Diff of the two buildlogs:

--
--- b1/build.log	2024-12-06 07:13:26.514671121 +0000
+++ b2/build.log	2024-12-06 07:21:15.657489861 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Thu Dec  5 19:03:47 -12 2024
-I: pbuilder-time-stamp: 1733468627
+I: Current time: Fri Dec  6 21:14:57 +14 2024
+I: pbuilder-time-stamp: 1733469297
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
 I: copying local configuration
@@ -38,52 +38,84 @@
 dpkg-source: info: applying fix_mpi.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/12177/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/23325/tmp/hooks/D01_modify_environment starting
+debug: Running on virt64z.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 Dec  6 07:15 /bin/sh -> /bin/bash
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/23325/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/23325/tmp/hooks/D02_print_environment starting
 I: set
-  BUILDDIR='/build/reproducible-path'
-  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
-  BUILDUSERNAME='pbuilder1'
-  BUILD_ARCH='armhf'
-  DEBIAN_FRONTEND='noninteractive'
-  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 '
-  DISTRIBUTION='trixie'
-  HOME='/root'
-  HOST_ARCH='armhf'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
+  BASH_VERSION='5.2.32(1)-release'
+  BUILDDIR=/build/reproducible-path
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=armhf
+  DEBIAN_FRONTEND=noninteractive
+  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 '
+  DIRSTACK=()
+  DISTRIBUTION=trixie
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=arm
+  HOST_ARCH=armhf
   IFS=' 	
   '
-  INVOCATION_ID='4245e9cfb62147eb8e147dd62a0e392f'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  MAIL='/var/mail/root'
-  OPTIND='1'
-  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
-  PBCURRENTCOMMANDLINEOPERATION='build'
-  PBUILDER_OPERATION='build'
-  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
-  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
-  PBUILDER_SYSCONFDIR='/etc'
-  PPID='12177'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=01f69b391fba46658e27697cf1eee058
+  LANG=C
+  LANGUAGE=it_CH:it
+  LC_ALL=C
+  MACHTYPE=arm-unknown-linux-gnueabihf
+  MAIL=/var/mail/root
+  OPTERR=1
+  OPTIND=1
+  OSTYPE=linux-gnueabihf
+  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+  PBCURRENTCOMMANDLINEOPERATION=build
+  PBUILDER_OPERATION=build
+  PBUILDER_PKGDATADIR=/usr/share/pbuilder
+  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+  PBUILDER_SYSCONFDIR=/etc
+  PIPESTATUS=([0]="0")
+  POSIXLY_CORRECT=y
+  PPID=23325
   PS4='+ '
-  PWD='/'
-  SHELL='/bin/bash'
-  SHLVL='2'
-  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6StvvwLx/pbuilderrc_PnuC --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6StvvwLx/b1 --logfile b1/build.log murasaki_1.68.6-14.dsc'
-  SUDO_GID='113'
-  SUDO_UID='107'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://10.0.0.15:3142/'
+  PWD=/
+  SHELL=/bin/bash
+  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+  SHLVL=3
+  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6StvvwLx/pbuilderrc_Lzlb --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6StvvwLx/b2 --logfile b2/build.log murasaki_1.68.6-14.dsc'
+  SUDO_GID=110
+  SUDO_UID=103
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://10.0.0.15:3142/
 I: uname -a
-  Linux virt32c 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux
 I: ls -l /bin
   lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/12177/tmp/hooks/D02_print_environment finished
+I: user script /srv/workspace/pbuilder/23325/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -201,7 +233,7 @@
 Get: 64 http://deb.debian.org/debian trixie/main armhf libterm-readkey-perl armhf 2.38-2+b4 [23.7 kB]
 Get: 65 http://deb.debian.org/debian trixie/main armhf libtext-wrapper-perl all 1.05-4 [10.3 kB]
 Get: 66 http://deb.debian.org/debian trixie/main armhf mpi-default-dev armhf 1.17 [3148 B]
-Fetched 61.2 MB in 2s (37.4 MB/s)
+Fetched 61.2 MB in 1s (99.7 MB/s)
 debconf: delaying package configuration, since apt-utils is not installed
 Selecting previously unselected package sensible-utils.
