############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL snpStats ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘snpStats’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c Runcertain.c -o Runcertain.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c bind.c -o bind.o bind.c: In function ‘snp_cbind’: bind.c:243:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=] 243 | error("Duplicated column name at column %d overall from column %d of object %d", ij+1, j+1, i+1); | ~^ ~~~~ | | | | int R_xlen_t {aka long int} | %ld gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c count_gt.c -o count_gt.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c covwin.c -o covwin.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c force_hom.c -o force_hom.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c fst.c -o fst.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c glm_test.c -o glm_test.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c glm_test_R.c -o glm_test_R.o glm_test_R.c: In function ‘snp_lhs_score’: glm_test_R.c:305:17: warning: too many arguments for format [-Wformat-extra-args] 305 | warning("Matrix not positive semi-definite in test ", t+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ glm_test_R.c: In function ‘snp_rhs_score’: glm_test_R.c:805:17: warning: too many arguments for format [-Wformat-extra-args] 805 | warning("Matrix not positive semi-definite in test ", test+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ glm_test_R.c:368:7: warning: unused variable ‘max_name_length’ [-Wunused-variable] 368 | int max_name_length = MAX_NAME_LENGTH -1; | ^~~~~~~~~~~~~~~ glm_test_R.c: In function ‘pool2_glm’: glm_test_R.c:937:17: warning: too many arguments for format [-Wformat-extra-args] 937 | warning("Matrix not positive semi-definite in pooled test ", i+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c hash_index.c -o hash_index.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c hphase.c -o hphase.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c imputation.c -o imputation.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c in.c -o in.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c input.c -o input.o input.c: In function ‘simplify_names’: input.c:788:5: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 788 | strncpy(back, front, MAX_FLD-1); | ^ input.c: In function ‘insnp_new’: input.c:442:11: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 442 | strncpy(gtype2, field, MAX_FLD-1); | ^ input.c:440:11: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 440 | strncpy(gtype1, field, MAX_FLD-1); | ^ input.c:438:11: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 438 | strncpy(gtype1, field, MAX_FLD-1); | ^ input.c:435:11: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 435 | strncpy(cscore, field, MAX_FLD-1); | ^ input.c:432:11: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 432 | strncpy(snpid, field, MAX_FLD-1); | ^ input.c:429:11: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 429 | strncpy(sampid, field, MAX_FLD-1); | ^ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c invert.c -o invert.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c ipf.c -o ipf.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c ld.c -o ld.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c misc.c -o misc.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c mla.c -o mla.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c mvphenotype.c -o mvphenotype.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c outdata.c -o outdata.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c plink.c -o plink.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c read_uncertain.c -o read_uncertain.o read_uncertain.c: In function ‘read_mach’: read_uncertain.c:103:36: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=] 103 | Rprintf("Reading SnpMatrix with %d rows and %d columns\n", lines, ncol); | ~^ ~~~~~ | | | | int long int | %ld gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c readped.c -o readped.o readped.c: In function ‘readped’: readped.c:234:33: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size between 0 and 127 [-Wformat-truncation=] 234 | snprintf(fmid, MAX_ID, "%s%c%d", fid, sepchar, memi); | ^~ In file included from /usr/include/stdio.h:980, from /home/biocbuild/bbs-3.21-bioc/R/include/R.h:44, from readped.c:3: In function ‘snprintf’, inlined from ‘readped’ at readped.c:234:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:54:10: note: ‘__builtin___snprintf_chk’ output between 3 and 140 bytes into a destination of size 128 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c single_snp_tests.c -o single_snp_tests.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c snp_summary.c -o snp_summary.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c snpmpy.c -o snpmpy.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c solve_cubic.c -o solve_cubic.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c structure.c -o structure.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c subset.c -o subset.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c switch.c -o switch.o switch.c: In function ‘test_switch’: switch.c:32:8: warning: variable ‘female2’ set but not used [-Wunused-but-set-variable] 32 | int *female2 = NULL; | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c tdt.c -o tdt.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c testBig.c -o testBig.o testBig.c: In function ‘snp_big’: testBig.c:31:27: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 31 | sprintf(name, "Subject%d", i+1); | ^~ testBig.c:31:19: note: directive argument in the range [1, 2147483647] 31 | sprintf(name, "Subject%d", i+1); | ^~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from /home/biocbuild/bbs-3.21-bioc/R/include/R.h:44, from testBig.c:1: In function ‘sprintf’, inlined from ‘snp_big’ at testBig.c:31:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 9 and 18 bytes into a destination of size 16 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c uncertain.c -o uncertain.o gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o snpStats.so Runcertain.o bind.o count_gt.o covwin.o force_hom.o fst.o glm_test.o glm_test_R.o hash_index.o hphase.o imputation.o in.o input.o invert.o ipf.o ld.o misc.o mla.o mvphenotype.o outdata.o plink.o read_uncertain.o readped.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o structure.o subset.o switch.o tdt.o testBig.o uncertain.o -lz -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-snpStats/00new/snpStats/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (snpStats)