Diff of the two buildlogs:
--
--- b1/build.log 2025-03-28 00:08:17.900453828 +0000
+++ b2/build.log 2025-03-28 00:14:02.788877476 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Wed Apr 29 18:22:33 -12 2026
-I: pbuilder-time-stamp: 1777530153
+I: Current time: Fri Mar 28 14:08:22 +14 2025
+I: pbuilder-time-stamp: 1743120502
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
@@ -41,52 +41,84 @@
dpkg-source: info: applying fix_ftbfs_with_gcc-15.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/900143/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/23253/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos11-amd64.
+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 Mar 28 00:08 /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/23253/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/23253/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='amd64'
- DEBIAN_FRONTEND='noninteractive'
- DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
- DISTRIBUTION='unstable'
- HOME='/root'
- HOST_ARCH='amd64'
+ 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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+ BASH_VERSION='5.2.37(1)-release'
+ BUILDDIR=/build/reproducible-path
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=amd64
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
+ DIRSTACK=()
+ DISTRIBUTION=unstable
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=x86_64
+ HOST_ARCH=amd64
IFS='
'
- INVOCATION_ID='6bd76dc7dc874485859e566720fa52ed'
- 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='900143'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=4b936954a9984e4d8e4db6daad4281e8
+ LANG=C
+ LANGUAGE=et_EE:et
+ LC_ALL=C
+ MACHTYPE=x86_64-pc-linux-gnu
+ MAIL=/var/mail/root
+ OPTERR=1
+ OPTIND=1
+ OSTYPE=linux-gnu
+ 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=23253
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.ahawirbV/pbuilderrc_aELG --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ahawirbV/b1 --logfile b1/build.log wise_2.4.1-27.dsc'
- SUDO_GID='111'
- SUDO_UID='106'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://213.165.73.152:3128'
+ 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.ahawirbV/pbuilderrc_blEQ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ahawirbV/b2 --logfile b2/build.log wise_2.4.1-27.dsc'
+ SUDO_GID=111
+ SUDO_UID=106
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://46.16.76.132:3128
I: uname -a
- Linux ionos15-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
+ Linux i-capture-the-hostname 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux
I: ls -l /bin
- lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/900143/tmp/hooks/D02_print_environment finished
+ lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/23253/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -334,7 +366,7 @@
Get: 198 http://deb.debian.org/debian unstable/main amd64 texlive-luatex all 2024.20250309-1 [29.1 MB]
Get: 199 http://deb.debian.org/debian unstable/main amd64 texlive-plain-generic all 2024.20250309-2 [29.0 MB]
Get: 200 http://deb.debian.org/debian unstable/main amd64 texlive-extra-utils all 2024.20250309-2 [67.6 MB]
-Fetched 253 MB in 6s (40.9 MB/s)
+Fetched 253 MB in 6s (43.0 MB/s)
Preconfiguring packages ...
Selecting previously unselected package m4.
(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 ... 19805 files and directories currently installed.)
@@ -995,8 +1027,8 @@
Setting up tzdata (2025b-1) ...
Current default time zone: 'Etc/UTC'
-Local time is now: Thu Apr 30 06:25:08 UTC 2026.
-Universal Time is now: Thu Apr 30 06:25:08 UTC 2026.
+Local time is now: Fri Mar 28 00:10:13 UTC 2025.
+Universal Time is now: Fri Mar 28 00:10:13 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up libsysprof-capture-4-dev:amd64 (48.0-2) ...
@@ -1211,7 +1243,11 @@
Building tag database...
-> Finished parsing the build-deps
I: Building the package
-I: Running cd /build/reproducible-path/wise-2.4.1/ && 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 > ../wise_2.4.1-27_source.changes
+I: user script /srv/workspace/pbuilder/23253/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/23253/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/wise-2.4.1/ && 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 > ../wise_2.4.1-27_source.changes