 (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19683 files and directories currently installed.)
@@ -483,7 +515,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/murasaki-1.68.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../murasaki_1.68.6-14_source.changes
+I: user script /srv/workspace/pbuilder/23325/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/23325/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/murasaki-1.68.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../murasaki_1.68.6-14_source.changes
 dpkg-buildpackage: info: source package murasaki
 dpkg-buildpackage: info: source version 1.68.6-14
 dpkg-buildpackage: info: source distribution unstable
@@ -493,7 +529,7 @@
  debian/rules clean
 dh clean
    dh_auto_clean
-	make -j3 clean
+	make -j4 clean
 make[1]: Entering directory '/build/reproducible-path/murasaki-1.68.6'
 rm -rf *.o *~ .*~ core
 make -C src clean
@@ -510,7 +546,7 @@
    debian/rules override_dh_auto_build
 make[1]: Entering directory '/build/reproducible-path/murasaki-1.68.6'
 dh_auto_build -- USE_MPI=YES
-	make -j3 "INSTALL=install --strip-program=true" USE_MPI=YES
+	make -j4 "INSTALL=install --strip-program=true" USE_MPI=YES
 make[2]: Entering directory '/build/reproducible-path/murasaki-1.68.6'
 make -C src all
 make[3]: Entering directory '/build/reproducible-path/murasaki-1.68.6/src'
@@ -518,6 +554,7 @@
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c timing.cc
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c dinkymath.cc
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c sequence.cc
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c msethash.cc
 In file included from murasaki.h:24,
                  from dinkymath.cc:27:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -534,14 +571,6 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)':
-dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
-   40 |   int last=0;
-      |       ^~~~
-dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)':
-dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
-   53 |   int last=0;
-      |       ^~~~
 In file included from murasaki.h:24,
                  from murasaki.cc:37:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -557,25 +586,14 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
-murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
- 1008 |   bool revZero=false;
-      |        ^~~~~~~
-murasaki.cc: In function 'bool convertPattern(std::string&)':
-murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<char*, __cxx11::basic_string<char> >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
- 1287 |   random_shuffle(randomStr.begin(),randomStr.end());
-      |   ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/algorithm:61,
-                 from /usr/include/boost/regex/v5/regex_workaround.hpp:23,
-                 from /usr/include/boost/regex/v5/regex.hpp:29,
-                 from /usr/include/boost/regex.hpp:34,
-                 from seqread.h:33,
-                 from binseq.hh:31,
-                 from sequence.h:32:
-/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here
- 4491 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
-      |     ^~~~~~~~~~~~~~
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c msethash.cc
+dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)':
+dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
+   40 |   int last=0;
+      |       ^~~~
+dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)':
+dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
+   53 |   int last=0;
+      |       ^~~~
 In file included from murasaki.h:24,
                  from sequence.cc:28:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -608,11 +626,29 @@
 /usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
   284 |     struct pair
       |            ^~~~
+murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
+murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
+ 1008 |   bool revZero=false;
+      |        ^~~~~~~
 sequence.cc: In destructor 'BitSequence::~BitSequence()':
 sequence.cc:1394:9: warning: 'throw' will always call 'terminate' [-Wterminate]
  1394 |         throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno));
       |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 sequence.cc:1394:9: note: in C++11 destructors default to 'noexcept'
+murasaki.cc: In function 'bool convertPattern(std::string&)':
+murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<char*, __cxx11::basic_string<char> >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
+ 1287 |   random_shuffle(randomStr.begin(),randomStr.end());
+      |   ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/algorithm:61,
+                 from /usr/include/boost/regex/v5/regex_workaround.hpp:23,
+                 from /usr/include/boost/regex/v5/regex.hpp:29,
+                 from /usr/include/boost/regex.hpp:34,
+                 from seqread.h:33,
+                 from binseq.hh:31,
+                 from sequence.h:32:
+/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here
+ 4491 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
+      |     ^~~~~~~~~~~~~~
 sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
 sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
  3332 |   SeqPos shortest=0,shortlen=length(spaces[0]);
@@ -649,6 +685,7 @@
 /usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair<long int, long int>' declared here
   284 |     struct pair
       |            ^~~~
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c options.cc
 In file included from msethash.cc:25:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
@@ -660,7 +697,7 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c options.cc
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecohash.cc
 In file included from options.h:28,
                  from options.cc:26:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -673,6 +710,20 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+In file included from ecolist.h:23,
+                 from ecohash.h:29,
+                 from ecohash.cc:26:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecolist.cc
