STRSXP) {
- cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
+ cl = R_class(Snps); /* S4 way of getting class attribute */
}
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
@@ -409,7 +409,7 @@ SEXP ibs_count(const SEXP Snps, const SEXP Uncertain) {
int *ifDiploid = NULL;
SEXP cl = GET_CLASS(Snps);
if (TYPEOF(cl) != STRSXP) {
- cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
+ cl = R_class(Snps); /* S4 way of getting class attribute */
}
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
diff --git a/src/subset.c b/src/subset.c
index cc7992d..4c2e2c4 100644
--- a/src/subset.c
+++ b/src/subset.c
@@ -55,7 +55,7 @@ SEXP subset(SEXP X, SEXP Rows, SEXP Cols) {
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
setAttrib(Rclass, install("package"), Package);
setAttrib(Result, R_ClassSymbol, Rclass);
- SET_S4_OBJECT(Result);
+ Rf_asS4(Result, TRUE, 0);
PROTECT(Rdim = allocVector(INTSXP, 2));
int *rdim = INTEGER(Rdim);
rdim[0] = nrows;
diff --git a/src/switch.c b/src/switch.c
index 60f7e6c..e2a3287 100644
--- a/src/switch.c
+++ b/src/switch.c
@@ -16,7 +16,7 @@ SEXP test_switch(const SEXP Snps, const SEXP Snps2, const SEXP Split,
int *female = NULL;
SEXP cl = GET_CLASS(Snps);
if (TYPEOF(cl) != STRSXP) {
- cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
+ cl = R_class(Snps); /* S4 way of getting class attribute */
}
SEXP diploid = NULL;
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
diff --git a/src/tdt.c b/src/tdt.c
index cece0d9..000d1c7 100644
--- a/src/tdt.c
+++ b/src/tdt.c
@@ -43,8 +43,8 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
/* SNPs ---- should be a SnpMatrix or an XSnpMatrix */
const char *classS = NULL;
- if (TYPEOF(R_data_class(Snps, FALSE)) == STRSXP) {
- classS = CHAR(STRING_ELT(R_data_class(Snps, FALSE), 0));
+ if (TYPEOF(R_class(Snps)) == STRSXP) {
+ classS = CHAR(STRING_ELT(R_class(Snps), 0));
} else {
classS = CHAR(STRING_ELT(getAttrib(Snps, R_ClassSymbol), 0));
}
@@ -84,8 +84,8 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
GTYPE **gt2ht = NULL;
if (!isNull(Rules)) {
const char *classR = NULL;
- if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
- classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
+ if (TYPEOF(R_class(Rules)) == STRSXP) {
+ classR = CHAR(STRING_ELT(R_class(Rules), 0));
} else {
classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
}
diff --git a/src/testBig.c b/src/testBig.c
index a6eb76f..3dca1da 100644
--- a/src/testBig.c
+++ b/src/testBig.c
@@ -18,7 +18,7 @@ SEXP snp_big(SEXP nrow, SEXP ncol) {
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
setAttrib(Class, install("package"), Package);
classgets(Result, Class);
- SET_S4_OBJECT(Result);
+ Rf_asS4(Result, TRUE, 0);
PROTECT(Dnames = allocVector(VECSXP, 2));
setAttrib(Result, R_DimNamesSymbol, Dnames);
--
2.52.0
gnu/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch
+149
View File
@@ -0,0 +1,149 @@
From a505297e347aa72510ecfc83e7009668693e1260 Mon Sep 17 00:00:00 2001
From: vjcitn <stvjc@channing.harvard.edu>
Date: Fri, 13 Mar 2026 04:06:37 -0400
Subject: [PATCH 2/2] fixed IS_S4_OBJECT
---
src/bind.c | 4 ++--
src/fst.c | 2 +-
src/glm_test_R.c | 8 ++++----
src/single_snp_tests.c | 2 +-
src/snp_summary.c | 6 +++---
src/tdt.c | 2 +-
6 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/src/bind.c b/src/bind.c
index fa87e7c..b3ef928 100644
--- a/src/bind.c
+++ b/src/bind.c
@@ -22,7 +22,7 @@ SEXP snp_rbind(SEXP args) {
Class = R_class(This);
}
const char *cli = CHAR(STRING_ELT(Class, 0));
- if(!IS_S4_OBJECT(This)) {
+ if(!Rf_isS4(This)) {