dpkg-buildpackage: info: source package wise
dpkg-buildpackage: info: source version 2.4.1-27
dpkg-buildpackage: info: source distribution unstable
@@ -1298,7 +1334,7 @@
# Also, it pre-depends on the libwisebase library, otherwise
# linking fails.
dh_auto_build --sourcedirectory=src/base -- libwisebase.a
- cd src/base && make -j42 "INSTALL=install --strip-program=true" libwisebase.a
+ cd src/base && make -j20 "INSTALL=install --strip-program=true" libwisebase.a
make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src/base'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseconfig.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisestring.c
@@ -1324,7 +1360,7 @@
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi
make[2]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/base'
dh_auto_build --sourcedirectory=src/dyc -- dyc
- cd src/dyc && make -j42 "INSTALL=install --strip-program=true" dyc
+ cd src/dyc && make -j20 "INSTALL=install --strip-program=true" dyc
make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src/dyc'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dyc.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dyna2.c
@@ -1346,18 +1382,6 @@
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ ftext.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ funcinfo.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ objectinfo.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ exprtree.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ compugen.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ docugen.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ input.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dpimpl.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dbthread.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ probal.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ telegraph.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dynadebug.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dyshatter.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ y.tab.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ lex.yy.c
dynashadow.dy: In function ‘optimised_shadow_GenericMatrix’:
dynashadow.dy:2180:31: warning: passing argument 2 of ‘write_main_shadow_block’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2180 | write_main_shadow_block(dfp,gm,"DC_OPT_SHADOW_MATRIX","mat","DC_OPT_SHADOW_SPECIAL","DC_OPT_SHADOW_MATRIX_SP","DC_OPT_SHADOW_SPECIAL_SP",7,TRUE,TRUE,0,TRUE);
@@ -1372,6 +1396,15 @@
dynashadow.h:189:63: note: expected ‘GenericMatrix *’ but argument is of type ‘const GenericMatrix *’
189 | void write_special_shadow_block(DYNFILE * dfp,GenericMatrix * gm,char * matrix,char * pointer_tag,char * special,char * shadow_main_tag,char * shadow_special_tag,int shadow_length,boolean shadow_on_special,int debug);
| ~~~~~~~~~~~~~~~~^~
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ exprtree.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ compugen.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ docugen.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ input.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dpimpl.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dbthread.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ probal.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ telegraph.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dynadebug.c
dynfile.dy: In function ‘warn_expr’:
dynfile.dy:699:16: warning: ‘%s’ directive writing up to 511 bytes into a region of size 506 [-Wformat-overflow=]
699 | sprintf(buf2,"warn(\"%s\");",buffer);
@@ -1389,11 +1422,14 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dyshatter.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ y.tab.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ lex.yy.c
cc -o dyc dyc.o dyna2.o dynfile.o wisec.o dynafunc.o module.o type.o method.o dynadb.o friend.o inputfile.o variable.o modulefunc.o api.o display.o dynashadow.o labelmaster.o ftext.o funcinfo.o objectinfo.o exprtree.o compugen.o docugen.o input.o dpimpl.o dbthread.o probal.o telegraph.o dynadebug.o dyshatter.o y.tab.o lex.yy.o -ll -lwisebase -Wl,-z,relro -Wl,-z,now -g -lm -L../base/ -lpthread
make[2]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/dyc'
PATH="$PATH:/build/reproducible-path/wise-2.4.1/src/dyc" \
dh_auto_build --sourcedirectory=src -- all
- cd src && make -j42 "INSTALL=install --strip-program=true" all
+ cd src && make -j20 "INSTALL=install --strip-program=true" all
make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src'
(cd base ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libwisebase.a )
make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/base'
@@ -1427,18 +1463,8 @@
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c interleaved.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c iupac.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c msf.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c revcomp.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c selex.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sqerror.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sqio.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sre_ctype.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sre_math.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sre_string.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c stack.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c translate.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c types.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c weight.c
gnuregex.c: In function ‘re_match_2’:
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c revcomp.c
gnuregex.c:3755:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
3755 | if ((int) old_regend[r] >= (int) regstart[r])
| ^
@@ -1559,6 +1585,8 @@
gnuregex.c:4281:11: note: in expansion of macro ‘POP_FAILURE_POINT’
4281 | POP_FAILURE_POINT (d, p,
| ^~~~~~~~~~~~~~~~~
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c selex.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sqerror.c
cluster.c: In function ‘Cluster’:
cluster.c:178:26: warning: argument 1 range [18446744065119617024, 18446744073709551612] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
178 | (diff = (float *) malloc ((N-1) * sizeof(float))) == NULL)
@@ -1568,6 +1596,14 @@
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
| ^~~~~~
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sqio.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sre_ctype.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sre_math.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sre_string.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c stack.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c translate.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c types.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c weight.c
ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o
a - alphabet.o
a - core_algorithms.o
@@ -1633,6 +1669,18 @@
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ seqalign.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hitlist.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsp.c
+aln.dy: In function ‘Wise2_mapped_ascii_AlnBlock’:
+packaln.dy: In function ‘Wise2_read_simple_PackAln’:
+packaln.dy:88:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
+ 88 | fgets(buffer,MAXLINE,ifp);
+ | ^~~~~~~~~~~~~~~~~~~~~~~~~
+matrixdebug.dy: In function ‘Wise2_user_DebugMatrix’:
+aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args]