 In file included from /usr/include/c++/14/bits/stl_algo.h:61:
 /usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Distance = int; _Tp = HashMethod; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
 /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
@@ -684,12 +735,6 @@
       |     ^~~~~~~~~~
 /usr/include/c++/14/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 /usr/include/c++/14/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
-In file included from /usr/include/c++/14/vector:72,
-                 from murasaki.cc:31:
-/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
-/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
-  700 |     vector<_Tp, _Alloc>::
-      |     ^~~~~~~~~~~~~~~~~~~
 /usr/include/c++/14/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
 /usr/include/c++/14/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
   340 |     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
@@ -700,6 +745,30 @@
  1770 |     __insertion_sort(_RandomAccessIterator __first,
       |     ^~~~~~~~~~~~~~~~
 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
+In file included from /usr/include/c++/14/vector:72,
+                 from murasaki.cc:31:
+/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
+/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
+  700 |     vector<_Tp, _Alloc>::
+      |     ^~~~~~~~~~~~~~~~~~~
+In file included from ecolist.h:23,
+                 from ecolist.cc:20:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+ecolist.cc:467:26: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  467 | struct less_map : public binary_function<const Ecolist::val_type&,const Ecolist::val_type&,bool> {
+      |                          ^~~~~~~~~~~~~~~
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/vector:66:
 In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
     inlined from 'void MurasakiRuntime::prep()' at murasaki.cc:378:26:
@@ -711,6 +780,8 @@
 /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  1037 |           _M_fill_insert(end(), __new_size - size(), __x);
       |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki_mpi.cc
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c arrayhash.cc
 In file included from /usr/include/c++/14/vector:72,
                  from scoring.h:27,
                  from sequence.h:31:
@@ -724,7 +795,50 @@
 /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  1037 |           _M_fill_insert(end(), __new_size - size(), __x);
       |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecohash.cc
+In file included from murasaki.h:24,
+                 from arrayhash.cc:28:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from murasaki.h:24,
+                 from murasaki_mpi.cc:33:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/ostream:40,
+                 from /usr/include/c++/14/iostream:41,
+                 from murasaki_mpi.cc:30:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+murasaki_mpi.cc:89:29: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+   89 | struct lt_mpi_worldMemory : binary_function<int,int,bool> {
+      |                             ^~~~~~~~~~~~~~~
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+murasaki_mpi.cc:95:29: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+   95 | struct gt_mpi_worldMemory : binary_function<int,int,bool> {
+      |                             ^~~~~~~~~~~~~~~
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+murasaki_mpi.cc: In function 'void mpi_hasher_client_mode(BitSequence*)':
+murasaki_mpi.cc:561:9: warning: variable 'send_done' set but not used [-Wunused-but-set-variable]
+  561 |     int send_done;
+      |         ^~~~~~~~~
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c seqread.cc
 /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
 /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
  1876 |     __introsort_loop(_RandomAccessIterator __first,
@@ -786,84 +900,14 @@
 /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
  1822 |         std::__insertion_sort(__first, __last, __comp);
       |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ecolist.h:23,
-                 from ecohash.h:29,
-                 from ecohash.cc:26:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecolist.cc
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki_mpi.cc
-In file included from ecolist.h:23,
-                 from ecolist.cc:20:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-ecolist.cc:467:26: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  467 | struct less_map : public binary_function<const Ecolist::val_type&,const Ecolist::val_type&,bool> {
-      |                          ^~~~~~~~~~~~~~~
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c arrayhash.cc
-In file included from murasaki.h:24,
-                 from murasaki_mpi.cc:33:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/ostream:40,
-                 from /usr/include/c++/14/iostream:41,
-                 from murasaki_mpi.cc:30:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-murasaki_mpi.cc:89:29: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-   89 | struct lt_mpi_worldMemory : binary_function<int,int,bool> {
-      |                             ^~~~~~~~~~~~~~~
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-murasaki_mpi.cc:95:29: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-   95 | struct gt_mpi_worldMemory : binary_function<int,int,bool> {
-      |                             ^~~~~~~~~~~~~~~
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-murasaki_mpi.cc: In function 'void mpi_hasher_client_mode(BitSequence*)':
-murasaki_mpi.cc:561:9: warning: variable 'send_done' set but not used [-Wunused-but-set-variable]
-  561 |     int send_done;
-      |         ^~~~~~~~~
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c seqread.cc
-In file included from murasaki.h:24,
-                 from arrayhash.cc:28:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
+seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)':
+seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations]
+  264 |     stitchPath=stitchfile.branch_path();
+      |                ~~~~~~~~~~~~~~~~~~~~~~^~
