############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL gpuMagic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘gpuMagic’ ... ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ using C++11 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/R/R/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS -DCL_SILENCE_DEPRECATION -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c C_Interface.cpp -o C_Interface.o C_Interface.cpp: In function ‘SEXPREC* getPlatformNum()’: C_Interface.cpp:16:28: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’? 16 | SEXP platformNum = ScalarInteger(kernelManager::getPlatformNum()); | ^~~~~~~~~~~~~ | Rf_ScalarInteger C_Interface.cpp: In function ‘SEXPREC* getDeviceNum(SEXP)’: C_Interface.cpp:22:68: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’? 22 | SEXP deviceNum = ScalarInteger(kernelManager::getDeviceNum(asInteger(platform))); | ^~~~~~~~~ | Rf_asInteger C_Interface.cpp:22:26: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’? 22 | SEXP deviceNum = ScalarInteger(kernelManager::getDeviceNum(asInteger(platform))); | ^~~~~~~~~~~~~ | Rf_ScalarInteger C_Interface.cpp: In function ‘SEXPREC* getDeviceInfo(SEXP, SEXP)’: C_Interface.cpp:28:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’? 28 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) }; | ^~~~~~~~~ | Rf_asInteger In file included from C_Interface.h:4, from C_Interface.cpp:10: C_Interface.cpp:30:31: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’? 30 | SEXP info_R = PROTECT(allocVector(VECSXP, 8)); | ^~~~~~~~~~~ /home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’ 388 | #define PROTECT(s) Rf_protect(s) | ^ C_Interface.cpp:32:43: error: ‘mkString’ was not declared in this scope; did you mean ‘asString’? 32 | SET_VECTOR_ELT(info_R, 0, PROTECT(mkString(info.device_name.c_str()))); | ^~~~~~~~ /home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’ 388 | #define PROTECT(s) Rf_protect(s) | ^ C_Interface.cpp:33:43: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’? 33 | SET_VECTOR_ELT(info_R, 1, PROTECT(ScalarInteger(info.device_type))); | ^~~~~~~~~~~~~ /home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’ 388 | #define PROTECT(s) Rf_protect(s) | ^ C_Interface.cpp:34:43: error: ‘ScalarReal’ was not declared in this scope; did you mean ‘Rf_ScalarReal’? 34 | SET_VECTOR_ELT(info_R, 2, PROTECT(ScalarReal(info.global_memory))); | ^~~~~~~~~~ /home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’ 388 | #define PROTECT(s) Rf_protect(s) | ^ C_Interface.cpp:36:43: error: ‘ScalarLogical’ was not declared in this scope; did you mean ‘Rf_ScalarLogical’? 36 | SET_VECTOR_ELT(info_R, 4, PROTECT(ScalarLogical(info.has_local_memory))); | ^~~~~~~~~~~~~ /home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’ 388 | #define PROTECT(s) Rf_protect(s) | ^ C_Interface.cpp:41:9: error: ‘unprotect’ was not declared in this scope; did you mean ‘Rf_unprotect’? 41 | unprotect(9); | ^~~~~~~~~ | Rf_unprotect C_Interface.cpp: In function ‘SEXPREC* upload(SEXP, SEXP, SEXP, SEXP, SEXP)’: C_Interface.cpp:48:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’? 48 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) }; | ^~~~~~~~~ | Rf_asInteger C_Interface.cpp:50:29: error: ‘asReal’ was not declared in this scope 50 | size_t dataLength = asReal(length); | ^~~~~~ C_Interface.cpp:84:17: error: ‘error’ was not declared in this scope; did you mean ‘perror’? 84 | error("Unsupported data structure!"); | ^~~~~ | perror C_Interface.cpp: In function ‘SEXPREC* gpuMalloc(SEXP, SEXP, SEXP, SEXP)’: C_Interface.cpp:96:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’? 96 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) }; | ^~~~~~~~~ | Rf_asInteger C_Interface.cpp:97:47: error: ‘asReal’ was not declared in this scope 97 | openArray* matrix = new openArray(id, asReal(length), (dtype)asInteger(type)); | ^~~~~~ C_Interface.cpp: In function ‘SEXPREC* download(SEXP)’: C_Interface.cpp:121:31: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’? 121 | res = PROTECT(allocVector(REALSXP, length)); | ^~~~~~~~~~~ /home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’ 388 | #define PROTECT(s) Rf_protect(s) | ^ C_Interface.cpp: In function ‘SEXPREC* hasKernel(SEXP, SEXP, SEXP, SEXP)’: C_Interface.cpp:156:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’? 156 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) }; | ^~~~~~~~~ | Rf_asInteger C_Interface.cpp:12:33: error: ‘asChar’ was not declared in this scope 12 | #define asString(x) string(CHAR(asChar(x))) | ^~~~~~ /home/biocbuild/R/R/include/Rinternals.h:203:24: note: in definition of macro ‘CHAR’ 203 | #define CHAR(x) R_CHAR(x) | ^ C_Interface.cpp:157:34: note: in expansion of macro ‘asString’ 157 | programSignature sig = { asString(signature) ,string(),string(),asString(kernel) }; | ^~~~~~~~ C_Interface.cpp:158:20: error: ‘ScalarLogical’ was not declared in this scope; did you mean ‘Rf_ScalarLogical’? 