+ 867 | fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml);
+ | ^~~~~~~~~~~~
+matrixdebug.dy:208:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
+ 208 | fgets(buffer,MAXLINE,in);
+ | ^~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspstream.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codon.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ compmat.c
@@ -1655,18 +1703,6 @@
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ genomicdb.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ randommodel.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ randomdb.c
-aln.dy: In function ‘Wise2_mapped_ascii_AlnBlock’:
-aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args]
- 867 | fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml);
- | ^~~~~~~~~~~~
-packaln.dy: In function ‘Wise2_read_simple_PackAln’:
-packaln.dy:88:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
- 88 | fgets(buffer,MAXLINE,ifp);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~
-matrixdebug.dy: In function ‘Wise2_user_DebugMatrix’:
-matrixdebug.dy:208:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
- 208 | fgets(buffer,MAXLINE,in);
- | ^~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ genomic.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ cdna.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ cdnadb.c
@@ -1707,15 +1743,12 @@
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ proteinindexcons.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dnaindexcons.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ staticseq.c
-hspthreadeddb.dy: In function ‘Wise2_threadeddb_scan_worker’:
-hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
- 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len);
- | ^
-hspthreadeddb.dy:154:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Wise2_HSPDatabaseSegment *’ [-Wformat=]
- 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~
- | |
- | Wise2_HSPDatabaseSegment *
+hsplookupthreaded.dy: In function ‘Wise2_one_off_ordered_HSPscan_scan_query_direct’:
+hsplookupthreaded.dy:263:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
+ 263 | fprintf(stderr,"retrieved array with %d elements\n",current_oph);
+ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~
+ | |
+ | long int
shadowseqindex.dy: In function ‘Wise2_dump_stats_ShadowSequenceIndex’:
shadowseqindex.dy:285:15: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘long unsigned int’ [-Wformat=]
285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000);
@@ -1869,12 +1902,15 @@
subseqhash.dy:189:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
189 | g_hash_table_insert(h,(gpointer)seq_number,p);
| ^
-hsplookupthreaded.dy: In function ‘Wise2_one_off_ordered_HSPscan_scan_query_direct’:
-hsplookupthreaded.dy:263:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
- 263 | fprintf(stderr,"retrieved array with %d elements\n",current_oph);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~
- | |
- | long int
+hspthreadeddb.dy: In function ‘Wise2_threadeddb_scan_worker’:
+hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
+ 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len);
+ | ^
+hspthreadeddb.dy:154:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Wise2_HSPDatabaseSegment *’ [-Wformat=]
+ 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len);
+ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~
+ | |
+ | Wise2_HSPDatabaseSegment *
ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar: creating libdyna_glib.a
@@ -1900,6 +1936,7 @@
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ functionserver.c
dyc -l -n Wise2_ -a _api.h -b _api.t -latex -perl functionclient.dy
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ anonobj.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ transferinterface.c
Warning Error
Could not open [methods] for MethodTypeSet reading
Warning Error
@@ -1907,7 +1944,6 @@
dynamite matrices. I will attempt to compile, but you cannot use
logical types. 'methods' should be either in the current directory,
the $WISECONFIGDIR or your $WISEPERSONALDIR
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ transferinterface.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ directsocketwrite.c
Warning Error
You have 3 undocumented functions
@@ -1940,7 +1976,6 @@
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models dnamapping.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c
dyc -l -n Wise2_ -pthreads -dbtrace 5 -nocwarn kmer_assembly_untangler.dy
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c
Warning Error
Could not open [methods] for MethodTypeSet reading
Warning Error
@@ -1948,28 +1983,29 @@
dynamite matrices. I will attempt to compile, but you cannot use
logical types. 'methods' should be either in the current directory,
the $WISECONFIGDIR or your $WISEPERSONALDIR
-dyc -l -n Wise2_ -pthreads -dbtrace 5 -nocwarn kmer_assembly_error.dy
Warning Error
kmer_assembly_untangler.dy:24:
For element long - got no good default. Returning 0
-Warning Errorcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly.c
-
- cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c
-Could not open [methods] for MethodTypeSet reading
+Warning Error
+ You have 14 undocumented functions
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c
+dyc -l -n Wise2_ -pthreads -dbtrace 5 -nocwarn kmer_assembly_error.dy
+Warning Error
+ Could not open [methods] for MethodTypeSet reading
Warning Error
You have no config file called 'methods'. This is bad news for
dynamite matrices. I will attempt to compile, but you cannot use
logical types. 'methods' should be either in the current directory,
the $WISECONFIGDIR or your $WISEPERSONALDIR
-Warning Error
- You have 14 undocumented functions
-Warning Error
- You have 10 undocumented functions
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c
dyc -l -n Wise2_ -pthreads -dbtrace 5 -nocwarn compressed_protein_index.dy
Warning Error
+ You have 10 undocumented functions
+Warning Error
Could not open [methods] for MethodTypeSet reading
Warning Error
You have no config file called 'methods'. This is bad news for
@@ -1977,9 +2013,9 @@
logical types. 'methods' should be either in the current directory,
the $WISECONFIGDIR or your $WISEPERSONALDIR
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c
Warning Error
You have 16 undocumented functions
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c
kmer_hash.dy: In function ‘Wise2_free_KmerHashIndex’:
kmer_hash.dy:318:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
@@ -2017,6 +2053,10 @@
kmer_assembly.dy:367:20: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=]
367 | fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
+kmer_assembly_untangler.dy: In function ‘Wise2_show_KmerAssemblyPath’:
+kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
+ 52 | fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base);
+ | ^
kmer_assembly_error.dy: In function ‘Wise2_mark_tangles_KmerAssembly’:
kmer_assembly_error.dy:93:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
93 | fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer);
@@ -2028,16 +2068,6 @@
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
| |
| kmer_t {aka long long int}
-kmer_assembly_error.dy: In function ‘Wise2_extend_indel_path_KmerAssembly’:
-kmer_assembly_error.dy:351:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int *’ [-Wformat=]
- 351 | fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
- | |
- | int *
-kmer_assembly_untangler.dy: In function ‘Wise2_show_KmerAssemblyPath’:
-kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
- 52 | fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base);
- | ^
kmer_assembly_untangler.dy: In function ‘Wise2_untangle_KmerAssembly’:
kmer_assembly_untangler.dy:120:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
120 | fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len);
@@ -2064,6 +2094,12 @@
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
| |
| kmer_t {aka long long int}
+kmer_assembly_error.dy: In function ‘Wise2_extend_indel_path_KmerAssembly’:
+kmer_assembly_error.dy:351:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int *’ [-Wformat=]
+ 351 | fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos);
+ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
+ | |
+ | int *
kmer_assembly_untangler.dy: In function ‘Wise2_old_attempt_forward_untangle_KmerAssembly’:
kmer_assembly_untangler.dy:444:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
444 | fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len);
@@ -2121,14 +2157,6 @@
dynamite matrices. I will attempt to compile, but you cannot use
logical types. 'methods' should be either in the current directory,
the $WISECONFIGDIR or your $WISEPERSONALDIR
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneutil.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneoutput.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ threestatemodel.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genefrequency.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ splicesitemodeler.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise4.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise6.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genestretch6.c
Warning Error
You have not documented new_GeneWiseRunPara_from_argv
Warning Error
@@ -2143,31 +2171,8 @@
You have not documented add_GeneWiseHSPmanager_HSPset
Warning Error
You have 6 undocumented functions
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise21.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneloop21.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneloop6.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genephase6.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwlite.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwlitemodel.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwrap.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ matchsum.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estwrap.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisemodel.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ phasemodel.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ cdparser.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genedisplay.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estwise3.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estslim3.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estloop3.c
-dnal.c: In function ‘show_version’:
-dnal.c:106:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
- 106 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
- | ^~~~~~~~~~~~
-pswdb.c: In function ‘show_version’:
-pswdb.c:97:106: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
- 97 | fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
- | ^~~~~~~~~~~~
-psw.c: In function ‘show_version’:
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneutil.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneoutput.c
dbac.c: In function ‘show_version’:
dbac.c:364:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
364 | fprintf(ofp," Compiled %s\n",COMPILE_DATE);
@@ -2179,17 +2184,45 @@
| | |
| int size_t {aka long unsigned int}
| %ld
+pswdb.c: In function ‘show_version’:
+pswdb.c:97:106: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
+ 97 | fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+ | ^~~~~~~~~~~~
+psw.c: In function ‘show_version’:
psw.c:261:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
261 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
| ^~~~~~~~~~~~
-genedisplay.dy: In function ‘Wise2_write_intron_desc’:
-genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args]
- 493 | sprintf(buffer," Intron ??? ",in_number);
- | ^~~~~~~~~~~~~~~~
+dnal.c: In function ‘show_version’:
+dnal.c:106:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
+ 106 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+ | ^~~~~~~~~~~~
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ threestatemodel.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genefrequency.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ splicesitemodeler.c
+estwise.c: In function ‘show_version’:
+estwise.c:559:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
+ 559 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+ | ^~~~~~~~~~~~
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise4.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise6.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genestretch6.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise21.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneloop21.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneloop6.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genephase6.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwlite.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwlitemodel.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwrap.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ matchsum.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estwrap.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisemodel.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ phasemodel.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ cdparser.c
phasemodel.dy: In function ‘Wise2_read_fasta_PhasedProtein’:
phasemodel.dy:241:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
241 | fgets(name,10000,ifp);
| ^~~~~~~~~~~~~~~~~~~~~
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genedisplay.c
phasemodel.dy:241:3: warning: ‘fgets’ writing 10000 bytes into a region of size 2000 overflows the destination [-Wstringop-overflow=]
241 | fgets(name,10000,ifp);
| ^~~~~~~~~~~~~~~~~~~~~
@@ -2206,13 +2239,21 @@
/usr/include/x86_64-linux-gnu/bits/stdio2.h:305:1: note: in a call to function ‘fgets’ declared with attribute ‘access (write_only, 1, 2)’
305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n,
| ^~~~~
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estwise3.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estslim3.c
+genedisplay.dy: In function ‘Wise2_write_intron_desc’:
+genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args]
+ 493 | sprintf(buffer," Intron ??? ",in_number);
+ | ^~~~~~~~~~~~~~~~
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estloop3.c
+In function ‘fgets’,
+ inlined from ‘Wise2_read_fasta_PhasedProtein’ at phasemodel.dy:241:3:
+/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
+ 316 | return __fgets_chk_warn (__s, __sz, __n, __stream);
+ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estfrag3.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estslimloop.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwquickdb.c
-estwise.c: In function ‘show_version’:
-estwise.c:559:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
- 559 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
- | ^~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ threestatedb.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pfamhmmer1db.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pwmdna.c
@@ -2223,24 +2264,27 @@