+In file included from seqread.cc:35:
+/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here
+ 1129 |     path branch_path() const { return parent_path(); }
+      |          ^~~~~~~~~~~
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c scoring.cc
 In file included from /usr/include/c++/14/vector:72,
                  from scoring.h:27,
@@ -890,14 +934,6 @@
 /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  1037 |           _M_fill_insert(end(), __new_size - size(), __x);
       |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)':
-seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations]
-  264 |     stitchPath=stitchfile.branch_path();
-      |                ~~~~~~~~~~~~~~~~~~~~~~^~
-In file included from seqread.cc:35:
-/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here
- 1129 |     path branch_path() const { return parent_path(); }
-      |          ^~~~~~~~~~~
 In file included from murasaki.h:24,
                  from scoring.cc:27:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -912,6 +948,8 @@
       |            ^~~~~~~~~~~~~~~
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c openhash.cc
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c genopts.cc
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c binseq.cc
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-image.cc
 In file included from ecolist.h:23,
                  from openhash.h:29,
                  from openhash.cc:26:
@@ -925,8 +963,7 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c binseq.cc
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-image.cc
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc
 binseq.cc: In member function 'bool SequenceBinary::save(std::string)':
 binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
    70 |   }catch(ofstream::failure e){
@@ -960,8 +997,6 @@
 /usr/include/c++/14/bits/stl_pair.h:284:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
   284 |     struct pair
       |            ^~~~
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-compare.cc
 cgr.cc: In member function 'void Cgr::merge(Cgr&)':
 cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable]
   140 |   int redist=(unsigned long)(rez*rez)<=seedcount;
@@ -974,6 +1009,8 @@
 cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
   435 |   int wordwidth=1;
       |       ^~~~~~~~~
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-compare.cc
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-random.cc
 cgr.cc: In member function 'std::pair<long unsigned int, long unsigned int> Cgr::sampleHighLow(double, double)':
 cgr.cc:339:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
   339 |   delete alt;
@@ -995,7 +1032,6 @@
 cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)'
   376 |   pix *alt=new pix[size];
       |                        ^
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-random.cc
 cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)':
 cgr.cc:557:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized]
   557 |   if(data.size()<(uint)(height*width))
@@ -1023,13 +1059,12 @@
   426 |   int width,height;
       |             ^~~~~~
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-sample.cc
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c testeco.cc
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-compare.cc
 cgr-sample.cc: In function 'int main(int, char**)':
 cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
    54 |   bool repeatmask=false,save=false;
       |        ^~~~~~~~~~
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c testeco.cc
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-compare.cc
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc
 In file included from ecolist.h:23,
                  from testeco.cc:20:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -1046,34 +1081,35 @@
 testeco.cc:29:41: warning: left shift count >= width of type [-Wshift-count-overflow]
    29 |   return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand())));
       |                  ~~~~~~~~~~~~~~~~~~~~~~~^~~~
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-or.cc
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c geneparse.cc
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-and.cc
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-best.cc
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-coverage.cc
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c getsegments.cc
 align-coverage.cc: In function 'int main(int, char**)':
 align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable]
   148 |     bool seqStats=true;
       |          ^~~~~~~~
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c getsegments.cc
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.cc
 getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list<std::pair<unsigned int, std::__cxx11::basic_string<char> > >&, std::string)':
 getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=]
   153 |     }catch(bad_lexical_cast e){
       |                             ^
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.cc
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o   -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o  genopts.o   -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o   -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o   -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o   -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
+mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
-mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 make[3]: Leaving directory '/build/reproducible-path/murasaki-1.68.6/src'
 make[2]: Leaving directory '/build/reproducible-path/murasaki-1.68.6'
@@ -1089,7 +1125,7 @@
 make[3]: Leaving directory '/build/reproducible-path/murasaki-1.68.6/src'
 make[2]: Leaving directory '/build/reproducible-path/murasaki-1.68.6'
 dh_auto_build -- USE_MPI=NO
-	make -j3 "INSTALL=install --strip-program=true" USE_MPI=NO
+	make -j4 "INSTALL=install --strip-program=true" USE_MPI=NO
 make[2]: Entering directory '/build/reproducible-path/murasaki-1.68.6'
 make -C src all
 make[3]: Entering directory '/build/reproducible-path/murasaki-1.68.6/src'
