Mock Version: 1.2.14
ENTER do(['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv6hl --nodeps /builddir/build/SPECS/R-Biostrings.spec'], timeout=0chrootPath='/var/lib/mock/fedora-23-armhfp-pidora-round2-root-15749/root'uid=1000gid=135env={'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'CCACHE_DIR': '/tmp/ccache', 'HOME': '/builddir', 'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'CCACHE_UMASK': '002'}logger=<mockbuild.trace_decorator.getLog object at 0xb5ef2610>shell=FalseprintOutput=Falseuser='mockbuild')
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv6hl --nodeps /builddir/build/SPECS/R-Biostrings.spec'] with env {'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'CCACHE_DIR': '/tmp/ccache', 'HOME': '/builddir', 'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'CCACHE_UMASK': '002'} and shell False
Building target platforms: armv6hl
Building for target armv6hl
Wrote: /builddir/build/SRPMS/R-Biostrings-2.36.1-3bs02npfc23.src.rpm
Child return code was: 0
LEAVE do --> 

ENTER do(['bash', '--login', '-c', "/usr/bin/rpmbuild -bb --target armv6hl --nodeps --define '__spec_check_template exit 0; ' /builddir/build/SPECS/R-Biostrings.spec "], timeout=0chrootPath='/var/lib/mock/fedora-23-armhfp-pidora-round2-root-15749/root'uid=1000gid=135env={'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'CCACHE_DIR': '/tmp/ccache', 'HOME': '/builddir', 'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'CCACHE_UMASK': '002'}logger=<mockbuild.trace_decorator.getLog object at 0xb5ef2610>shell=Falseprivate_network=TrueprintOutput=Falseuser='mockbuild')
Executing command: ['bash', '--login', '-c', "/usr/bin/rpmbuild -bb --target armv6hl --nodeps --define '__spec_check_template exit 0; ' /builddir/build/SPECS/R-Biostrings.spec "] with env {'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'CCACHE_DIR': '/tmp/ccache', 'HOME': '/builddir', 'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'CCACHE_UMASK': '002'} and shell False
Building target platforms: armv6hl
Building for target armv6hl
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.OrjRZO
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf Biostrings
+ /usr/bin/mkdir -p Biostrings
+ cd Biostrings
+ /usr/bin/gzip -dc /builddir/build/SOURCES/Biostrings_2.36.1.tar.gz
+ /usr/bin/tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
Patch #0 (R-Biostrings-no-zlibbioc.patch):
+ echo 'Patch #0 (R-Biostrings-no-zlibbioc.patch):'
+ /usr/bin/cat /builddir/build/SOURCES/R-Biostrings-no-zlibbioc.patch
+ /usr/bin/patch -p1 -b --suffix .no-zlibbioc --fuzz=0
patching file Biostrings/DESCRIPTION
patching file Biostrings/NAMESPACE
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.S8aQmV
+ umask 022
+ cd /builddir/build/BUILD
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.4h5Bb2
+ cd Biostrings
+ exit 0
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-Biostrings-2.36.1-3bs02npfc23.arm '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.36.1-3bs02npfc23.arm
++ dirname /builddir/build/BUILDROOT/R-Biostrings-2.36.1-3bs02npfc23.arm
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-Biostrings-2.36.1-3bs02npfc23.arm
+ cd Biostrings
+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.36.1-3bs02npfc23.arm
+ mkdir -p /builddir/build/BUILDROOT/R-Biostrings-2.36.1-3bs02npfc23.arm/usr/lib/R/library
+ R CMD INSTALL Biostrings -l /builddir/build/BUILDROOT/R-Biostrings-2.36.1-3bs02npfc23.arm/usr/lib/R/library
* installing *source* package 'Biostrings' ...
