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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL ShortRead
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘ShortRead’ ...
** this is package ‘ShortRead’ version ‘1.69.3’
** using staged installation
checking for gcc... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 accepts -g... yes
checking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c R_init_ShortRead.c -o R_init_ShortRead.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c alphabet.c -o alphabet.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c count.c -o count.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c io.c -o io.o
io.c: In function ‘read_prb_as_character’:
io.c:227:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘const char *’ [-Wformat=]
  227 |         error("could not read file '%f'", translateChar(STRING_ELT(fname, 0)));
      |                                     ~^
      |                                      |
      |                                      double
      |                                     %s
io.c: In function ‘_read_solexa_export_file’:
io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
  658 |                 error("invalid 'strand' field '%s', %s:%d",
      |                                                ~^
      |                                                 |
      |                                                 char *
      |                                                %d
  659 |                       *elt[13], fname, lineno);
      |                       ~~~~~~~~                   
      |                       |
      |                       int
io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
  676 |             error("invalid 'filtering' field '%s', %s:%d",
      |                                               ~^
      |                                                |
      |                                                char *
      |                                               %d
  677 |                   *elt[21], fname, lineno);
      |                   ~~~~~~~~                      
      |                   |
      |                   int
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c io_bowtie.c -o io_bowtie.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c io_soap.c -o io_soap.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/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  -g -O2  -Wall -Werror=format-security  -c readBfaToc.cc -o readBfaToc.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/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  -g -O2  -Wall -Werror=format-security  -c read_maq_map.cc -o read_maq_map.o
In file included from read_maq_map.cc:13:
maqmap_m.h: In function ‘maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 128]’:
maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free]
  102 |             Rf_error("MAQ format '%d' not supported", mm->format);
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 128]’,
    inlined from ‘void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 128]’ at maqmap_m.h:74:35,
    inlined from ‘maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 128]’ at maqmap_m.h:101:30:
maqmap_m.h:84:14: note: call to ‘void free(void*)’ here
   84 |     std::free(mm);
      |     ~~~~~~~~~^~~~
maqmap_m.h: In function ‘maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 64]’:
maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free]
  102 |             Rf_error("MAQ format '%d' not supported", mm->format);
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 64]’,
    inlined from ‘void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 64]’ at maqmap_m.h:74:35,
    inlined from ‘maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 64]’ at maqmap_m.h:101:30:
maqmap_m.h:84:14: note: call to ‘void free(void*)’ here
   84 |     std::free(mm);
      |     ~~~~~~~~~^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c sampler.c -o sampler.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c trim.c -o trim.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c util.c -o util.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c xsnap.c -o xsnap.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -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 -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-ShortRead/00new/ShortRead/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘Rsamtools’:
 class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'
Execution halted
ERROR: lazy loading failed for package ‘ShortRead’
* removing ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/ShortRead’
* restoring previous ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/ShortRead’