@@ -1097,32 +1133,21 @@
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c timing.cc
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c dinkymath.cc
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c sequence.cc
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c msethash.cc
 In file included from murasaki.h:24,
-                 from dinkymath.cc:27:
+                 from sequence.cc:28:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
       |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/ostream:40,
-                 from /usr/include/c++/14/iostream:41,
-                 from dinkymath.h:24,
-                 from dinkymath.cc:26:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)':
-dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
-   40 |   int last=0;
-      |       ^~~~
-dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)':
-dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
-   53 |   int last=0;
-      |       ^~~~
 In file included from murasaki.h:24,
-                 from murasaki.cc:37:
+                 from dinkymath.cc:27:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
       |                   ^~~~~~~~~~~~~~~
@@ -1132,38 +1157,8 @@
                  from /usr/include/c++/14/ios:44,
                  from /usr/include/c++/14/ostream:40,
                  from /usr/include/c++/14/iostream:41,
-                 from murasaki.cc:29:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
-murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
- 1008 |   bool revZero=false;
-      |        ^~~~~~~
-murasaki.cc: In function 'bool convertPattern(std::string&)':
-murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<char*, __cxx11::basic_string<char> >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
- 1287 |   random_shuffle(randomStr.begin(),randomStr.end());
-      |   ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/algorithm:61,
-                 from /usr/include/boost/regex/v5/regex_workaround.hpp:23,
-                 from /usr/include/boost/regex/v5/regex.hpp:29,
-                 from /usr/include/boost/regex.hpp:34,
-                 from seqread.h:33,
-                 from binseq.hh:31,
-                 from sequence.h:32:
-/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here
- 4491 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
-      |     ^~~~~~~~~~~~~~
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c msethash.cc
-In file included from murasaki.h:24,
-                 from sequence.cc:28:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
+                 from dinkymath.h:24,
+                 from dinkymath.cc:26:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -1182,10 +1177,33 @@
 /usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
   284 |     struct pair
       |            ^~~~
+dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)':
+dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
+   40 |   int last=0;
+      |       ^~~~
+dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)':
+dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
+   53 |   int last=0;
+      |       ^~~~
 sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
 sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
  3332 |   SeqPos shortest=0,shortlen=length(spaces[0]);
       |          ^~~~~~~~
+In file included from murasaki.h:24,
+                 from murasaki.cc:37:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/ostream:40,
+                 from /usr/include/c++/14/iostream:41,
+                 from murasaki.cc:29:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 In file included from sequence.cc:41:
 hashing.h: In instantiation of 'SBox<T>::SBox(int) [with T = short unsigned int]':
 sequence.cc:162:29:   required from here
@@ -1218,6 +1236,24 @@
 /usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair<long int, long int>' declared here
   284 |     struct pair
       |            ^~~~
+murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
+murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
+ 1008 |   bool revZero=false;
+      |        ^~~~~~~
+murasaki.cc: In function 'bool convertPattern(std::string&)':
+murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<char*, __cxx11::basic_string<char> >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
+ 1287 |   random_shuffle(randomStr.begin(),randomStr.end());
+      |   ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/algorithm:61,
+                 from /usr/include/boost/regex/v5/regex_workaround.hpp:23,
+                 from /usr/include/boost/regex/v5/regex.hpp:29,
+                 from /usr/include/boost/regex.hpp:34,
+                 from seqread.h:33,
+                 from binseq.hh:31,
+                 from sequence.h:32:
+/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here
+ 4491 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
+      |     ^~~~~~~~~~~~~~
 In file included from msethash.cc:25:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
@@ -1230,6 +1266,7 @@
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c options.cc
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c ecohash.cc
 In file included from options.h:28,
                  from options.cc:26:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -1242,6 +1279,20 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+In file included from ecolist.h:23,
+                 from ecohash.h:29,
+                 from ecohash.cc:26:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c ecolist.cc
 In file included from /usr/include/c++/14/bits/stl_algo.h:61:
 /usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Distance = int; _Tp = HashMethod; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
 /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
@@ -1263,6 +1314,27 @@
  1770 |     __insertion_sort(_RandomAccessIterator __first,
       |     ^~~~~~~~~~~~~~~~
 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
+In file included from ecolist.h:23,
