############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data FindMyFriends ### ############################################################################## ############################################################################## * checking for file ‘FindMyFriends/DESCRIPTION’ ... OK * preparing ‘FindMyFriends’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘FindMyFriends’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit-bombs.cpp -o cdhit-bombs.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit-common.cpp -o cdhit-common.o cdhit-common.cpp:341:9: warning: unused variable 'tm' [-Wunused-variable] time_t tm = time(NULL); ^ cdhit-common.cpp:394:14: warning: unused variable 'message' [-Wunused-variable] const char *message = "Your word length is %i, using %i may be faster!\n"; ^ cdhit-common.cpp:517:8: warning: unused variable 'bip' [-Wunused-variable] INTs *bip; ^ cdhit-common.cpp:866:8: warning: unused variable 's1' [-Wunused-variable] int s1, k0, back; ^ cdhit-common.cpp:866:12: warning: unused variable 'k0' [-Wunused-variable] int s1, k0, back; ^ cdhit-common.cpp:778:6: warning: unused variable 'iden_no1' [-Wunused-variable] int iden_no1; ^ cdhit-common.cpp:777:6: warning: unused variable 'jj' [-Wunused-variable] int jj, kk; ^ cdhit-common.cpp:777:10: warning: unused variable 'kk' [-Wunused-variable] int jj, kk; ^ cdhit-common.cpp:917:14: warning: unused variable 'letters' [-Wunused-variable] const char *letters = "acgtnx"; ^ cdhit-common.cpp:918:14: warning: unused variable 'letters2' [-Wunused-variable] const char *letters2 = "ACGTNX"; ^ cdhit-common.cpp:1200:6: warning: unused variable 'i' [-Wunused-variable] int i; ^ cdhit-common.cpp:1419:6: warning: unused variable 'ix1' [-Wunused-variable] int ix1, ix2, ix3, ix4; ^ cdhit-common.cpp:1417:6: warning: unused variable 'S' [-Wunused-variable] int S = frag_count ? frag_count : sequences.size(); ^ cdhit-common.cpp:1419:11: warning: unused variable 'ix2' [-Wunused-variable] int ix1, ix2, ix3, ix4; ^ cdhit-common.cpp:1419:16: warning: unused variable 'ix3' [-Wunused-variable] int ix1, ix2, ix3, ix4; ^ cdhit-common.cpp:1419:21: warning: unused variable 'ix4' [-Wunused-variable] int ix1, ix2, ix3, ix4; ^ cdhit-common.cpp:1418:25: warning: unused variable 'm' [-Wunused-variable] int j, k, j0, j1, k1, m; ^ cdhit-common.cpp:1469:6: warning: unused variable 'i' [-Wunused-variable] int i; ^ cdhit-common.cpp:1511:6: warning: unused variable 'i' [-Wunused-variable] int i, m = size, n = strlen( s ); ^ cdhit-common.cpp:1517:6: warning: unused variable 'i' [-Wunused-variable] int i, m = size < n ? size : n; ^ cdhit-common.cpp:1533:6: warning: unused variable 'i' [-Wunused-variable] int i, m = size < n ? size : n; ^ cdhit-common.cpp:1622:12: warning: unused variable 'last' [-Wunused-variable] Sequence *last = NULL; ^ cdhit-common.cpp:1755:9: warning: unused variable 'j' [-Wunused-variable] int i, j, k, len; ^ cdhit-common.cpp:1755:12: warning: unused variable 'k' [-Wunused-variable] int i, j, k, len; ^ cdhit-common.cpp:1944:12: warning: unused variable 'k' [-Wunused-variable] int i, k, N = sequences.size(); ^ cdhit-common.cpp:2098:7: warning: unused variable 'k' [-Wunused-variable] int k = len_eff < invd ? len_eff : invd; ^ cdhit-common.cpp:2103:7: warning: unused variable 'ks3' [-Wunused-variable] int ks3 = int((len_eff - band + 1.0)*(1.0 - options.distance_thd * ss)); ^ cdhit-common.cpp:2104:7: warning: unused variable 'kn3' [-Wunused-variable] int kn3 = int((len_eff - band + 1.0)*(1.0 - options.distance_thd * NAA)); ^ cdhit-common.cpp:2255:7: warning: unused variable 'size' [-Wunused-variable] int size = rep_seqs.size(); ^ cdhit-common.cpp:2337:6: warning: unused variable 'len' [-Wunused-variable] int len, len_bound; ^ cdhit-common.cpp:2337:11: warning: unused variable 'len_bound' [-Wunused-variable] int len, len_bound; ^ cdhit-common.cpp:2365:6: warning: unused variable 'K' [-Wunused-variable] int K = N - 100 * T; ^ cdhit-common.cpp:2367:9: warning: unused variable 'mem_limit' [-Wunused-variable] size_t mem_limit = MemoryLimit( mem_need, options ); ^ cdhit-common.cpp:2329:9: warning: unused variable 'j' [-Wunused-variable] int i, j, k; ^ cdhit-common.cpp:2338:6: warning: unused variable 'flag' [-Wunused-variable] int flag; ^ cdhit-common.cpp:2536:17: warning: unused variable 'aap_list' [-Wunused-variable] Vector & aap_list = buf.aap_list; ^ cdhit-common.cpp:2537:17: warning: unused variable 'aap_begin' [-Wunused-variable] Vector & aap_begin = buf.aap_begin; ^ cdhit-common.cpp:2545:6: warning: unused variable 'j' [-Wunused-variable] int j, k, j1, len = seq->size; ^ cdhit-common.cpp:2589:6: warning: unused variable 'best1' [-Wunused-variable] int best1, sum; ^ cdhit-common.cpp:2590:8: warning: unused variable 'lookptr' [-Wunused-variable] INTs *lookptr; ^ cdhit-common.cpp:2579:6: warning: unused variable 'M' [-Wunused-variable] int M = frag_size ? table.frag_count : S; ^ cdhit-common.cpp:2539:17: warning: unused variable 'taap' [-Wunused-variable] Vector & taap = buf.taap; ^ cdhit-common.cpp:2699:17: warning: unused variable 'aap_list' [-Wunused-variable] Vector & aap_list = buf.aap_list; ^ cdhit-common.cpp:2702:17: warning: unused variable 'taap' [-Wunused-variable] Vector & taap = buf.taap; ^ cdhit-common.cpp:2700:17: warning: unused variable 'aap_begin' [-Wunused-variable] Vector & aap_begin = buf.aap_begin; ^ cdhit-common.cpp:2876:55: warning: unused variable 'required_aa1' [-Wunused-variable] int band_width1, band_left, band_center, band_right, required_aa1; ^ cdhit-common.cpp:3024:9: warning: unused variable 'p0' [-Wunused-variable] float p0 = 0; ^ cdhit-common.cpp:2979:14: warning: unused variable 'mega' [-Wunused-variable] size_t mem, mega = 1000000; ^ cdhit-common.cpp:2978:9: warning: unused variable 'mem_limit' [-Wunused-variable] size_t mem_limit = MemoryLimit( mem_need, options ); ^ cdhit-common.cpp:2950:6: warning: unused variable 'flag' [-Wunused-variable] int flag; ^ cdhit-common.cpp:2979:9: warning: unused variable 'mem' [-Wunused-variable] size_t mem, mega = 1000000; ^ cdhit-common.cpp:2949:11: warning: unused variable 'len_bound' [-Wunused-variable] int len, len_bound; ^ cdhit-common.cpp:2949:6: warning: unused variable 'len' [-Wunused-variable] int len, len_bound; ^ cdhit-common.cpp:3145:11: warning: unused variable 'seqi' [-Wunused-variable] char *seqi = seq->data; ^ cdhit-common.cpp:3097:9: warning: unused variable 'mem_limit' [-Wunused-variable] size_t mem_limit = MemoryLimit( mem_need, options ); ^ cdhit-common.cpp:3063:9: warning: unused variable 'is' [-Wunused-variable] int i, is, js, flag; ^ cdhit-common.cpp:3063:13: warning: unused variable 'js' [-Wunused-variable] int i, is, js, flag; ^ cdhit-common.cpp:61:12: warning: unused variable 'aa' [-Wunused-const-variable] const char aa[] = {"ARNDCQEGHILKMFPSTWYVBZX"}; ^ 58 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit-est.cpp -o cdhit-est.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit.cpp -o cdhit.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fastaFunctions.cpp -o fastaFunctions.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fmf-common.cpp -o fmf-common.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c linearKernel.cpp -o linearKernel.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c neighborhoodSim.cpp -o neighborhoodSim.o neighborhoodSim.cpp:432:9: warning: unused variable 'maxO' [-Wunused-variable] int maxO = 0; ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c panSim.cpp -o panSim.o panSim.cpp:19:9: warning: unused variable 'iVal' [-Wunused-variable] int iVal; ^ panSim.cpp:16:9: warning: unused variable 'k' [-Wunused-variable] int k; ^ panSim.cpp:20:9: warning: unused variable 'jVal' [-Wunused-variable] int jVal; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c progress.cpp -o progress.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c smallgraph.cpp -o smallgraph.o smallgraph.cpp:28:32: warning: unused variable 'itvec' [-Wunused-variable] std::vector::iterator itvec; ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o FindMyFriends.so RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o fastaFunctions.o fmf-common.o linearKernel.o neighborhoodSim.o panSim.o progress.o smallgraph.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /private/tmp/RtmpDHTB0i/Rinst204c8b89389/00LOCK-FindMyFriends/00new/FindMyFriends/libs ** R Error in .install_package_code_files(".", instdir) : files in 'Collate' field missing from '/private/tmp/RtmpDHTB0i/Rbuild204c36f2f516/FindMyFriends/R': zzz.R ERROR: unable to collate and parse R files for package ‘FindMyFriends’ * removing ‘/private/tmp/RtmpDHTB0i/Rinst204c8b89389/FindMyFriends’ ----------------------------------- ERROR: package installation failed