* installing *source* package 'GenABEL' ... Using auto-selected zip option '--use-zip-data' ** libs making DLL ... make[1]: Entering directory `/cygdrive/d/Rcompile/CRANpkg/local/2.11/GenABEL/src' g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c AbstractMatrix.cpp -o AbstractMatrix.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c AbstractMatrix_R.cpp -o AbstractMatrix_R.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c CastUtils.cpp -o CastUtils.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c Chip.cpp -o Chip.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c FileVector.cpp -o FileVector.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c FilteredMatrix.cpp -o FilteredMatrix.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c FilteredMatrix_R.cpp -o FilteredMatrix_R.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c Logger.cpp -o Logger.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c RealHandlerWrapper.cpp -o RealHandlerWrapper.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c ReusableFileHandle.cpp -o ReusableFileHandle.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c Transposer.cpp -o Transposer.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c bartlett_test.cpp -o bartlett_test.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c chinv2.cpp -o chinv2.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c cholesky2.cpp -o cholesky2.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c chsolve2.cpp -o chsolve2.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c convert.snp.affymetrix.cpp -o convert.snp.affymetrix.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c convert_snp_illumina.cpp -o convert_snp_illumina.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c convert_snp_merlin.cpp -o convert_snp_merlin.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c convert_snp_merlin_wslash.cpp -o convert_snp_merlin_wslash.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c convert_snp_tped.cpp -o convert_snp_tped.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c convert_util.cpp -o convert_util.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c coxfit2.cpp -o coxfit2.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c dautil.cpp -o dautil.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c dmatrix.cpp -o dmatrix.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c dometa.cpp -o dometa.o gcc -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -O3 -Wall -std=gnu99 -c fexact.c -o fexact.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c frutil.cpp -o frutil.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c gtps_container.cpp -o gtps_container.o gtps_container.cpp: In member function 'char gtps_container::get(unsigned int, unsigned int)': gtps_container.cpp:108: warning: unused variable 'our_byte_vallue' gtps_container.cpp: In member function 'char* gtps_container::get_gtps_array_for_snp(unsigned int)': gtps_container.cpp:132: warning: comparison between signed and unsigned integer expressions gtps_container.cpp: In member function 'char gtps_container::get_coding(unsigned int)': gtps_container.cpp:162: warning: control reaches end of non-void function gtps_container.cpp: In member function 'char gtps_container::get_strand(unsigned int)': gtps_container.cpp:154: warning: control reaches end of non-void function gcc -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -O3 -Wall -std=gnu99 -c gwaa.c -o gwaa.o gwaa.c: In function 'hom': gwaa.c:1019: warning: unused variable 'varhomweight' gwaa.c: In function 'r2new': gwaa.c:1289: warning: unused variable 'nsnps' g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c gwaa_cpp.cpp -o gwaa_cpp.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c gwaa_data.cpp -o gwaa_data.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c gwaautil.cpp -o gwaautil.