* installing *source* package ‘ShortRead’ ...
** this is package ‘ShortRead’ version ‘1.69.3-2’
** using staged installation
checking for gcc... clang-22 -std=gnu23
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang-22 -std=gnu23 accepts -g... yes
checking for clang-22 -std=gnu23 option to accept ISO C89... unsupported
checking for gzeof in -lz... yes
checking how to run the C preprocessor... clang-22 -std=gnu23 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 8
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘clang version 22.1.3 (https://github.com/llvm/llvm-project e9846648fd6183ee6d8cbdb4502213fcf902a211)’
using C++ compiler: ‘clang version 22.1.3 (https://github.com/llvm/llvm-project e9846648fd6183ee6d8cbdb4502213fcf902a211)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/ShortRead/src'
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Biostrings_stubs.c -o Biostrings_stubs.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c IRanges_stubs.c -o IRanges_stubs.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_init_ShortRead.c -o R_init_ShortRead.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c XVector_stubs.c -o XVector_stubs.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c alphabet.c -o alphabet.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c count.c -o count.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c io.c -o io.o
io.c:227:43: warning: format specifies type 'double' but the argument has type 'const char *' [-Wformat]
227 | error("could not read file '%f'", translateChar(STRING_ELT(fname, 0)));
| ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| %s
/data/gannet/ripley/R/R-clang/include/Rinternals.h:1036:24: note: expanded from macro 'translateChar'
1036 | #define translateChar Rf_translateChar
| ^
io.c:659:23: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
658 | error("invalid 'strand' field '%s', %s:%d",
| ~~
| %c
659 | *elt[13], fname, lineno);
| ^~~~~~~~
io.c:677:19: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
676 | error("invalid 'filtering' field '%s', %s:%d",
| ~~
| %c
677 | *elt[21], fname, lineno);
| ^~~~~~~~
3 warnings generated.
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c io_bowtie.c -o io_bowtie.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c io_soap.c -o io_soap.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c readBfaToc.cc -o readBfaToc.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c read_maq_map.cc -o read_maq_map.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c sampler.c -o sampler.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c trim.c -o trim.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c util.c -o util.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/S4Vectors/include' -I'/data/gannet/ripley/R/test-clang/IRanges/include' -I'/data/gannet/ripley/R/test-clang/XVector/include' -I'/data/gannet/ripley/R/test-clang/Biostrings/include' -I'/data/gannet/ripley/R/test-clang/Rhtslib/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c xsnap.c -o xsnap.o
clang++-22 -stdlib=libc++ -std=gnu++20 -shared -L/usr/local/clang/lib64 -L/usr/local/clang22/lib -L/usr/local/clang22/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/ShortRead/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/ShortRead/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/ShortRead/src'
installing to /data/gannet/ripley/R/packages/tests-clang/ShortRead.Rcheck/00LOCK-ShortRead/00new/ShortRead/libs
** R
** 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 (ShortRead)