* installing *source* package ‘tidysq’ ...
** package ‘tidysq’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 18.1.4’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/tidysq/src'
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c apply_R_function.cpp -o apply_R_function.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/tidysq.h:5:
In file included from ./../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/tidysq.h:5:
In file included from ./../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from apply_R_function.cpp:1:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from apply_R_function.cpp:1:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c bite.cpp -o bite.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c collapse.cpp -o collapse.o
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c complement.cpp -o complement.o
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c find_invalid_letters.cpp -o find_invalid_letters.o
In file included from bite.cpp:1:
In file included from ../inst/include/tidysq/ops/bite.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from bite.cpp:3:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from collapse.cpp:1:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from collapse.cpp:1:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c find_motifs.cpp -o find_motifs.o
In file included from complement.cpp:3:
In file included from ../inst/include/tidysq/ops/complement.h:4:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from complement.cpp:4:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from find_invalid_letters.cpp:1:
In file included from ../inst/include/tidysq/ops/find_invalid_letters.h:4:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from find_invalid_letters.cpp:2:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c get_standard_alphabet.cpp -o get_standard_alphabet.o
2 warnings generated.
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c guess_standard_alph.cpp -o guess_standard_alph.o
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c has.cpp -o has.o
In file included from find_motifs.cpp:1:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from find_motifs.cpp:1:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from get_standard_alphabet.cpp:3:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from get_standard_alphabet.cpp:3:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from guess_standard_alph.cpp:1:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from guess_standard_alph.cpp:1:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from has.cpp:1:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from has.cpp:1:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
2 warnings generated.
2 warnings generated.
2 warnings generated.
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c obtain_alphabet.cpp -o obtain_alphabet.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c pack.cpp -o pack.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c paste.cpp -o paste.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c random_sq.cpp -o random_sq.o
In file included from obtain_alphabet.cpp:1:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from obtain_alphabet.cpp:1:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from paste.cpp:1:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from paste.cpp:1:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from pack.cpp:1:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from pack.cpp:1:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from random_sq.cpp:3:
In file included from ../inst/include/tidysq/ops/random_sq.h:5:
In file included from ../inst/include/tidysq/ops/pack.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from random_sq.cpp:4:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c read_fasta.cpp -o read_fasta.o
2 warnings generated.
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c remove_NA.cpp -o remove_NA.o
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c remove_ambiguous.cpp -o remove_ambiguous.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c reverse.cpp -o reverse.o
In file included from read_fasta.cpp:3:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from read_fasta.cpp:3:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c sqapply.cpp -o sqapply.o
In file included from remove_NA.cpp:3:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from remove_NA.cpp:3:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c substitute_letters.cpp -o substitute_letters.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c test-pack.cpp -o test-pack.o
In file included from remove_ambiguous.cpp:3:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from remove_ambiguous.cpp:3:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from reverse.cpp:1:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from reverse.cpp:1:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c test-runner.cpp -o test-runner.o
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c translate.cpp -o translate.o
In file included from sqapply.cpp:1:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c typify.cpp -o typify.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c unpack.cpp -o unpack.o
1 warning generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c write_fasta.cpp -o write_fasta.o
In file included from test-pack.cpp:3:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from test-pack.cpp:3:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from substitute_letters.cpp:3:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from substitute_letters.cpp:3:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
2 warnings generated.
2 warnings generated.
In file included from translate.cpp:1:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from translate.cpp:1:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from typify.cpp:3:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from typify.cpp:3:
In file included from ../inst/include/tidysq/Rcpp-import.h:3:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from unpack.cpp:3:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from unpack.cpp:3:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
In file included from write_fasta.cpp:1:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h:13:14: warning: extension used [-Wlanguage-extension-token]
13 | for (typeof(vector_in.size()) i = 0; i < vector_in.size(); i++) {
| ^
In file included from write_fasta.cpp:1:
In file included from ../inst/include/tidysq.h:5:
In file included from ../inst/include/tidysq/Sq.h:5:
In file included from ../inst/include/tidysq/ops/unpack.h:6:
../inst/include/tidysq/ProtoSq.h:68:17: warning: extension used [-Wlanguage-extension-token]
68 | for (typeof(content_.size()) i = 0; i < content_.size(); i++) {
| ^
2 warnings generated.
2 warnings generated.
2 warnings generated.
2 warnings generated.
2 warnings generated.
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o tidysq.so RcppExports.o apply_R_function.o bite.o collapse.o complement.o find_invalid_letters.o find_motifs.o get_standard_alphabet.o guess_standard_alph.o has.o obtain_alphabet.o pack.o paste.o random_sq.o read_fasta.o remove_NA.o remove_ambiguous.o reverse.o sqapply.o substitute_letters.o test-pack.o test-runner.o translate.o typify.o unpack.o write_fasta.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/tidysq/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/tidysq/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/tidysq/src'
installing to /data/gannet/ripley/R/packages/tests-clang/tidysq.Rcheck/00LOCK-tidysq/00new/tidysq/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (tidysq)