+                 from ecolist.cc:20:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+ecolist.cc:467:26: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  467 | struct less_map : public binary_function<const Ecolist::val_type&,const Ecolist::val_type&,bool> {
+      |                          ^~~~~~~~~~~~~~~
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c murasaki_mpi.cc
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c arrayhash.cc
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c seqread.cc
 In file included from /usr/include/c++/14/vector:72,
                  from scoring.h:27,
                  from sequence.h:31:
@@ -1276,7 +1348,27 @@
 /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  1037 |           _M_fill_insert(end(), __new_size - size(), __x);
       |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c ecohash.cc
+In file included from murasaki.h:24,
+                 from arrayhash.cc:28:
+sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
+      |                   ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from cmultiset.h:33,
+                 from sequence.h:30:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c scoring.cc
+seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)':
+seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations]
+  264 |     stitchPath=stitchfile.branch_path();
+      |                ~~~~~~~~~~~~~~~~~~~~~~^~
+In file included from seqread.cc:35:
+/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here
+ 1129 |     path branch_path() const { return parent_path(); }
+      |          ^~~~~~~~~~~
 /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
 /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
  1876 |     __introsort_loop(_RandomAccessIterator __first,
@@ -1338,63 +1430,6 @@
 /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
  1822 |         std::__insertion_sort(__first, __last, __comp);
       |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ecolist.h:23,
-                 from ecohash.h:29,
-                 from ecohash.cc:26:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c ecolist.cc
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c murasaki_mpi.cc
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c arrayhash.cc
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c seqread.cc
-In file included from ecolist.h:23,
-                 from ecolist.cc:20:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-ecolist.cc:467:26: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  467 | struct less_map : public binary_function<const Ecolist::val_type&,const Ecolist::val_type&,bool> {
-      |                          ^~~~~~~~~~~~~~~
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from murasaki.h:24,
-                 from arrayhash.cc:28:
-sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
-      |                   ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from cmultiset.h:33,
-                 from sequence.h:30:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c scoring.cc
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c openhash.cc
-seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)':
-seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations]
-  264 |     stitchPath=stitchfile.branch_path();
-      |                ~~~~~~~~~~~~~~~~~~~~~~^~
-In file included from seqread.cc:35:
-/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here
- 1129 |     path branch_path() const { return parent_path(); }
-      |          ^~~~~~~~~~~
 In file included from murasaki.h:24,
                  from scoring.cc:27:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -1407,6 +1442,10 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c openhash.cc
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c genopts.cc
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c binseq.cc
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-image.cc
 In file included from ecolist.h:23,
                  from openhash.h:29,
                  from openhash.cc:26:
@@ -1420,9 +1459,7 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c genopts.cc
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c binseq.cc
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-image.cc
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr.cc
 binseq.cc: In member function 'bool SequenceBinary::save(std::string)':
 binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
    70 |   }catch(ofstream::failure e){
@@ -1456,8 +1493,6 @@
 /usr/include/c++/14/bits/stl_pair.h:284:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
   284 |     struct pair
       |            ^~~~
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr.cc
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-compare.cc
 cgr.cc: In member function 'void Cgr::merge(Cgr&)':
 cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable]
   140 |   int redist=(unsigned long)(rez*rez)<=seedcount;
@@ -1470,6 +1505,7 @@
 cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
   435 |   int wordwidth=1;
       |       ^~~~~~~~~
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-compare.cc
 cgr.cc: In member function 'std::pair<long unsigned int, long unsigned int> Cgr::sampleHighLow(double, double)':
 cgr.cc:339:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
   339 |   delete alt;
@@ -1491,6 +1527,7 @@
 cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)'
   376 |   pix *alt=new pix[size];
       |                        ^
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-random.cc
 cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)':
 cgr.cc:557:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized]
   557 |   if(data.size()<(uint)(height*width))
@@ -1517,14 +1554,13 @@
 cgr.cc:426:13: note: 'height' was declared here
   426 |   int width,height;
       |             ^~~~~~
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-random.cc
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-sample.cc
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c testeco.cc
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c align-compare.cc
 cgr-sample.cc: In function 'int main(int, char**)':
 cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
    54 |   bool repeatmask=false,save=false;