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c interactions_rare_recesive_alleles.cpp -o interactions_rare_recesive_alleles.o interactions_rare_recesive_alleles.cpp: In member function 'int snp_snp_interaction_results::push_chi2(float, unsigned int, unsigned int)': interactions_rare_recesive_alleles.cpp:107: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp:110: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp: In member function 'unsigned int snp_snp_interaction_results::get_current_window(unsigned int)': interactions_rare_recesive_alleles.cpp:146: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp: In function 'float maximumValue(float*, unsigned int)': interactions_rare_recesive_alleles.cpp:164: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp:181: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp: In function 'double independence_test_2x2(int*, int*, int*, int, unsigned int, unsigned int, INDEPENDENCE_TEST_NAME_ENUM, int)': interactions_rare_recesive_alleles.cpp:321: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp: In function 'SEXPREC* interaction_rare_recesive_allele_C_(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)': interactions_rare_recesive_alleles.cpp:521: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp:529: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp:533: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp:540: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp:572: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp:583: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp:592: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp:604: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp:606: warning: comparison between signed and unsigned integer expressions interactions_rare_recesive_alleles.cpp:619: warning: right-hand operand of comma has no effect interactions_rare_recesive_alleles.cpp: In function 'double independence_test_2x2(double (*)[2], INDEPENDENCE_TEST_NAME_ENUM, int)': interactions_rare_recesive_alleles.cpp:258: warning: control reaches end of non-void function interactions_rare_recesive_alleles.cpp: In function 'SEXPREC* interaction_rare_recesive_allele_C_(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)': interactions_rare_recesive_alleles.cpp:431: warning: 'test_name' may be used uninitialized in this function g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c iterator.cpp -o iterator.o g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c iterator_functions.cpp -o iterator_functions.o iterator_functions.cpp: In function 'void qtscoreProcessor(double*, double*, int*, int*, int*, int*, double*)': iterator_functions.cpp:104: warning: unused variable 'i1' iterator_functions.cpp:169: warning: 'igt' is used uninitialized in this function g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c lm_gwaa.cpp -o lm_gwaa.o In file included from lm_gwaa.cpp:18: reg1.h: In constructor 'linear_reg::linear_reg(regdata, int)': reg1.h:40: warning: format '%Lf' expects type 'long double', but argument 2 has type 'double' g++ -I"d:/Rcompile/recent/R32-2.11.1/include" -I"d:/RCompile/CRANpkg/extralibs/local/include" -DCOMPILE_WITH_R -O2 -Wall -c merge.snp.data.cpp -o merge.snp.data.o merge.snp.data.cpp: In function 'void coding_error(unsigned int, unsigned int, unsigned int, unsigned int*, unsigned int*, char*, char*, unsigned int*, int*)': merge.snp.data.cpp:191: warning: comparison between signed and unsigned integer expressions merge.snp.data.cpp: In function 'void fast_merge_C_(char*, int*, int*, char*, int*, int*, unsigned int*, unsigned int*, unsigned int*, unsigned int*, bool*, char*, char*, char*, char*, char*, char**, unsigned int*, char*, unsigned int*, unsigned int*, unsigned int*, unsigned int*, unsigned int*, char*, char*, unsigned int*, char*, char*, bool*, char*)': merge.snp.data.cpp:558: warning: comparison between signed and unsigned integer expressions merge.snp.data.cpp:569: warning: comparison between signed and unsigned integer expressions g++ -shared -s -static-libgcc -o GenABEL.dll tmp.def AbstractMatrix.o AbstractMatrix_R.o CastUtils.o Chip.o FileVector.o FilteredMatrix.o FilteredMatrix_R.o Logger.o RealHandlerWrapper.o ReusableFileHandle.o Transposer.o bartlett_test.o chinv2.o cholesky2.o chsolve2.o convert.snp.affymetrix.o convert_snp_illumina.o convert_snp_merlin.o convert_snp_merlin_wslash.o convert_snp_tped.o convert_util.o coxfit2.o dautil.o dmatrix.o dometa.o fexact.o frutil.o gtps_container.o gwaa.o gwaa_cpp.o gwaa_data.o gwaautil.o interactions_rare_recesive_alleles.o iterator.o iterator_functions.o lm_gwaa.o merge.snp.data.o -Ld:/RCompile/CRANpkg/extralibs/local/lib -Ld:/Rcompile/recent/R32-2.11.1/bin -lR make[1]: Leaving directory `/cygdrive/d/Rcompile/CRANpkg/local/2.11/GenABEL/src' installing to d:/Rcompile/CRANpkg/lib/2.11/GenABEL/libs ... done ** R ** data *** resaving rda files ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded GenABEL v. 1.6-5 (February 07, 2011) loaded * MD5 sums packaged installation of 'GenABEL' as GenABEL_1.6-5.zip * DONE (GenABEL)