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneparser4.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estquick3.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
-In function ‘fgets’,
- inlined from ‘Wise2_read_fasta_PhasedProtein’ at phasemodel.dy:241:3:
-/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
- 316 | return __fgets_chk_warn (__s, __sz, __n, __stream);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/
+genewise.c: In function ‘show_version’:
+genewise.c:860:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
+ 860 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+ | ^~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genomewise.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genomewise9.c
+estwisedb.c: In function ‘show_version’:
+estwisedb.c:838:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
+ 838 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+ | ^~~~~~~~~~~~
genomewise.c: In function ‘show_version’:
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genome_evidence.c
genomewise.c:18:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
18 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
| ^~~~~~~~~~~~
-genewise.c: In function ‘show_version’:
-genewise.c:860:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
- 860 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genomewise9.c
+genewisedb.c: In function ‘show_version’:
+genewisedb.c:1005:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
+ 1005 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
| ^~~~~~~~~~~~
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genome_evidence.c
dyc -l -D -n Wise2_ -a _api.h -b _api.t -latex -perl -pthreads -dbtrace 5 -nocwarn est_evidence.dy
Warning Error
Could not open [methods] for MethodTypeSet reading
@@ -2284,48 +2328,39 @@
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ sywise.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ sywise20.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ syexonmodel.c
-genewisedb.c: In function ‘show_version’:
-genewisedb.c:1005:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
- 1005 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
- | ^~~~~~~~~~~~
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pseudowise.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pseudowise7.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ localdba.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c
sywise.c: In function ‘show_version’:
sywise.c:14:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
14 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
| ^~~~~~~~~~~~
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pseudowise.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pseudowise7.c
pseudowise.c: In function ‘show_version’:
pseudowise.c:15:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
15 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
| ^~~~~~~~~~~~
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ localdba.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c
+promoterwise.c: In function ‘show_version’:
+promoterwise.c:17:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
+ 17 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+ | ^~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ localcispara.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ motifmatrix.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ motifmatrixdp.c
-estwisedb.c: In function ‘show_version’:
-estwisedb.c:838:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
- 838 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
- | ^~~~~~~~~~~~
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ transfactor.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pairwiseshortdna.c
motifmatrix.c: In function ‘Wise2_MotifConsMatrix_alloc_matrix’:
motifmatrix.c:408:24: warning: assignment to ‘char’ from ‘void *’ makes integer from pointer without a cast [-Wint-conversion]
408 | for(i=0;i<leni;i++) {
| ^
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ motifmatrixdp.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ transfactor.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pairwiseshortdna.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c
-promoterwise.c: In function ‘show_version’:
-promoterwise.c:17:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
- 17 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
- | ^~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` hsp2aln_sw.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisehsp.c
-cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ est_evidence.c
scanwisep.c: In function ‘show_version’:
scanwisep.c:423:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
423 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
| ^~~~~~~~~~~~
+cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm
transfactor.dy: In function ‘Wise2_read_ben_IUPAC_TransFactorSet’:
transfactor.dy:680:21: warning: ‘%s’ directive writing up to 511 bytes into a region of size between 495 and 504 [-Wformat-overflow=]
680 | sprintf(sbuffer,"motif_%d_%s",motif_no,buffer);
@@ -2344,14 +2379,15 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
-cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm
cc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm
cc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm
+cc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisehsp.c
+cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ est_evidence.c
cc -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -lpthread -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0`
cc -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm `pkg-config --libs glib-2.0` -lpthread
-cc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm
-cc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm
cc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm
+cc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm
cc -g -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0`
cc -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0`
cc -g -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0`
@@ -6271,18 +6307,18 @@
chmod -R u\+rw,go=rX debian/wise-doc/usr/share/doc
install -p -m0644 debian/copyright debian/wise-doc/usr/share/doc/wise-doc/copyright
install -m0755 -d debian/wise-doc/usr/share/doc-base/
+ install -p -m0644 debian/wise-doc.doc-base.api debian/wise-doc/usr/share/doc-base/wise-doc.wise-api
install -p -m0644 debian/wise-doc.doc-base.dynamite debian/wise-doc/usr/share/doc-base/wise-doc.wise-dynamite
install -p -m0644 debian/wise-doc.doc-base.wise debian/wise-doc/usr/share/doc-base/wise-doc.wise
- install -p -m0644 debian/wise-doc.doc-base.api debian/wise-doc/usr/share/doc-base/wise-doc.wise-api
install -m0755 -d debian/wise-data/usr/share/doc/wise-data
install -p -m0644 debian/copyright debian/wise-data/usr/share/doc/wise-data/copyright
dh_installchangelogs
+ install -m0755 -d debian/wise-doc/usr/share/doc/wise-doc
+ install -p -m0644 debian/.debhelper/generated/wise-doc/dh_installchangelogs.dch.trimmed debian/wise-doc/usr/share/doc/wise-doc/changelog.Debian
install -m0755 -d debian/wise-data/usr/share/doc/wise-data
install -p -m0644 debian/.debhelper/generated/wise-data/dh_installchangelogs.dch.trimmed debian/wise-data/usr/share/doc/wise-data/changelog.Debian
install -m0755 -d debian/wise/usr/share/doc/wise
install -p -m0644 debian/.debhelper/generated/wise/dh_installchangelogs.dch.trimmed debian/wise/usr/share/doc/wise/changelog.Debian
- install -m0755 -d debian/wise-doc/usr/share/doc/wise-doc