158 | SEXP res = ScalarLogical(kernelManager::hasKernel(id, sig)); | ^~~~~~~~~~~~~ | Rf_ScalarLogical C_Interface.cpp: In function ‘SEXPREC* createKernel(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: C_Interface.cpp:166:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’? 166 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) }; | ^~~~~~~~~ | Rf_asInteger C_Interface.cpp:12:33: error: ‘asChar’ was not declared in this scope 12 | #define asString(x) string(CHAR(asChar(x))) | ^~~~~~ /home/biocbuild/R/R/include/Rinternals.h:203:24: note: in definition of macro ‘CHAR’ 203 | #define CHAR(x) R_CHAR(x) | ^ C_Interface.cpp:167:34: note: in expansion of macro ‘asString’ 167 | programSignature sig = { asString(signature) ,asString(flag),asString(code),asString(kernel) }; | ^~~~~~~~ C_Interface.cpp: In function ‘SEXPREC* setParameter(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: C_Interface.cpp:178:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’? 178 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) }; | ^~~~~~~~~ | Rf_asInteger C_Interface.cpp:12:33: error: ‘asChar’ was not declared in this scope 12 | #define asString(x) string(CHAR(asChar(x))) | ^~~~~~ /home/biocbuild/R/R/include/Rinternals.h:203:24: note: in definition of macro ‘CHAR’ 203 | #define CHAR(x) R_CHAR(x) | ^ C_Interface.cpp:179:34: note: in expansion of macro ‘asString’ 179 | programSignature sig = { asString(signature),string(),string(),asString(kernel) }; | ^~~~~~~~ C_Interface.cpp: In function ‘SEXPREC* setSharedParameter(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: C_Interface.cpp:190:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’? 190 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) }; | ^~~~~~~~~ | Rf_asInteger C_Interface.cpp:12:33: error: ‘asChar’ was not declared in this scope 12 | #define asString(x) string(CHAR(asChar(x))) | ^~~~~~ /home/biocbuild/R/R/include/Rinternals.h:203:24: note: in definition of macro ‘CHAR’ 203 | #define CHAR(x) R_CHAR(x) | ^ C_Interface.cpp:191:34: note: in expansion of macro ‘asString’ 191 | programSignature sig = { asString(signature),string(),string(),asString(kernel) }; | ^~~~~~~~ C_Interface.cpp: In function ‘SEXPREC* launchKernel(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: C_Interface.cpp:203:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’? 203 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) }; | ^~~~~~~~~ | Rf_asInteger C_Interface.cpp:12:33: error: ‘asChar’ was not declared in this scope 12 | #define asString(x) string(CHAR(asChar(x))) | ^~~~~~ /home/biocbuild/R/R/include/Rinternals.h:203:24: note: in definition of macro ‘CHAR’ 203 | #define CHAR(x) R_CHAR(x) | ^ C_Interface.cpp:205:34: note: in expansion of macro ‘asString’ 205 | programSignature sig = { asString(signature),string(),string(),asString(kernel) }; | ^~~~~~~~ C_Interface.cpp: In function ‘SEXPREC* getPreferredGroupSize(SEXP, SEXP, SEXP, SEXP)’: C_Interface.cpp:230:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’? 230 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) }; | ^~~~~~~~~ | Rf_asInteger C_Interface.cpp:12:33: error: ‘asChar’ was not declared in this scope 12 | #define asString(x) string(CHAR(asChar(x))) | ^~~~~~ /home/biocbuild/R/R/include/Rinternals.h:203:24: note: in definition of macro ‘CHAR’ 203 | #define CHAR(x) R_CHAR(x) | ^ C_Interface.cpp:231:34: note: in expansion of macro ‘asString’ 231 | programSignature sig = { asString(signature),string(),string(),asString(kernel) }; | ^~~~~~~~ C_Interface.cpp:239:20: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’? 239 | SEXP res = ScalarInteger(prefferedSize); | ^~~~~~~~~~~~~ | Rf_ScalarInteger C_Interface.cpp: In function ‘SEXPREC* getDeviceStatus(SEXP, SEXP)’: C_Interface.cpp:246:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’? 246 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) }; | ^~~~~~~~~ | Rf_asInteger C_Interface.cpp:252:24: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’? 252 | return(ScalarInteger(status)); | ^~~~~~~~~~~~~ | Rf_ScalarInteger C_Interface.cpp:272:16: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’? 272 | return(ScalarInteger(status)); | ^~~~~~~~~~~~~ | Rf_ScalarInteger C_Interface.cpp: In function ‘SEXPREC* getTrueAd(SEXP)’: C_Interface.cpp:281:16: error: ‘ScalarReal’ was not declared in this scope; did you mean ‘Rf_ScalarReal’? 281 | return(ScalarReal(ad_double)); | ^~~~~~~~~~ | Rf_ScalarReal C_Interface.cpp: In function ‘SEXPREC* asMatrix(SEXP, SEXP)’: C_Interface.cpp:286:9: error: ‘setAttrib’ was not declared in this scope; did you mean ‘Rf_setAttrib’? 286 | setAttrib(data, R_DimSymbol, dim); | ^~~~~~~~~ | Rf_setAttrib C_Interface.cpp: In function ‘SEXPREC* getDeviceFullInfo(SEXP, SEXP)’: C_Interface.cpp:292:27: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’? 292 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) }; | ^~~~~~~~~ | Rf_asInteger make: *** [/home/biocbuild/R/R/etc/Makeconf:204: C_Interface.o] Error 1 ERROR: compilation failed for package ‘gpuMagic’ * removing ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/gpuMagic’