warning("rbinding SnpMatrix object without S4 object bit");
}
int nci = ncols(This);
@@ -151,7 +151,7 @@ SEXP snp_cbind(SEXP args) {
Class = R_class(This);
}
const char *cli = CHAR(STRING_ELT(Class, 0));
- if(!IS_S4_OBJECT(This)) {
+ if(!Rf_isS4(This)) {
warning("cbinding SnpMatrix object without S4 object bit");
}
SEXP Di = R_NilValue;
diff --git a/src/fst.c b/src/fst.c
index bbc39c0..5451a51 100644
--- a/src/fst.c
+++ b/src/fst.c
@@ -23,7 +23,7 @@ SEXP Fst(SEXP Snps, SEXP Group, SEXP HapMap) {
ifX = 0; /* to avoid warning message */
error("Argument error - class(Snps)");
}
- if(!IS_S4_OBJECT(Snps)) {
+ if(!Rf_isS4(Snps)) {
error("Argument error - Snps is not S4 object");
}
diff --git a/src/glm_test_R.c b/src/glm_test_R.c
index dc8ebef..fe9d9c8 100644
--- a/src/glm_test_R.c
+++ b/src/glm_test_R.c
@@ -24,7 +24,7 @@ SEXP snp_lhs_score(const SEXP Y, const SEXP X, const SEXP Stratum,
} else {
classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
}
- if(!IS_S4_OBJECT(Y)) {
+ if(!Rf_isS4(Y)) {
error("Y in snp_lhs_score is missing S4 Object bit");
}
int ifX = 0;
@@ -443,7 +443,7 @@ SEXP snp_rhs_score(SEXP Y, SEXP family, SEXP link,
ifX = 1;
else
error("Argument error - class(Z)");
- if (!IS_S4_OBJECT(Z)) {
+ if (!Rf_isS4(Z)) {
error("Z in snp_rhs_score is missing S4 Object bit");
}
@@ -1008,7 +1008,7 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
} else {
classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
}
- if(!IS_S4_OBJECT(Y)) {
+ if(!Rf_isS4(Y)) {
error("Y in snp_lhs_score is missing S4 Object bit");
}
int ifX = 0;
@@ -1365,7 +1365,7 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
} else {
classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
}
- if(!IS_S4_OBJECT(Z)) {
+ if(!Rf_isS4(Z)) {
error("Z in snp_rhs_score is missing S4 Object bit");
}
int ifX = 0;
diff --git a/src/single_snp_tests.c b/src/single_snp_tests.c
index 08bd098..b577300 100644
--- a/src/single_snp_tests.c
+++ b/src/single_snp_tests.c
@@ -67,7 +67,7 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
ifX = 0; /* to avoid warning message */
error("Argument error - class(Snps)");
}
- if(!IS_S4_OBJECT(Snps)) {
+ if(!Rf_isS4(Snps)) {
error("Argument error - Snps is not S4 object");
}
diff --git a/src/snp_summary.c b/src/snp_summary.c
index 6f181c9..c2f1c73 100644
--- a/src/snp_summary.c
+++ b/src/snp_summary.c
@@ -24,7 +24,7 @@ SEXP X_snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
if (Snps == R_NilValue) {
error("Argument error - Snps = NULL");
}
- if(!IS_S4_OBJECT(Snps)) {
+ if(!Rf_isS4(Snps)) {
error("Argument error - Snps is not S4 object");
}
const unsigned char *snps = RAW(Snps);
@@ -298,7 +298,7 @@ SEXP snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
if (Snps == R_NilValue) {
error("Argument error - Snps = NULL");
}
- if(!IS_S4_OBJECT(Snps)) {
+ if(!Rf_isS4(Snps)) {
error("Argument error - Snps is not S4 object");
}
const unsigned char *snps = RAW(Snps);
@@ -538,7 +538,7 @@ SEXP row_summary(const SEXP Snps) {
if (Snps == R_NilValue) {
error("Argument error - Snps = NULL");
}
- if(!IS_S4_OBJECT(Snps)) {
+ if(!Rf_isS4(Snps)) {
error("Argument error - Snps is not S4 object");
}
const unsigned char *snps = RAW(Snps);
diff --git a/src/tdt.c b/src/tdt.c
index 000d1c7..634e1b3 100644
--- a/src/tdt.c
+++ b/src/tdt.c
@@ -57,7 +57,7 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
ifX = 0; /* to avoid warning message */
error("Argument error - class(Snps)");
}
- if(!IS_S4_OBJECT(Snps)) {
+ if(!Rf_isS4(Snps)) {
error("Argument error - Snps is not S4 object");
}
--
2.52.0