- install -p -m0644 debian/.debhelper/generated/wise-doc/dh_installchangelogs.dch.trimmed debian/wise-doc/usr/share/doc/wise-doc/changelog.Debian
debian/rules override_dh_installexamples-indep
make[1]: Entering directory '/build/reproducible-path/wise-2.4.1'
dh_installexamples
@@ -6346,73 +6382,73 @@
install -m0755 -d debian/wise/usr/share/man/man1/
install -p -m0644 ./debian/manpages.d/scanwise_server.1 debian/wise/usr/share/man/man1/scanwise_server.1
man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/dba.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/dnal.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/estwise.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/pswdb.1
man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/estwisedb.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genomewise.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/promoterwise.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/estwise.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/dnal.1
man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genewise.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genewisedb.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/scanwise.1
man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/psw.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/pswdb.1
man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/scanwise_server.1
- mv debian/wise/usr/share/man/man1/estwise.1.dh-new debian/wise/usr/share/man/man1/estwise.1
- chmod 0644 -- debian/wise/usr/share/man/man1/estwise.1
- mv debian/wise/usr/share/man/man1/dnal.1.dh-new debian/wise/usr/share/man/man1/dnal.1
- chmod 0644 -- debian/wise/usr/share/man/man1/dnal.1
- mv debian/wise/usr/share/man/man1/psw.1.dh-new debian/wise/usr/share/man/man1/psw.1
- chmod 0644 -- debian/wise/usr/share/man/man1/psw.1
- mv debian/wise/usr/share/man/man1/dba.1.dh-new debian/wise/usr/share/man/man1/dba.1
- chmod 0644 -- debian/wise/usr/share/man/man1/dba.1
- mv debian/wise/usr/share/man/man1/genewisedb.1.dh-new debian/wise/usr/share/man/man1/genewisedb.1
- chmod 0644 -- debian/wise/usr/share/man/man1/genewisedb.1
- mv debian/wise/usr/share/man/man1/estwisedb.1.dh-new debian/wise/usr/share/man/man1/estwisedb.1
- chmod 0644 -- debian/wise/usr/share/man/man1/estwisedb.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/scanwise.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genomewise.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/promoterwise.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genewisedb.1
mv debian/wise/usr/share/man/man1/promoterwise.1.dh-new debian/wise/usr/share/man/man1/promoterwise.1
chmod 0644 -- debian/wise/usr/share/man/man1/promoterwise.1
- mv debian/wise/usr/share/man/man1/genewise.1.dh-new debian/wise/usr/share/man/man1/genewise.1
- chmod 0644 -- debian/wise/usr/share/man/man1/genewise.1
+ mv debian/wise/usr/share/man/man1/psw.1.dh-new debian/wise/usr/share/man/man1/psw.1
+ chmod 0644 -- debian/wise/usr/share/man/man1/psw.1
mv debian/wise/usr/share/man/man1/pswdb.1.dh-new debian/wise/usr/share/man/man1/pswdb.1
chmod 0644 -- debian/wise/usr/share/man/man1/pswdb.1
+ mv debian/wise/usr/share/man/man1/genewise.1.dh-new debian/wise/usr/share/man/man1/genewise.1
+ chmod 0644 -- debian/wise/usr/share/man/man1/genewise.1
+ mv debian/wise/usr/share/man/man1/dnal.1.dh-new debian/wise/usr/share/man/man1/dnal.1
+ chmod 0644 -- debian/wise/usr/share/man/man1/dnal.1
mv debian/wise/usr/share/man/man1/scanwise.1.dh-new debian/wise/usr/share/man/man1/scanwise.1
chmod 0644 -- debian/wise/usr/share/man/man1/scanwise.1
- mv debian/wise/usr/share/man/man1/scanwise_server.1.dh-new debian/wise/usr/share/man/man1/scanwise_server.1
- chmod 0644 -- debian/wise/usr/share/man/man1/scanwise_server.1
mv debian/wise/usr/share/man/man1/genomewise.1.dh-new debian/wise/usr/share/man/man1/genomewise.1
chmod 0644 -- debian/wise/usr/share/man/man1/genomewise.1
+ mv debian/wise/usr/share/man/man1/estwisedb.1.dh-new debian/wise/usr/share/man/man1/estwisedb.1
+ chmod 0644 -- debian/wise/usr/share/man/man1/estwisedb.1
+ mv debian/wise/usr/share/man/man1/dba.1.dh-new debian/wise/usr/share/man/man1/dba.1
+ chmod 0644 -- debian/wise/usr/share/man/man1/dba.1
+ mv debian/wise/usr/share/man/man1/genewisedb.1.dh-new debian/wise/usr/share/man/man1/genewisedb.1
+ chmod 0644 -- debian/wise/usr/share/man/man1/genewisedb.1
+ mv debian/wise/usr/share/man/man1/estwise.1.dh-new debian/wise/usr/share/man/man1/estwise.1
+ chmod 0644 -- debian/wise/usr/share/man/man1/estwise.1
+ mv debian/wise/usr/share/man/man1/scanwise_server.1.dh-new debian/wise/usr/share/man/man1/scanwise_server.1
+ chmod 0644 -- debian/wise/usr/share/man/man1/scanwise_server.1
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
- cd debian/wise-data
- cd debian/wise-doc
cd debian/wise
- chmod a-x usr/share/doc/wise-doc/changelog.Debian usr/share/doc/wise/api.pdf usr/share/doc/wise/dynamite.pdf usr/share/doc/wise/wise2.pdf
- gzip -9nf usr/share/doc/wise-doc/changelog.Debian usr/share/doc/wise/api.pdf usr/share/doc/wise/dynamite.pdf usr/share/doc/wise/wise2.pdf
+ cd debian/wise-doc
+ cd debian/wise-data
chmod a-x usr/share/doc/wise-data/changelog.Debian
+ chmod a-x usr/share/doc/wise-doc/changelog.Debian usr/share/doc/wise/api.pdf usr/share/doc/wise/dynamite.pdf usr/share/doc/wise/wise2.pdf
gzip -9nf usr/share/doc/wise-data/changelog.Debian
+ gzip -9nf usr/share/doc/wise-doc/changelog.Debian usr/share/doc/wise/api.pdf usr/share/doc/wise/dynamite.pdf usr/share/doc/wise/wise2.pdf
chmod a-x usr/share/doc/wise/changelog.Debian usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewise.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1
- cd '/build/reproducible-path/wise-2.4.1'
gzip -9nf usr/share/doc/wise/changelog.Debian usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewise.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1
cd '/build/reproducible-path/wise-2.4.1'
cd '/build/reproducible-path/wise-2.4.1'
+ cd '/build/reproducible-path/wise-2.4.1'
rm -f debian/wise-data.debhelper.log debian/wise-doc.debhelper.log
debian/rules override_dh_fixperms
make[1]: Entering directory '/build/reproducible-path/wise-2.4.1'
dh_fixperms
find debian/wise ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
- find debian/wise-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/wise-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
- find debian/wise-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/wise-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/wise-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/wise-data/usr/share/doc -type f -a -true -a ! -regex 'debian/wise-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/wise/usr/share/doc -type f -a -true -a ! -regex 'debian/wise/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/wise-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
+ find debian/wise-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/wise-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/wise-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/wise/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
+ find debian/wise-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
+ find debian/wise/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/wise-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/wise-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/wise/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/wise -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/wise/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian -iname "*.hmm" -exec chmod -x \{\} \;
