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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data snpStats
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* checking for file ‘snpStats/DESCRIPTION’ ... OK
* preparing ‘snpStats’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to process help pages)
-----------------------------------
* installing *source* package ‘snpStats’ ...
** this is package ‘snpStats’ version ‘1.61.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c Runcertain.c -o Runcertain.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c bind.c -o bind.o
bind.c: In function ‘snp_rbind’:
bind.c:25:9: warning: implicit declaration of function ‘IS_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
25 | if(!IS_S4_OBJECT(This)) {
| ^~~~~~~~~~~~
| SET_OBJECT
bind.c:69:3: warning: implicit declaration of function ‘SET_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
69 | SET_S4_OBJECT(Result);
| ^~~~~~~~~~~~~
| SET_OBJECT
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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c count_gt.c -o count_gt.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c covwin.c -o covwin.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c force_hom.c -o force_hom.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fst.c -o fst.o
fst.c: In function ‘Fst’:
fst.c:26:7: warning: implicit declaration of function ‘IS_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
26 | if(!IS_S4_OBJECT(Snps)) {
| ^~~~~~~~~~~~
| SET_OBJECT
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c glm_test.c -o glm_test.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function ‘snp_lhs_score’:
glm_test_R.c:27:7: warning: implicit declaration of function ‘IS_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
27 | if(!IS_S4_OBJECT(Y)) {
| ^~~~~~~~~~~~
| SET_OBJECT
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
glm_test_R.c: In function ‘snp_lhs_estimate’:
glm_test_R.c:1289:3: warning: implicit declaration of function ‘SET_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
1289 | SET_S4_OBJECT(Estimates);
| ^~~~~~~~~~~~~
| SET_OBJECT
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c hash_index.c -o hash_index.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c hphase.c -o hphase.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c imputation.c -o imputation.o
imputation.c: In function ‘snp_impute’:
imputation.c:398:3: warning: implicit declaration of function ‘SET_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
398 | SET_S4_OBJECT(Result);
| ^~~~~~~~~~~~~
| SET_OBJECT
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c in.c -o in.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c input.c -o input.o
input.c: In function ‘insnp_new’:
input.c:333:3: warning: implicit declaration of function ‘SET_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
333 | SET_S4_OBJECT(Result);
| ^~~~~~~~~~~~~
| SET_OBJECT
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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c invert.c -o invert.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ipf.c -o ipf.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ld.c -o ld.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c misc.c -o misc.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c mla.c -o mla.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c mvphenotype.c -o mvphenotype.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c outdata.c -o outdata.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c plink.c -o plink.o
plink.c: In function ‘readbed’:
plink.c:62:3: warning: implicit declaration of function ‘SET_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
62 | SET_S4_OBJECT(Result);
| ^~~~~~~~~~~~~
| SET_OBJECT
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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
read_uncertain.c:140:3: warning: implicit declaration of function ‘SET_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
140 | SET_S4_OBJECT(Result);
| ^~~~~~~~~~~~~
| SET_OBJECT
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c readped.c -o readped.o
readped.c: In function ‘readped’:
readped.c:330:3: warning: implicit declaration of function ‘SET_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
330 | SET_S4_OBJECT(Smat);
| ^~~~~~~~~~~~~
| SET_OBJECT
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-3.23-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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c single_snp_tests.c -o single_snp_tests.o
single_snp_tests.c: In function ‘score_single’:
single_snp_tests.c:70:7: warning: implicit declaration of function ‘IS_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
70 | if(!IS_S4_OBJECT(Snps)) {
| ^~~~~~~~~~~~
| SET_OBJECT
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c snp_summary.c -o snp_summary.o
snp_summary.c: In function ‘X_snp_summary’:
snp_summary.c:27:7: warning: implicit declaration of function ‘IS_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
27 | if(!IS_S4_OBJECT(Snps)) {
| ^~~~~~~~~~~~
| SET_OBJECT
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c snpmpy.c -o snpmpy.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c solve_cubic.c -o solve_cubic.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c structure.c -o structure.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c subset.c -o subset.o
subset.c: In function ‘subset’:
subset.c:58:3: warning: implicit declaration of function ‘SET_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
58 | SET_S4_OBJECT(Result);
| ^~~~~~~~~~~~~
| SET_OBJECT
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c tdt.c -o tdt.o
tdt.c: In function ‘score_tdt’:
tdt.c:60:7: warning: implicit declaration of function ‘IS_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
60 | if(!IS_S4_OBJECT(Snps)) {
| ^~~~~~~~~~~~
| SET_OBJECT
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c testBig.c -o testBig.o
testBig.c: In function ‘snp_big’:
testBig.c:21:3: warning: implicit declaration of function ‘SET_S4_OBJECT’; did you mean ‘SET_OBJECT’? [-Wimplicit-function-declaration]
21 | SET_S4_OBJECT(Result);
| ^~~~~~~~~~~~~
| SET_OBJECT
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-3.23-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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c uncertain.c -o uncertain.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-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-3.23-bioc/R/lib -lR
installing to /tmp/Rtmpab2dvh/Rinst1c32fad2d07eb/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
Error: package or namespace load failed for ‘snpStats’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/tmp/Rtmpab2dvh/Rinst1c32fad2d07eb/00LOCK-snpStats/00new/snpStats/libs/snpStats.so':
/tmp/Rtmpab2dvh/Rinst1c32fad2d07eb/00LOCK-snpStats/00new/snpStats/libs/snpStats.so: undefined symbol: IS_S4_OBJECT
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/tmp/Rtmpab2dvh/Rinst1c32fad2d07eb/snpStats’
-----------------------------------
ERROR: package installation failed
