cpanse
commented
9 months ago #!/bin/bash
export CXX=clang++-17
export CC=clang-17
export PKG_CFLAG="-pendantic -O2 -Wall"
export PKG_CXXFLAGS="-pedantic -O2 -Wall"
Rpkg="protViz"
while true;
do
R CMD build --no-build-vignettes ${Rpkg} && R CMD INSTALL ${Rpkg}_0.7.8.tar.gz
sleep 10;
done
exit 0
^~ ~/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 57 | REprintf("%.s", num, s); |^~ ~In file included from deisotoper.cpp:1: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:181: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] 30 | Rf_warningcall(call, s.c_str()); | ^~~~~ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this 30 | Rf_warningcall(call, s.c_str()); | ^ | "%s", /usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c aa2mass.cpp -o aa2mass.o deisotoper.cpp:14:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security] 14 | ::Rf_warning(s.c_str()); | ^~~~~ deisotoper.cpp:14:15: note: treat the string as an argument to avoid this 14 | ::Rf_warning(s.c_str()); | ^ | "%s", In file included from aa2mass.cpp:32: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:128: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/routines.h:26: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 53 | Rprintf("%.s", num, s); |^~ ~/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 57 | REprintf("%.s", num, s); |^~ ~In file included from aa2mass.cpp:32: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:181: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] 30 | Rf_warningcall(call, s.c_str()); | ^~~~~ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this 30 | Rf_warningcall(call, s.c_str()); | ^ | "%s", 4 warnings generated. /usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFYSOURCE=3 -c findNN.cpp -o findNN_.o /usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFYSOURCE=3 -c computeFragmentIons.c -o computeFragmentIons.o In file included from findNN.cpp:4: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:128: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/routines.h:26: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 53 | Rprintf("%.s", num, s); |^~ ~/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 57 | REprintf("%.s", num, s); |^~ ~In file included from findNN_.cpp:4: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:181: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] 30 | Rf_warningcall(call, s.c_str()); | ^~~~~ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this 30 | Rf_warningcall(call, s.c_str()); | ^ | "%s", /usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c computeParentIonMass.c -o computeParentIonMass.o 3 warnings generated. /usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c findNN.c -o findNN.o /usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o /usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c fasta.cpp -o fasta.o In file included from RcppExports.cpp:4: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:128: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/routines.h:26: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 53 | Rprintf("%.s", num, s); |^~ ~/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 57 | REprintf("%.s", num, s); |^~ ~In file included from RcppExports.cpp:4: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:181: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] 30 | Rf_warningcall(call, s.c_str()); | ^~~~~ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this 30 | Rf_warningcall(call, s.c_str()); | ^ | "%s", In file included from fasta.cpp:10: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:128: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/routines.h:26: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 53 | Rprintf("%.s", num, s); |^~ ~/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 57 | REprintf("%.*s", num, s); |^~ ~In file included from fasta.cpp:10: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27: In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:181: /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] 30 | Rf_warningcall(call, s.c_str()); | ^~~~~ /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this 30 | Rf_warningcall(call, s.c_str()); | ^ | "%s", 3 warnings generated. 3 warnings generated. 3 warnings generated. /usr/local/clang17/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang17/lib -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o protViz.so protVizinit.o deisotoper.o aa2mass.o findNN.o computeFragmentIons.o computeParentIonMass.o findNN.o RcppExports.o fasta.o make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/protViz/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/protViz/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/protViz/src' installing to /data/gannet/ripley/R/packages/tests-clang/protViz.Rcheck/00LOCK-protViz/00new/protViz/libs R data * moving datasets to lazyload DB demo exec 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