** libs
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c BAB_class.c -o BAB_class.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c BitMatrix.c -o BitMatrix.o
BitMatrix.c: In function 'debug_BitMatrix':
BitMatrix.c:382:41: warning: left shift count >= width of type [-Wshift-count-overflow]
   bitcol0 = _new_BitCol(40, 33UL + (1UL << 39));
                                         ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:193:18: warning: unused variable 'poffsets_order' [-Wunused-variable]
  IntAE poffsets, poffsets_order;
                  ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c SparseList_utils.c -o SparseList_utils.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:123:3: warning: 'lkup_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
   ^
XStringSet_class.c:102:18: note: 'lkup_length' was declared here
  int ans_length, lkup_length, i;
                  ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function 'parse_FASTQ_file':
XStringSet_io.c:815:7: warning: 'load_rec' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (load_rec && loader->load_qual != NULL)
       ^
XStringSet_io.c:737:19: note: 'load_rec' was declared here
      lineinrecno, load_rec;
                   ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c XString_class.c -o XString_class.o
XString_class.c: In function 'new_XString_from_CHARACTER':
XString_class.c:184:2: warning: 'lkup_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
  _copy_CHARSXP_to_Chars_holder(&ans_holder, x_elt,
  ^
XString_class.c:168:6: note: 'lkup_length' was declared here
  int lkup_length;
      ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c XVector_stubs.c -o XVector_stubs.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:173:22: warning: 'sc' may be used uninitialized in this function [-Wmaybe-uninitialized]
  INTEGER(ans_elt)[0] = score;
                      ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned':
align_utils.c:254:14: warning: 'indelWidthSubject' may be used uninitialized in this function [-Wmaybe-uninitialized]
     jPattern += indelWidthSubject;
              ^
align_utils.c:235:42: warning: 'indelStartSubject' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
                                          ^
align_utils.c:225:26: warning: 'indelWidthPattern' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
                          ^
align_utils.c:236:50: warning: 'indelStartPattern' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
                                                  ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c find_palindromes.c -o find_palindromes.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c gtestsim.c -o gtestsim.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c inject_code.c -o inject_code.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c io_utils.c -o io_utils.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function 'XStringSet_two_way_letter_frequency':
letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
   int x_width, y_width, x_length, *ans_mat, i, x_pos;
                                                ^
letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
   SEXP ans, ans_dimnames;
             ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c match_BOC.c -o match_BOC.o
match_BOC.c: In function 'BOC_exact_search':
match_BOC.c:331:3: warning: label 'continue0' defined but not used [-Wunused-label]
   continue0: ;
   ^
match_BOC.c:268:68: warning: unused variable 'noffsets' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                    ^
match_BOC.c:268:59: warning: unused variable 'offsets' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                           ^
match_BOC.c:268:55: warning: unused variable 'j' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                       ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function 'BOC2_exact_search':
match_BOC2.c:288:3: warning: label 'continue0' defined but not used [-Wunused-label]
   continue0: ;
   ^
match_BOC2.c:234:68: warning: unused variable 'noffsets' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                    ^
match_BOC2.c:234:59: warning: unused variable 'offsets' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                           ^
match_BOC2.c:234:55: warning: unused variable 'j' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                       ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c match_PWM.c -o match_PWM.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c match_pattern.c -o match_pattern.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c match_pattern_indels.c -o match_pattern_indels.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'match_pdict':
match_pdict.c:59:26: warning: variable 'fixedP' set but not used [-Wunused-but-set-variable]
  int max_nmis, min_nmis, fixedP, fixedS;
                          ^
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:442:12: warning: 'ans_col' may be used uninitialized in this function [-Wmaybe-uninitialized]
    ans_col += tb_length;
            ^
match_pdict.c:415:58: note: 'ans_col' was declared here
  int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
                                                          ^
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:493:13: warning: 'ans_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
     ans_elt += P_length;
             ^
match_pdict.c:464:57: note: 'ans_elt' was declared here
  int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
                                                         ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function 'split_and_move_pointers':
match_pdict_ACtree2.c:1069:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^
match_pdict_ACtree2.c: In function 'merge_pointers':
match_pdict_ACtree2.c:1114:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^
match_pdict_ACtree2.c: At top level:
match_pdict_ACtree2.c:640:21: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used [-Wunused-function]
 static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
                     ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_Twobit.c: In function 'build_Twobit':
match_pdict_Twobit.c:91:2: warning: 'twobit_sign2pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
  PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos));
  ^
match_pdict_Twobit.c:126:12: note: 'twobit_sign2pos' was declared here
  SEXP ans, twobit_sign2pos;
            ^
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:665:49: warning: unused variable 'ncol' [-Wunused-variable]
  int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
                                                 ^
