I: pbuilder: network access will be disabled during build I: Current time: Sun Mar 28 18:49:59 -12 2021 I: pbuilder-time-stamp: 1617000599 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [readseq_1-13.dsc] I: copying [./readseq_1.orig.tar.gz] I: copying [./readseq_1-13.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Jun 23 07:54:48 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./readseq_1-13.dsc dpkg-source: info: extracting readseq in readseq-1 dpkg-source: info: unpacking readseq_1.orig.tar.gz dpkg-source: info: unpacking readseq_1-13.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 20-Formats.patch dpkg-source: info: applying 20-Makefile.patch dpkg-source: info: applying 30-arb-code-patches.patch dpkg-source: info: applying 552830.patch dpkg-source: info: applying gcc-4.6_format-security.patch dpkg-source: info: applying enable_tests.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying buffer_overflow.patch dpkg-source: info: applying fix_tests.patch I: using fakeroot in build. I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), ncbi-tools-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19231 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on ncbi-tools-dev; however: Package ncbi-tools-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncbi6{a} libncbi6-dev{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} ncbi-data{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx ncbi-tools-bin shared-mime-info wget xdg-user-dirs 0 packages upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 32.7 MB of archives. After unpacking 132 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 10 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 11 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 14 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 24 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6 [8443 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 30 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main i386 ncbi-data all 6.1.20170106+dfsg1-0+deb10u2 [3552 kB] Get: 35 http://deb.debian.org/debian buster/main i386 libncbi6 i386 6.1.20170106+dfsg1-0+deb10u2 [4193 kB] Get: 36 http://deb.debian.org/debian buster/main i386 libncbi6-dev i386 6.1.20170106+dfsg1-0+deb10u2 [5647 kB] Fetched 32.7 MB in 1s (39.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19231 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... 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Setting up autopoint (0.19.8.1-9) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libbsd0:i386 (0.9.1-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up libncbi6:i386 (6.1.20170106+dfsg1-0+deb10u2) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libncbi6-dev:i386 (6.1.20170106+dfsg1-0+deb10u2) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:i386 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/readseq-1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package readseq dpkg-buildpackage: info: source version 1-13 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Liubov Chuprikova dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean dh_auto_clean make -j18 clean make[1]: Entering directory '/build/readseq-1' rm -f *.o core test.* readseq make[1]: Leaving directory '/build/readseq-1' debian/rules override_dh_clean make[1]: Entering directory '/build/readseq-1' dh_clean rm -f readseq make[1]: Leaving directory '/build/readseq-1' debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j18 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/readseq-1' Compiling readseq with NCBI toolkit support and ARB patches gcc -o readseq -I/usr/include/ncbi -g -O2 -ffile-prefix-map=/build/readseq-1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -DNCBI -I/usr/include/ncbi -DARB readseq.c ureadseq.c ureadasn.c -lncbi -lncbiobj -lncbicdr -lncbiacc -lncbitool -lncbimmdb -lncbiid1 -lnetcli -lm -Wl,-z,relro -Wl,-z,now readseq.c: In function 'formatstr': readseq.c:267:41: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] case kASNseqset : return formats[kASN1-1]; ~~~~~~~^~~~~~~~~ readseq.c:269:45: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] case kPhylipSequential: return formats[kPhylip-1]; ~~~~~~~^~~~~~~~~~~ readseq.c:273:22: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] else return formats[format-1]; ~~~~~~~^~~~~~~~~~ readseq.c: In function 'Nlm_Main': readseq.c:801:5: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] gets(oname= onamestore); ^~~~ fgets readseq.c:936:33: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] sprintf( stemp,"%s_%d", oname, whichSeq); ~^ ~~~~~~~~ %ld readseq.c:938:48: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf( stderr,"Writing sequence %d to file %s\n", whichSeq, stemp); ~^ ~~~~~~~~ %ld readseq.c:980:39: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", ~^ %ld whichSeq, seqlen, checksum, formatstr(format), seqidptr); ~~~~~~~~ readseq.c:980:51: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", ~^ %ld whichSeq, seqlen, checksum, formatstr(format), seqidptr); ~~~~~~ readseq.c:980:65: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", ~^ %lX whichSeq, seqlen, checksum, formatstr(format), seqidptr); ~~~~~~~~ readseq.c:998:53: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); ~^ ~ %ld readseq.c:998:56: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); ~^ ~~~~~~ %ld readseq.c:999:39: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] else fprintf(foo," %d %d YF\n", i, seqlen); ~^ ~ %ld readseq.c:999:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] else fprintf(foo," %d %d YF\n", i, seqlen); ~^ ~~~~~~ %ld readseq.c:1117:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */ ~^ %ld cp, seqlen, timestr, checkall); ~~~~~~ readseq.c:1117:55: warning: format '%d' expects argument of type 'int', but argument 6 has type 'long unsigned int' [-Wformat=] fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */ ~^ %ld cp, seqlen, timestr, checkall); ~~~~~~~~ readseq.c:1133:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] if (phylvers >= 4) fprintf(foo," %d %d\n", seqout, seqlen); ~^ ~~~~~~ %ld readseq.c:1134:28: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] else fprintf(foo," %d %d YF\n", seqout, seqlen); ~^ ~~~~~~ %ld readseq.c:1158:49: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(foo," dimensions ntax=%d nchar=%d;\n", seqout, seqlen); ~^ ~~~~~~ %ld ureadseq.c: In function 'seqFileFormatFp': ureadseq.c:1535:19: warning: format '%d' expects argument of type 'int *', but argument 3 has type 'long int *' [-Wformat=] sscanf( sp, "%d%d", &nspp, &nlen); ~^ ~~~~~ %ld ureadseq.c:1535:21: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long int *' [-Wformat=] sscanf( sp, "%d%d", &nspp, &nlen); ~^ ~~~~~ %ld ureadseq.c: In function 'writeSeq': ureadseq.c:1784:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] sprintf(numform, "%d", seqlen); ~^ ~~~~~~ %ld ureadseq.c:1813:43: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,"LOCUS %s %d bp\n", idword, seqlen); ~^ ~~~~~~ %ld ureadseq.c:1814:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~ %ld ureadseq.c:1814:48: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~~~ %lX ureadseq.c:1828:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~ %ld ureadseq.c:1828:52: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~~~ %lX ureadseq.c:1838:53: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] for (j= 5; j<=width; j += 5) fprintf(outf,"%10d",j); ~~~^ ~ %10ld ureadseq.c:1848:26: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~ %ld ureadseq.c:1848:36: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~~~ %lX ureadseq.c:1857:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~ %ld ureadseq.c:1857:41: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~~~ %lX ureadseq.c:1858:37: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf(outf,"SQ %d BP\n", seqlen); ~^ ~~~~~~ %ld ureadseq.c:1869:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum); ~^ ~~~~~~ %ld ureadseq.c:1869:58: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum); ~^ ~~~~~~~~ %ld ureadseq.c:1878:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum); ~^ ~~~~~~ %ld ureadseq.c:1878:52: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum); ~^ ~~~~~~~~ %lX ureadseq.c:1884:26: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~ %ld ureadseq.c:1884:36: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~~~ %lX ureadseq.c:1915:53: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf," repr raw, mol %s, length %d, topology linear,\n", cp, seqlen); ~^ ~~~~~~ %ld ureadseq.c:1937:41: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum); ~~^ ~~~~~~ %6ld ureadseq.c:1937:53: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum); ~~^ ~~~~~~~~ %8lX ureadseq.c:1954:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum); ~~^ ~~~~~~ %6ld ureadseq.c:1954:54: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum); ~~^ ~~~~~~~~ %8lX ureadseq.c:1960:40: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", ~~^ %6ld idword, seqlen, checksum); ~~~~~~ ureadseq.c:1960:52: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", ~~^ %5ld