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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL snpStats
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘snpStats’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Runcertain.c -o Runcertain.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -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-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c count_gt.c -o count_gt.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c covwin.c -o covwin.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c force_hom.c -o force_hom.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fst.c -o fst.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glm_test.c -o glm_test.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -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-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hash_index.c -o hash_index.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hphase.c -o hphase.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c imputation.c -o imputation.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c in.c -o in.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -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-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c invert.c -o invert.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ipf.c -o ipf.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ld.c -o ld.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c misc.c -o misc.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mla.c -o mla.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mvphenotype.c -o mvphenotype.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c outdata.c -o outdata.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c plink.c -o plink.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -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-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -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-3.20-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-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c single_snp_tests.c -o single_snp_tests.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c snp_summary.c -o snp_summary.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c snpmpy.c -o snpmpy.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c solve_cubic.c -o solve_cubic.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c structure.c -o structure.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c subset.c -o subset.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -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-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tdt.c -o tdt.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -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-3.20-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-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c uncertain.c -o uncertain.o
gcc -shared -L/home/biocbuild/bbs-3.20-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-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-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)
