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Define R_NO_REMAP and STRICT_R_HEADERS
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@stewid
stewid committed Nov 2, 2019
1 parent da55652 commit 8020699
Showing 1 changed file with 35 additions and 32 deletions.
67 changes: 35 additions & 32 deletions src/trace.cpp
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
// Copyright 2013-2017 Stefan Widgren and Maria Noremark,
// Copyright 2013-2019 Stefan Widgren and Maria Noremark,
// National Veterinary Institute, Sweden
//
// Licensed under the EUPL, Version 1.1 or - as soon they
Expand All @@ -18,6 +18,9 @@
// See the Licence for the specific language governing
// permissions and limitations under the Licence.

#define R_NO_REMAP
#define STRICT_R_HEADERS

#include <algorithm>
#include <map>
#include <set>
Expand Down Expand Up @@ -327,40 +330,40 @@ SEXP shortestPaths(const SEXP src,
}

SEXP result, names, vec;
PROTECT(result = allocVector(VECSXP, 6));
PROTECT(names = allocVector(STRSXP, 6));
PROTECT(result = Rf_allocVector(VECSXP, 6));
PROTECT(names = Rf_allocVector(STRSXP, 6));

SET_VECTOR_ELT(result, 0, vec = allocVector(INTSXP, inDistance.size()));
SET_VECTOR_ELT(result, 0, vec = Rf_allocVector(INTSXP, inDistance.size()));
for (size_t i = 0; i < inDistance.size(); ++i)
INTEGER(vec)[i] = inDistance[i];
SET_STRING_ELT(names, 0, mkChar("inDistance"));
SET_STRING_ELT(names, 0, Rf_mkChar("inDistance"));

SET_VECTOR_ELT(result, 1, vec = allocVector(INTSXP, inRowid.size()));
SET_VECTOR_ELT(result, 1, vec = Rf_allocVector(INTSXP, inRowid.size()));
for (size_t i = 0; i < inRowid.size(); ++i)
INTEGER(vec)[i] = inRowid[i];
SET_STRING_ELT(names, 1, mkChar("inRowid"));
SET_STRING_ELT(names, 1, Rf_mkChar("inRowid"));

SET_VECTOR_ELT(result, 2, vec = allocVector(INTSXP, inIndex.size()));
SET_VECTOR_ELT(result, 2, vec = Rf_allocVector(INTSXP, inIndex.size()));
for (size_t i = 0; i < inIndex.size(); ++i)
INTEGER(vec)[i] = inIndex[i];
SET_STRING_ELT(names, 2, mkChar("inIndex"));
SET_STRING_ELT(names, 2, Rf_mkChar("inIndex"));

SET_VECTOR_ELT(result, 3, vec = allocVector(INTSXP, outDistance.size()));
SET_VECTOR_ELT(result, 3, vec = Rf_allocVector(INTSXP, outDistance.size()));
for (size_t i = 0; i < outDistance.size(); ++i)
INTEGER(vec)[i] = outDistance[i];
SET_STRING_ELT(names, 3, mkChar("outDistance"));
SET_STRING_ELT(names, 3, Rf_mkChar("outDistance"));

SET_VECTOR_ELT(result, 4, vec = allocVector(INTSXP, outRowid.size()));
SET_VECTOR_ELT(result, 4, vec = Rf_allocVector(INTSXP, outRowid.size()));
for (size_t i = 0; i < outRowid.size(); ++i)
INTEGER(vec)[i] = outRowid[i];
SET_STRING_ELT(names, 4, mkChar("outRowid"));
SET_STRING_ELT(names, 4, Rf_mkChar("outRowid"));

SET_VECTOR_ELT(result, 5, vec = allocVector(INTSXP, outIndex.size()));
SET_VECTOR_ELT(result, 5, vec = Rf_allocVector(INTSXP, outIndex.size()));
for (size_t i = 0; i < outIndex.size(); ++i)
INTEGER(vec)[i] = outIndex[i];
SET_STRING_ELT(names, 5, mkChar("outIndex"));
SET_STRING_ELT(names, 5, Rf_mkChar("outIndex"));

setAttrib(result, R_NamesSymbol, names);
Rf_setAttrib(result, R_NamesSymbol, names);
UNPROTECT(2);

return result;
Expand Down Expand Up @@ -465,7 +468,7 @@ SEXP traceContacts(const SEXP src,
std::vector<int> resultRowid;
std::vector<int> resultDistance;

PROTECT(result = allocVector(VECSXP, 4 * LENGTH(root)));
PROTECT(result = Rf_allocVector(VECSXP, 4 * LENGTH(root)));
for (size_t i = 0, end = LENGTH(root); i < end; ++i) {
resultRowid.clear();
resultDistance.clear();
Expand All @@ -481,11 +484,11 @@ SEXP traceContacts(const SEXP src,
resultDistance,
INTEGER(maxDistance)[0]);

