* installing *source* package ‘seqminer’ ... ** package ‘seqminer’ successfully unpacked and MD5 sums checked ** using staged installation configure: CC = gcc-13 configure: CFLAGS = -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes configure: CXX = g++-13 -std=gnu++11 configure: CXXFLAGS = -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++-13 -std=gnu++11 accepts -g... yes checking how to run the C++ preprocessor... g++-13 -std=gnu++11 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for BZ2_bzDecompressInit in -lbz2... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes configure: Will use system-wide bzip2 library checking for ZSTD_compress in -lzstd... yes checking zstd.h usability... yes checking zstd.h presence... yes checking for zstd.h... yes configure: Will use system-wide zstd library checking for sqlite3_open in -lsqlite3... yes checking sqlite3.h usability... yes checking sqlite3.h presence... yes checking for sqlite3.h... yes configure: Will use system-wide sqlite library checking for regcomp in -lc... yes checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking for working REG_STARTEND... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/config.h ** libs using C compiler: ‘gcc-13 (GCC) 13.2.0’ using C++ compiler: ‘g++-13 (GCC) 13.2.0’ using C++17 make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-noRemap/seqminer/src' have bzip2 g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c BCFReader.cpp -o BCFReader.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c BGenFile.cpp -o BGenFile.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c BGenIndex.cpp -o BGenIndex.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c BGenVariant.cpp -o BGenVariant.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c Exception.cpp -o Exception.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c FileIO.cpp -o FileIO.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c GeneLoader.cpp -o GeneLoader.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c MmapFile.cpp -o MmapFile.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c PatternMatch.cpp -o PatternMatch.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c PeopleSet.cpp -o PeopleSet.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c PlinkInputFile.cpp -o PlinkInputFile.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c PlinkOutputFile.cpp -o PlinkOutputFile.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c Profiler.cpp -o Profiler.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c R_CPP_interface.cpp -o R_CPP_interface.o R_CPP_interface.cpp: In function 'void extractStringArray(SEXP, std::vector >*)': R_CPP_interface.cpp:15:27: error: 'length' was not declared in this scope 15 | for (R_len_t i = 0; i < length(in); i++) { | ^~~~~~ R_CPP_interface.cpp: In function 'void extractIntArray(SEXP, std::vector*)': R_CPP_interface.cpp:26:27: error: 'length' was not declared in this scope 26 | for (R_len_t i = 0; i < length(in); i++) { | ^~~~~~ R_CPP_interface.cpp: In function 'void extractStringSet(SEXP, std::set >*)': R_CPP_interface.cpp:33:27: error: 'length' was not declared in this scope 33 | for (R_len_t i = 0; i < length(in); i++) { | ^~~~~~ R_CPP_interface.cpp: In function 'SEXPREC* getListElement(SEXP, const char*)': R_CPP_interface.cpp:43:16: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'? 43 | SEXP names = getAttrib(list, R_NamesSymbol); | ^~~~~~~~~ | Rf_getAttrib R_CPP_interface.cpp:44:27: error: 'length' was not declared in this scope 44 | for (R_len_t i = 0; i < length(list); i++) | ^~~~~~ In file included from /data/gannet/ripley/R/R-devel/include/Rdefines.h:41, from R_CPP_interface.h:9, from R_CPP_interface.cpp:1: R_CPP_interface.cpp: In function 'void storeResult(const std::vector&, SEXPREC*&, int)': R_CPP_interface.cpp:66:15: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 66 | PROTECT(s = allocVector(LGLSXP, n)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp: In function 'void storeResult(const std::vector&, SEXPREC*&, int)': R_CPP_interface.cpp:77:15: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 77 | PROTECT(s = allocVector(INTSXP, n)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp: In function 'void storeResult(const std::vector >&, SEXP, int)': R_CPP_interface.cpp:88:15: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 88 | PROTECT(s = allocVector(STRSXP, n)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp:90:26: error: 'mkChar' was not declared in this scope 90 | SET_STRING_ELT(s, i, mkChar(in[i].c_str())); | ^~~~~~ R_CPP_interface.cpp: In function 'void storeResult(const std::vector&, SEXPREC*&, int)': R_CPP_interface.cpp:100:15: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 100 | PROTECT(s = allocVector(REALSXP, n)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp: In function 'void storeIntResult(const std::vector >&, SEXPREC*&, int)': R_CPP_interface.cpp:112:15: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 112 | PROTECT(s = allocVector(INTSXP, n)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp: In function 'void storeDoubleResult(const std::vector >&, SEXPREC*&, int)': R_CPP_interface.cpp:127:15: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 127 | PROTECT(s = allocVector(REALSXP, n)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp: In function 'void storeResult(const std::vector >&, SEXPREC*&, int)': R_CPP_interface.cpp:143:15: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 