       |        ^~~~~~~~~~
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c testeco.cc
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c align-compare.cc
 In file included from ecolist.h:23,
                  from testeco.cc:20:
 sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -1563,13 +1599,13 @@
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o   -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o   -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
+g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
-g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o  -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now 
 make[3]: Leaving directory '/build/reproducible-path/murasaki-1.68.6/src'
 make[2]: Leaving directory '/build/reproducible-path/murasaki-1.68.6'
@@ -1636,41 +1672,41 @@
    dh_strip -a
    dh_makeshlibs -a
    dh_shlibdeps -a
-dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-best-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
 dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-coverage-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
-dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-compare-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
-dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-and-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
-dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-image-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
-dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/mbfa-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
-dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-image contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
-dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-sample-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
-dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-or contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
 dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/geneparse-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
-dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-coverage contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
-dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-or-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki/usr/bin/murasaki contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-and-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-sample contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
 dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-compare-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki/usr/bin/mbfa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-or-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
 dpkg-shlibdeps: warning: debian/murasaki/usr/bin/geneparse contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/mbfa-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
 dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-and contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
-dpkg-shlibdeps: warning: debian/murasaki/usr/bin/mbfa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
 dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
-dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-sample contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-image-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-coverage contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-best-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-or contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-compare-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-best contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
 dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
-dpkg-shlibdeps: warning: debian/murasaki/usr/bin/murasaki contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-sample-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
+dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-image contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
 dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/murasaki-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
-dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-best contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
    dh_installdeb
    dh_gencontrol
-dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined
 dpkg-gencontrol: warning: Depends field of package murasaki-common: substitution variable ${misc:perl} used, but is not defined
 dpkg-gencontrol: warning: package murasaki-common: substitution variable ${perl:Depends} unused, but is defined
 dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined
+dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined
    dh_md5sums
    dh_builddeb
 dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-14_armhf.deb'.
 dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-14_armhf.deb'.
 dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-14_all.deb'.
-dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-14_armhf.deb'.
 dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-14_armhf.deb'.
+dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-14_armhf.deb'.
  dpkg-genbuildinfo --build=binary -O../murasaki_1.68.6-14_armhf.buildinfo
  dpkg-genchanges --build=binary -O../murasaki_1.68.6-14_armhf.changes
 dpkg-genchanges: info: binary-only upload (no source code included)
@@ -1678,12 +1714,14 @@
 dpkg-buildpackage: info: binary-only upload (no source included)
 dpkg-genchanges: info: not including original source code in upload
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/23325/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/23325/tmp/hooks/B01_cleanup finished
 I: unmounting dev/ptmx filesystem
 I: unmounting dev/pts filesystem
 I: unmounting dev/shm filesystem
 I: unmounting proc filesystem
 I: unmounting sys filesystem
 I: cleaning the build env 
-I: removing directory /srv/workspace/pbuilder/12177 and its subdirectories
-I: Current time: Thu Dec  5 19:13:22 -12 2024
-I: pbuilder-time-stamp: 1733469202
+I: removing directory /srv/workspace/pbuilder/23325 and its subdirectories
+I: Current time: Fri Dec  6 21:21:11 +14 2024
+I: pbuilder-time-stamp: 1733469671