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:723:6: warning: unused variable 'nelt' [-Wunused-variable]
  int nelt, nkey0, nkey1, nkey2, i;
      ^
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:823:44: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                            ^
match_pdict_utils.c:823:27: warning: unused variable 'total_NFC' [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                           ^
match_pdict_utils.c:822:33: warning: unused variable 'NFC' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                 ^
match_pdict_utils.c:822:26: warning: unused variable 'nloci' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                          ^
match_pdict_utils.c:822:20: warning: unused variable 'ndup' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                    ^
match_pdict_utils.c: At top level:
match_pdict_utils.c:275:13: warning: 'match_headtail_by_loc' defined but not used [-Wunused-function]
 static void match_headtail_by_loc(const HeadTail *headtail,
             ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c match_reporting.c -o match_reporting.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c matchprobes.c -o matchprobes.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c pmatchPattern.c -o pmatchPattern.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c replace_letter_at.c -o replace_letter_at.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c strutils.c -o strutils.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c translate.c -o translate.o
translate.c: In function 'DNAStringSet_translate':
translate.c:101:8: warning: 'if_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (if_ambig == TRANSLATE_ERROR) {
        ^
translate.c:126:29: note: 'if_ambig0' was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
                             ^
translate.c:97:8: warning: 'if_non_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (if_non_ambig == TRANSLATE_TO_X)
        ^
translate.c:126:14: note: 'if_non_ambig0' was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
              ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature':
utils.c:210:9: warning: 'twobit_sign' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return twobit_sign;
         ^
utils.c: In function '_get_twobit_signature_at':
utils.c:217:12: warning: 'twobit_sign' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, twobit_sign;
            ^
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp  -c xscat.c -o xscat.o
xscat.c: In function 'XString_xscat':
xscat.c:38:2: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
  PROTECT(ans_tag = NEW_RAW(ans_length));
  ^
xscat.c:52:2: warning: 'ans_classname' may be used uninitialized in this function [-Wmaybe-uninitialized]
  PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag));
  ^
xscat.c: In function 'XStringSet_xscat':
xscat.c:92:2: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
  PROTECT(ans_width = NEW_INTEGER(ans_length));
  ^
gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o io_utils.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -lz -L/usr/lib/R/lib -lR
installing to /builddir/build/BUILDROOT/R-Biostrings-2.36.1-3bs02npfc23.arm/usr/lib/R/library/Biostrings/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'setequal' from package 'base' in package 'Biostrings'
Creating a generic function for 'ls' from package 'base' in package 'Biostrings'
Creating a new generic function for 'offset' in package 'Biostrings'
** help
*** installing help indices
  converting help for package 'Biostrings'
    finding HTML links ... done
    AAString-class                          html  
    AMINO_ACID_CODE                         html  
    AlignedXStringSet-class                 html  
    BOC_SubjectString-class                 html  
    Biostrings-internals                    html  
    DNAString-class                         html  
    GENETIC_CODE                            html  
    HNF4alpha                               html  
    IUPAC_CODE_MAP                          html  
    InDel-class                             html  
    MIndex-class                            html  
    MaskedXString-class                     html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/MaskedXString-class.Rd:182: missing file link 'Views'
    MultipleAlignment-class                 html  
    finding level-2 HTML links ... done
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/MultipleAlignment-class.Rd:124: missing file link 'narrow'
    PDict-class                             html  
    PairwiseAlignments-class                html  
    PairwiseAlignments-io                   html  
    QualityScaledXStringSet-class           html  
    RNAString-class                         html  
    XString-class                           html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XString-class.Rd:179: missing file link 'subseq'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XString-class.Rd:187: missing file link 'compact'
    XStringPartialMatches-class             html  
    XStringQuality-class                    html  
    XStringSet-class                        html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:94: missing file link 'narrow'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:181: missing file link 'subseq'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:201: missing file link 'IRanges'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:203: missing file link 'XVector'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:209: missing file link 'IRanges'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:215: missing file link 'threebands'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:220: missing file link 'subseq<-'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:221: missing file link 'XVector'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:222: missing file link 'subseq<-'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:320: missing file link 'subseq'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:321: missing file link 'narrow'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:323: missing file link 'compact'
    XStringSet-comparison                   html  
    XStringSet-io                           html  
    XStringSetList-class                    html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSetList-class.Rd:70: missing file link 'List'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSetList-class.Rd:77: missing file link 'elementLengths'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSetList-class.Rd:78: missing file link 'PartitioningByEnd'
    XStringViews-class                      html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringViews-class.Rd:150: missing file link 'gaps'