143 | PROTECT(s = allocVector(VECSXP, n)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp: In function 'void storeResult(const std::vector > >&, SEXPREC*&, int)': R_CPP_interface.cpp:159:15: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 159 | PROTECT(s = allocVector(VECSXP, n)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp: In function 'void storeResult(const std::string&, const std::vector >&, SEXP, int)': R_CPP_interface.cpp:174:15: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 174 | PROTECT(s = allocVector(STRSXP, n)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp:176:26: error: 'mkChar' was not declared in this scope 176 | SET_STRING_ELT(s, i, mkChar(val[i].c_str())); | ^~~~~~ R_CPP_interface.cpp: In function 'void storeResult(const std::string&, const std::vector&, SEXPREC*&, int)': R_CPP_interface.cpp:186:15: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 186 | PROTECT(s = allocVector(INTSXP, n)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp: In function 'void setDim(int, int, SEXP)': R_CPP_interface.cpp:196:17: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 196 | PROTECT(dim = allocVector(INTSXP, 2)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp:199:3: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 199 | setAttrib(s, R_DimSymbol, dim); | ^~~~~~~~~ | Rf_setAttrib R_CPP_interface.cpp: In function 'void setDim(int, int, int, SEXP)': R_CPP_interface.cpp:205:17: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 205 | PROTECT(dim = allocVector(INTSXP, 3)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp:209:3: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 209 | setAttrib(s, R_DimSymbol, dim); | ^~~~~~~~~ | Rf_setAttrib R_CPP_interface.cpp: In function 'void setDimNames(const std::vector >&, const std::vector >&, SEXP)': R_CPP_interface.cpp:226:22: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 226 | PROTECT(dimnames = allocVector(VECSXP, 2)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp:231:3: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 231 | setAttrib(s, R_DimNamesSymbol, dimnames); | ^~~~~~~~~ | Rf_setAttrib R_CPP_interface.cpp: In function 'void setDimNames(const std::vector >&, const std::vector >&, const std::vector >&, SEXP)': R_CPP_interface.cpp:240:22: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 240 | PROTECT(dimnames = allocVector(VECSXP, 3)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp:246:3: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 246 | setAttrib(s, R_DimNamesSymbol, dimnames); | ^~~~~~~~~ | Rf_setAttrib R_CPP_interface.cpp: In function 'void setListNames(std::vector >&, SEXPREC**)': R_CPP_interface.cpp:275:24: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 275 | PROTECT(sListNames = allocVector(STRSXP, names.size())); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp:277:35: error: 'mkChar' was not declared in this scope 277 | SET_STRING_ELT(sListNames, i, mkChar(names[i].c_str())); | ^~~~~~ R_CPP_interface.cpp:279:3: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 279 | setAttrib((*s), R_NamesSymbol, sListNames); | ^~~~~~~~~ | Rf_setAttrib R_CPP_interface.cpp: In function 'void initDoubleArray(SEXP)': R_CPP_interface.cpp:285:23: error: 'length' was not declared in this scope 285 | for (int i = 0; i < length(s); i++) { | ^~~~~~ R_CPP_interface.cpp: In function 'void initIntArray(SEXP)': R_CPP_interface.cpp:292:23: error: 'length' was not declared in this scope 292 | for (int i = 0; i < length(s); i++) { | ^~~~~~ R_CPP_interface.cpp: In function 'void initStringArray(SEXP)': R_CPP_interface.cpp:298:23: error: 'length' was not declared in this scope 298 | for (int i = 0; i < length(s); i++) { | ^~~~~~ R_CPP_interface.cpp: In function 'void storeResult(const std::vector >&, SEXPREC**)': R_CPP_interface.cpp:305:20: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 305 | PROTECT((*ret) = allocVector(STRSXP, in.size())); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp:308:31: error: 'mkChar' was not declared in this scope 308 | SET_STRING_ELT((*ret), i, mkChar(in[i].c_str())); | ^~~~~~ R_CPP_interface.cpp: In function 'void storeResult(const std::vector&, SEXPREC**)': R_CPP_interface.cpp:315:20: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 315 | PROTECT((*ret) = allocVector(REALSXP, in.size())); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp: In function 'void storeResult(const std::vector >&, SEXPREC**)': R_CPP_interface.cpp:325:20: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 325 | PROTECT((*ret) = allocVector(VECSXP, in.size())); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ R_CPP_interface.cpp: In function 'int getDim(SEXP, std::vector*)': R_CPP_interface.cpp:340:12: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'? 340 | SEXP r = getAttrib(s, R_DimSymbol); | ^~~~~~~~~ | Rf_getAttrib R_CPP_interface.cpp:341:7: error: 'isNull' was not declared in this scope 341 | if (isNull(r)) return -1; | ^~~~~~ R_CPP_interface.cpp:342:11: error: 'length' was not declared in this scope 342 | int n = length(r); | ^~~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:202: R_CPP_interface.o] Error 1 make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-noRemap/seqminer/src' ERROR: compilation failed for package ‘seqminer’ * removing ‘/data/gannet/ripley/R/packages/tests-noRemap/Libs/seqminer-lib/seqminer’ Command exited with non-zero status 1 Time 1:00.85, 47.99 + 6.27