@@ -6424,66 +6460,66 @@
objcopy --compress-debug-sections debian/wise/usr/lib/debug/.dwz/x86_64-linux-gnu/wise.debug
chmod 0644 -- debian/wise/usr/lib/debug/.dwz/x86_64-linux-gnu/wise.debug
dh_strip -a
- install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76
- objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76/c74e3e3fdd0bb25887022bc7cdbacf56a96ff5.debug
- chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76/c74e3e3fdd0bb25887022bc7cdbacf56a96ff5.debug
- strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise
- objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76/c74e3e3fdd0bb25887022bc7cdbacf56a96ff5.debug debian/wise/usr/bin/genewise
- install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/07
- objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise_server debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/07/9d5a6e5a0ce0c8a3ed39982eb649968c646d22.debug
- chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/07/9d5a6e5a0ce0c8a3ed39982eb649968c646d22.debug
- strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server
- objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/07/9d5a6e5a0ce0c8a3ed39982eb649968c646d22.debug debian/wise/usr/bin/scanwise_server
- install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e9
- objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e9/81b8f629ea2027febaa5caf4f45fab7b26fdc2.debug
- chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e9/81b8f629ea2027febaa5caf4f45fab7b26fdc2.debug
- strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise
- objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e9/81b8f629ea2027febaa5caf4f45fab7b26fdc2.debug debian/wise/usr/bin/estwise
install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b
objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/psw debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b/a1da17c9fa2608d2efad9c49a17eda4ae2c248.debug
chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b/a1da17c9fa2608d2efad9c49a17eda4ae2c248.debug
strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/psw
objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b/a1da17c9fa2608d2efad9c49a17eda4ae2c248.debug debian/wise/usr/bin/psw
- install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2
- objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2/cfd039f4b5c2c3322bdd6d1ce5f7dda764312d.debug
- chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2/cfd039f4b5c2c3322bdd6d1ce5f7dda764312d.debug
- strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise
- objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2/cfd039f4b5c2c3322bdd6d1ce5f7dda764312d.debug debian/wise/usr/bin/scanwise
- install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da
- objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da/0a6b4ff7e8c7e75d66ea075a0060a26dbef12a.debug
- chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da/0a6b4ff7e8c7e75d66ea075a0060a26dbef12a.debug
- strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb
- objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da/0a6b4ff7e8c7e75d66ea075a0060a26dbef12a.debug debian/wise/usr/bin/genewisedb
install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/71
objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/71/bed81c42b18899c7f95c58cebd9b1fe1757901.debug
chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/71/bed81c42b18899c7f95c58cebd9b1fe1757901.debug
strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/pswdb
objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/71/bed81c42b18899c7f95c58cebd9b1fe1757901.debug debian/wise/usr/bin/pswdb
- install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0
- objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0/8d9e4cd3a7917c950168f89ea6600f3e57b30b.debug
- chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0/8d9e4cd3a7917c950168f89ea6600f3e57b30b.debug
- strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb
- objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0/8d9e4cd3a7917c950168f89ea6600f3e57b30b.debug debian/wise/usr/bin/estwisedb
- install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ec
- objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ec/ed32d8309f7db0a3781f21a4438709986a14cc.debug
- chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ec/ed32d8309f7db0a3781f21a4438709986a14cc.debug
- strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise
- objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ec/ed32d8309f7db0a3781f21a4438709986a14cc.debug debian/wise/usr/bin/promoterwise
+ install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45
+ objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45/c1055d3673bc15d240d26700bd6e22e74166d4.debug
+ chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45/c1055d3673bc15d240d26700bd6e22e74166d4.debug
+ strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba
+ objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45/c1055d3673bc15d240d26700bd6e22e74166d4.debug debian/wise/usr/bin/dba
+ install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e9
+ objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e9/81b8f629ea2027febaa5caf4f45fab7b26fdc2.debug
+ chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e9/81b8f629ea2027febaa5caf4f45fab7b26fdc2.debug
+ strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise
+ objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e9/81b8f629ea2027febaa5caf4f45fab7b26fdc2.debug debian/wise/usr/bin/estwise
install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/37
objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/37/03ce9069d93d1de8fd10d61a0f400c072e2286.debug
chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/37/03ce9069d93d1de8fd10d61a0f400c072e2286.debug
strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genomewise
objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/37/03ce9069d93d1de8fd10d61a0f400c072e2286.debug debian/wise/usr/bin/genomewise
+ install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76
+ objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76/c74e3e3fdd0bb25887022bc7cdbacf56a96ff5.debug
+ chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76/c74e3e3fdd0bb25887022bc7cdbacf56a96ff5.debug
+ strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise
+ objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76/c74e3e3fdd0bb25887022bc7cdbacf56a96ff5.debug debian/wise/usr/bin/genewise
+ install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/07
+ objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise_server debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/07/9d5a6e5a0ce0c8a3ed39982eb649968c646d22.debug
+ chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/07/9d5a6e5a0ce0c8a3ed39982eb649968c646d22.debug
+ strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server
+ objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/07/9d5a6e5a0ce0c8a3ed39982eb649968c646d22.debug debian/wise/usr/bin/scanwise_server
install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/08
objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/08/8a7890e21636ac4f2f8da5a09c2eaeecdf5afd.debug
chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/08/8a7890e21636ac4f2f8da5a09c2eaeecdf5afd.debug
strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal
objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/08/8a7890e21636ac4f2f8da5a09c2eaeecdf5afd.debug debian/wise/usr/bin/dnal
- install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45
- objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45/c1055d3673bc15d240d26700bd6e22e74166d4.debug
- chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45/c1055d3673bc15d240d26700bd6e22e74166d4.debug
- strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba
- objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45/c1055d3673bc15d240d26700bd6e22e74166d4.debug debian/wise/usr/bin/dba
+ install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ec
+ objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ec/ed32d8309f7db0a3781f21a4438709986a14cc.debug
+ chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ec/ed32d8309f7db0a3781f21a4438709986a14cc.debug
+ strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise
+ objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ec/ed32d8309f7db0a3781f21a4438709986a14cc.debug debian/wise/usr/bin/promoterwise
+ install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0
+ objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0/8d9e4cd3a7917c950168f89ea6600f3e57b30b.debug
+ chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0/8d9e4cd3a7917c950168f89ea6600f3e57b30b.debug
+ strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb
+ objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0/8d9e4cd3a7917c950168f89ea6600f3e57b30b.debug debian/wise/usr/bin/estwisedb
+ install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2
+ objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2/cfd039f4b5c2c3322bdd6d1ce5f7dda764312d.debug
+ chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2/cfd039f4b5c2c3322bdd6d1ce5f7dda764312d.debug
+ strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise
+ objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2/cfd039f4b5c2c3322bdd6d1ce5f7dda764312d.debug debian/wise/usr/bin/scanwise
+ install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da
+ objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da/0a6b4ff7e8c7e75d66ea075a0060a26dbef12a.debug
+ chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da/0a6b4ff7e8c7e75d66ea075a0060a26dbef12a.debug
+ strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb
+ objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da/0a6b4ff7e8c7e75d66ea075a0060a26dbef12a.debug debian/wise/usr/bin/genewisedb
install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/wise/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/wise/usr/lib/debug/.dwz
@@ -6495,7 +6531,7 @@
rm -f debian/wise/DEBIAN/shlibs
dh_shlibdeps -a
install -m0755 -d debian/wise/DEBIAN
- dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/genewise debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/estwise debian/wise/usr/bin/psw debian/wise/usr/bin/scanwise debian/wise/usr/bin/genewisedb debian/wise/usr/bin/pswdb debian/wise/usr/bin/estwisedb debian/wise/usr/bin/promoterwise debian/wise/usr/bin/genomewise debian/wise/usr/bin/dnal debian/wise/usr/bin/dba
+ dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/psw debian/wise/usr/bin/pswdb debian/wise/usr/bin/dba debian/wise/usr/bin/estwise debian/wise/usr/bin/genomewise debian/wise/usr/bin/genewise debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/dnal debian/wise/usr/bin/promoterwise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/scanwise debian/wise/usr/bin/genewisedb
dh_installdeb
install -m0755 -d debian/wise/DEBIAN
install -m0755 -d debian/wise-doc/DEBIAN
@@ -6505,29 +6541,29 @@
echo misc:Depends= >> debian/wise-doc.substvars
echo misc:Pre-Depends= >> debian/wise-doc.substvars
dpkg-gencontrol -pwise-doc -ldebian/changelog -Tdebian/wise-doc.substvars -cdebian/control -Pdebian/wise-doc
- install -m0755 -d debian/wise-data/DEBIAN
- echo misc:Depends= >> debian/wise-data.substvars
- echo misc:Pre-Depends= >> debian/wise-data.substvars
- dpkg-gencontrol -pwise-data -ldebian/changelog -Tdebian/wise-data.substvars -cdebian/control -Pdebian/wise-data
install -m0755 -d debian/wise/DEBIAN
echo misc:Depends= >> debian/wise.substvars
echo misc:Pre-Depends= >> debian/wise.substvars
install -m0755 -d debian/.debhelper/wise/dbgsym-root/DEBIAN
dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -cdebian/control -Pdebian/.debhelper/wise/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=wise-dbgsym "-DDepends=wise (= \${binary:Version})" "-DDescription=debug symbols for wise" "-DBuild-Ids=079d5a6e5a0ce0c8a3ed39982eb649968c646d22 088a7890e21636ac4f2f8da5a09c2eaeecdf5afd 3703ce9069d93d1de8fd10d61a0f400c072e2286 45c1055d3673bc15d240d26700bd6e22e74166d4 71bed81c42b18899c7f95c58cebd9b1fe1757901 76c74e3e3fdd0bb25887022bc7cdbacf56a96ff5 8ba1da17c9fa2608d2efad9c49a17eda4ae2c248 b08d9e4cd3a7917c950168f89ea6600f3e57b30b b2cfd039f4b5c2c3322bdd6d1ce5f7dda764312d da0a6b4ff7e8c7e75d66ea075a0060a26dbef12a e981b8f629ea2027febaa5caf4f45fab7b26fdc2 eced32d8309f7db0a3781f21a4438709986a14cc" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
- chmod 0644 -- debian/wise-data/DEBIAN/control
+ install -m0755 -d debian/wise-data/DEBIAN
+ echo misc:Depends= >> debian/wise-data.substvars
+ echo misc:Pre-Depends= >> debian/wise-data.substvars
+ dpkg-gencontrol -pwise-data -ldebian/changelog -Tdebian/wise-data.substvars -cdebian/control -Pdebian/wise-data
chmod 0644 -- debian/wise-doc/DEBIAN/control
+ chmod 0644 -- debian/wise-data/DEBIAN/control
chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -cdebian/control -Pdebian/wise
chmod 0644 -- debian/wise/DEBIAN/control
dh_md5sums
- install -m0755 -d debian/wise-doc/DEBIAN
install -m0755 -d debian/wise/DEBIAN
+ install -m0755 -d debian/wise-doc/DEBIAN
+ cd debian/wise >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
install -m0755 -d debian/wise-data/DEBIAN
cd debian/wise-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/wise-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
- cd debian/wise >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
- chmod 0644 -- debian/wise-data/DEBIAN/md5sums
chmod 0644 -- debian/wise-doc/DEBIAN/md5sums
+ chmod 0644 -- debian/wise-data/DEBIAN/md5sums
chmod 0644 -- debian/wise/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/wise/dbgsym-root/DEBIAN
cd debian/.debhelper/wise/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
@@ -6535,12 +6571,12 @@
dh_builddeb
dpkg-deb --root-owner-group --build debian/wise ..
dpkg-deb --root-owner-group --build debian/wise-doc ..
- dpkg-deb --root-owner-group --build debian/.debhelper/wise/dbgsym-root ..
dpkg-deb --root-owner-group --build debian/wise-data ..
-dpkg-deb: building package 'wise-data' in '../wise-data_2.4.1-27_all.deb'.
+ dpkg-deb --root-owner-group --build debian/.debhelper/wise/dbgsym-root ..
dpkg-deb: building package 'wise' in '../wise_2.4.1-27_amd64.deb'.
-dpkg-deb: building package 'wise-dbgsym' in '../wise-dbgsym_2.4.1-27_amd64.deb'.
+dpkg-deb: building package 'wise-data' in '../wise-data_2.4.1-27_all.deb'.
dpkg-deb: building package 'wise-doc' in '../wise-doc_2.4.1-27_all.deb'.
+dpkg-deb: building package 'wise-dbgsym' in '../wise-dbgsym_2.4.1-27_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../wise_2.4.1-27_amd64.buildinfo
dpkg-genchanges --build=binary -O../wise_2.4.1-27_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
@@ -6548,12 +6584,14 @@
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/23253/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/23253/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/900143 and its subdirectories
-I: Current time: Wed Apr 29 18:31:17 -12 2026
-I: pbuilder-time-stamp: 1777530677
+I: removing directory /srv/workspace/pbuilder/23253 and its subdirectories
+I: Current time: Fri Mar 28 14:14:01 +14 2025
+I: pbuilder-time-stamp: 1743120841