idword, seqlen, checksum); ~~~~~~~~ ureadseq.c:1972:27: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~ %ld ureadseq.c:1972:37: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~~~ %lX ureadseq.c:1979:18: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf(outf,"%4d %-60s\n",seqlen,seqname); ~~^ ~~~~~~ %4ld ureadseq.c:2002:27: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~ %ld ureadseq.c:2002:37: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ ~~~~~~~~ %lX ureadseq.c:2043:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] if (numline==1) fprintf(outf,"%-9d ",i+1); ~~~^ ~~~ %-9ld ureadseq.c:2007:45: warning: '%d' directive writing between 1 and 6 bytes into a region of size between 2 and 7 [-Wformat-overflow=] if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); ^~ ureadseq.c:2007:39: note: directive argument in the range [-32768, 32767] if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); ^~~~~~~~~~~ ureadseq.c:2007:21: note: 'sprintf' output between 7 and 17 bytes into a destination of size 10 if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadseq.c:1780:3: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy( seqnamestore, seqid, l); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ureadseq.c:27: ureadseq.c:1779:16: note: length computed here l = min(128, strlen(seqid)); ^~~~~~~~~~~~~ ureadseq.h:15:26: note: in definition of macro 'min' #define min(a,b) (a ;nucleic/amino, , 228 bases, 1B5655D0 checksum. > nucleic/amino, make[1]: [Makefile:70: test] Error 1 (ignored) Test for multiple-sequence format conversions: ./readseq -p -f=ig multi.std -otest.m-ig ./readseq -p -f=gb test.m-ig -otest.m-gb ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf ./readseq -p -f=embl test.m-nbrf -otest.m-embl ./readseq -p -f=fasta test.m-embl -otest.m-fasta ./readseq -p -f=pir test.m-fasta -otest.m-pir ./readseq -p -f=msf test.m-pir -otest.m-msf ./readseq -p -f=paup test.m-msf -otest.m-paup ./readseq -p -f=ig test.m-paup -otest.m-ig-b diff test.m-ig test.m-ig-b 1,2c1,2 < ;acarr58sst , 183 bases, 64754A4D checksum. < acarr58sst --- > ;acarr58ss, 183 bases, 64754A4D checksum. > acarr58ss 7c7 < ;amgrrbst , 183 bases, C886D2FB checksum. --- > ;amgrrbst, 183 bases, C886D2FB checksum. 13c13 < ;bmorrbst , 183 bases, 3E9C23D6 checksum. --- > ;bmorrbst, 183 bases, 3E9C23D6 checksum. 19c19 < ;crerrbst , 183 bases, AC88A337 checksum. --- > ;crerrbst, 183 bases, AC88A337 checksum. 25,26c25,26 < ;ddirr58sst , 183 bases, 1E3D23B8 checksum. < ddirr58sst --- > ;ddirr58ss, 183 bases, 1E3D23B8 checksum. > ddirr58ss make[1]: [Makefile:82: test] Error 1 (ignored) Expect differences in the header lines due to different format headers. If any sequence lines differ, or if the checksums differ, there is a problem. ---------------------- To clean up test files, command me: make clean make[1]: Leaving directory '/build/readseq-1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_installdirs dh_auto_install make -j18 install DESTDIR=/build/readseq-1/debian/readseq AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/readseq-1' install readseq /build/readseq-1/debian/readseq/usr/bin install *.std /build/readseq-1/debian/readseq/usr/share/doc/readseq/tests install Makefile /build/readseq-1/debian/readseq/usr/share/doc/readseq/tests make[1]: Leaving directory '/build/readseq-1' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/readseq/usr/bin/readseq was not linked against libnetcli.so.6 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/readseq/usr/bin/readseq was not linked against libncbitool.so.6 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/readseq/usr/bin/readseq was not linked against libncbiid1.so.6 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/readseq/usr/bin/readseq was not linked against libncbimmdb.so.6 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/readseq/usr/bin/readseq was not linked against libncbicdr.so.6 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/readseq/usr/bin/readseq was not linked against libncbiNacc.so.6 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/readseq/usr/bin/readseq was not linked against libm.so.6 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'readseq' in '../readseq_1-13_i386.deb'. dpkg-deb: building package 'readseq-dbgsym' in '../readseq-dbgsym_1-13_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../readseq_1-13_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration 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/23013 and its subdirectories I: Current time: Sun Mar 28 18:50:17 -12 2021 I: pbuilder-time-stamp: 1617000617