SET_VECTOR_ELT(result, 4 * i, vec = allocVector(INTSXP, resultRowid.size()));
SET_VECTOR_ELT(result, 4 * i, vec = Rf_allocVector(INTSXP, resultRowid.size()));
for (size_t j = 0; j < resultRowid.size(); ++j)
INTEGER(vec)[j] = resultRowid[j];

SET_VECTOR_ELT(result, 4 * i + 1, vec = allocVector(INTSXP, resultDistance.size()));
SET_VECTOR_ELT(result, 4 * i + 1, vec = Rf_allocVector(INTSXP, resultDistance.size()));
for (size_t j = 0; j < resultDistance.size(); ++j)
INTEGER(vec)[j] = resultDistance[j];

Expand All @@ -503,11 +506,11 @@ SEXP traceContacts(const SEXP src,
resultDistance,
INTEGER(maxDistance)[0]);

SET_VECTOR_ELT(result, 4 * i + 2, vec = allocVector(INTSXP, resultRowid.size()));
SET_VECTOR_ELT(result, 4 * i + 2, vec = Rf_allocVector(INTSXP, resultRowid.size()));
for (size_t j = 0; j < resultRowid.size(); ++j)
INTEGER(vec)[j] = resultRowid[j];

SET_VECTOR_ELT(result, 4 * i + 3, vec = allocVector(INTSXP, resultDistance.size()));
SET_VECTOR_ELT(result, 4 * i + 3, vec = Rf_allocVector(INTSXP, resultDistance.size()));
for (size_t j = 0; j < resultDistance.size(); ++j)
INTEGER(vec)[j] = resultDistance[j];
}
Expand Down Expand Up @@ -654,30 +657,30 @@ SEXP networkSummary(const SEXP src,
}

SEXP result, names, vec;
PROTECT(result = allocVector(VECSXP, 4));
PROTECT(names = allocVector(STRSXP, 4));
PROTECT(result = Rf_allocVector(VECSXP, 4));
PROTECT(names = Rf_allocVector(STRSXP, 4));

SET_VECTOR_ELT(result, 0, vec = allocVector(INTSXP, inDegree.size()));
SET_VECTOR_ELT(result, 0, vec = Rf_allocVector(INTSXP, inDegree.size()));
for (size_t i = 0; i < inDegree.size(); ++i)
INTEGER(vec)[i] = inDegree[i];
SET_STRING_ELT(names, 0, mkChar("inDegree"));
SET_STRING_ELT(names, 0, Rf_mkChar("inDegree"));

SET_VECTOR_ELT(result, 1, vec = allocVector(INTSXP, outDegree.size()));
SET_VECTOR_ELT(result, 1, vec = Rf_allocVector(INTSXP, outDegree.size()));
for (size_t i = 0; i < outDegree.size(); ++i)
INTEGER(vec)[i] = outDegree[i];
SET_STRING_ELT(names, 1, mkChar("outDegree"));
SET_STRING_ELT(names, 1, Rf_mkChar("outDegree"));

SET_VECTOR_ELT(result, 2, vec = allocVector(INTSXP, ingoingContactChain.size()));
SET_VECTOR_ELT(result, 2, vec = Rf_allocVector(INTSXP, ingoingContactChain.size()));
for (size_t i = 0; i < ingoingContactChain.size(); ++i)
INTEGER(vec)[i] = ingoingContactChain[i];
SET_STRING_ELT(names, 2, mkChar("ingoingContactChain"));
SET_STRING_ELT(names, 2, Rf_mkChar("ingoingContactChain"));

SET_VECTOR_ELT(result, 3, vec = allocVector(INTSXP, outgoingContactChain.size()));
SET_VECTOR_ELT(result, 3, vec = Rf_allocVector(INTSXP, outgoingContactChain.size()));
for (size_t i = 0; i < outgoingContactChain.size(); ++i)
INTEGER(vec)[i] = outgoingContactChain[i];
SET_STRING_ELT(names, 3, mkChar("outgoingContactChain"));
SET_STRING_ELT(names, 3, Rf_mkChar("outgoingContactChain"));

setAttrib(result, R_NamesSymbol, names);
Rf_setAttrib(result, R_NamesSymbol, names);
UNPROTECT(2);

return result;
Expand Down

1 comment on commit 8020699

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R/network-summary.R:262:1: style: functions should have cyclomatic complexity of less than 15, this has 38.

​setMethod("NetworkSummary",
^

R/report.R:290:1: style: Lines should not be more than 80 characters.

​##' @param template the Sweave template file to use. If none is provided, the default
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/shortest-paths.R:169:1: style: functions should have cyclomatic complexity of less than 15, this has 41.

​setMethod("ShortestPaths",
^

R/trace.R:161:1: style: functions should have cyclomatic complexity of less than 15, this has 56.

​Trace <- function(movements,
^

R/tree.R:135:1: style: functions should have cyclomatic complexity of less than 15, this has 48.

​position_tree <- function(tree,
^

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