    align-utils                             html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/align-utils.Rd:87: missing file link 'coverage'
    chartr                                  html  
    detail                                  html  
    dinucleotideFrequencyTest               html  
    findPalindromes                         html  
    getSeq                                  html  
    gregexpr2                               html  
    injectHardMask                          html  
    letter                                  html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/letter.Rd:49: missing file link 'subseq'
    letterFrequency                         html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/letterFrequency.Rd:290: missing file link 'coverage'
    longestConsecutive                      html  
    lowlevel-matching                       html  
    maskMotif                               html  
    match-utils                             html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/match-utils.Rd:42: missing file link 'coverage'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/match-utils.Rd:48: missing file link 'coverage'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/match-utils.Rd:72: missing file link 'Rle'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/match-utils.Rd:74: missing file link 'coverage'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/match-utils.Rd:87: missing file link 'coverage'
    matchLRPatterns                         html  
    matchPDict-exact                        html  
    matchPDict-inexact                      html  
    matchPWM                                html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/matchPWM.Rd:84: missing file link 'Views'
    matchPattern                            html  
    matchProbePair                          html  
    matchprobes                             html  
    misc                                    html  
    needwunsQS                              html  
    nucleotideFrequency                     html  
    padAndClip                              html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/padAndClip.Rd:33: missing file link 'Ranges'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/padAndClip.Rd:108: missing file link 'Ranges'
    pairwiseAlignment                       html  
    phiX174Phage                            html  
    pid                                     html  
    pmatchPattern                           html  
    replaceAt                               html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:36: missing file link 'Ranges'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:37: missing file link 'RangesList'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:43: missing file link 'IntegerList'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:51: missing file link 'Ranges'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:52: missing file link 'RangesList'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:53: missing file link 'RangesList'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:72: missing file link 'CharacterList'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:98: missing file link 'subseq'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:103: missing file link 'Ranges'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:110: missing file link 'subseq'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:110: missing file link 'subseq<-'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:115: missing file link 'unstrsplit'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:127: missing file link 'Ranges'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:127: missing file link 'RangesList'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:128: missing file link 'IntegerList'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:128: missing file link 'CharacterList'
    replaceLetterAt                         html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceLetterAt.Rd:43: missing file link 'Rle'
    reverseComplement                       html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/reverseComplement.Rd:48: missing file link 'reverse'
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/reverseComplement.Rd:71: missing file link 'reverse'
    stringDist                              html  
    substitution_matrices                   html  
    toComplex                               html  
    translate                               html  
    trimLRPatterns                          html  
    xscat                                   html  
    yeastSEQCHR1                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Biostrings)
+ test -d Biostrings/src
+ cd Biostrings/src
+ rm -f BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o io_utils.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o Biostrings.so
+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.36.1-3bs02npfc23.arm/usr/lib/R/library/R.css
+ rm -f /builddir/build/BUILDROOT/R-Biostrings-2.36.1-3bs02npfc23.arm/usr/lib/R/library/Biostrings/doc/GenomeSearching.R
+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 /builddir/build/BUILD/Biostrings
extracting debug info from /builddir/build/BUILDROOT/R-Biostrings-2.36.1-3bs02npfc23.arm/usr/lib/R/library/Biostrings/libs/Biostrings.so
dwz: Too few files for multifile optimization
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
872 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-java-repack-jars
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.GWVN7N
Processing files: R-Biostrings-2.36.1-3bs02npfc23.armv6hl
Provides: R-Biostrings = 2.36.1-3bs02npfc23 R-Biostrings(armv6hl-32) = 2.36.1-3bs02npfc23
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: ld-linux-armhf.so.3 ld-linux-armhf.so.3(GLIBC_2.4) libR.so libc.so.6 libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libgcc_s.so.1 libgcc_s.so.1(GCC_3.5) libz.so.1 rtld(GNU_HASH)
Processing files: R-Biostrings-devel-2.36.1-3bs02npfc23.armv6hl
Provides: R-Biostrings-devel = 2.36.1-3bs02npfc23 R-Biostrings-devel(armv6hl-32) = 2.36.1-3bs02npfc23
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-Biostrings-debuginfo-2.36.1-3bs02npfc23.armv6hl
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-Biostrings-2.36.1-3bs02npfc23.arm
Wrote: /builddir/build/RPMS/R-Biostrings-2.36.1-3bs02npfc23.armv6hl.rpm
Wrote: /builddir/build/RPMS/R-Biostrings-devel-2.36.1-3bs02npfc23.armv6hl.rpm
Wrote: /builddir/build/RPMS/R-Biostrings-debuginfo-2.36.1-3bs02npfc23.armv6hl.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.ra2V4O
+ umask 022
+ cd /builddir/build/BUILD
+ cd Biostrings
+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.36.1-3bs02npfc23.arm
+ exit 0
Child return code was: 0
LEAVE do -->