Mock Version: 1.4.14 Mock Version: 1.4.14 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/glimmer.spec'], chrootPath='/var/lib/mock/f31-build-55646-28134/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=345600uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/glimmer.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1548892800 Wrote: /builddir/build/SRPMS/glimmer-3.02b-13.fc31.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/glimmer.spec'], chrootPath='/var/lib/mock/f31-build-55646-28134/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=345600uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/glimmer.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1548892800 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.A3zyah + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf glimmer3.02 + /usr/bin/gzip -dc /builddir/build/SOURCES/glimmer302b.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd glimmer3.02 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + rm -f sample-run/g3-from-scratch.csh sample-run/g3-from-training.csh sample-run/g3-iterated.csh + sed -i s+/fs/szgenefinding/Glimmer3/bin+/usr/libexec/glimmer3+ scripts/g3-from-scratch.csh scripts/g3-from-training.csh scripts/g3-iterated.csh + sed -i s+/fs/szgenefinding/Glimmer3/scripts+/usr/share/glimmer3+ scripts/g3-from-scratch.csh scripts/g3-from-training.csh scripts/g3-iterated.csh + sed -i s+/nfshomes/adelcher/bin/elph+/usr/bin/elph+ scripts/g3-from-scratch.csh scripts/g3-from-training.csh scripts/g3-iterated.csh + sed -i 's/@ if/if/' src/c_make.gen + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.ctRV1e + umask 022 + cd /builddir/build/BUILD + cd glimmer3.02 + make -C src -j4 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' BUILDSTDERR: make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition make: Entering directory '/builddir/build/BUILD/glimmer3.02/src' * Make Target is all ##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Common all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Common' if [ -e gene.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc gene.cc \ | sed '\''s/gene\\.o[ :]*/& gene.d/g'\'' > gene.d' ; \ fi ; if [ -e fasta.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc fasta.cc \ | sed '\''s/fasta\\.o[ :]*/& fasta.d/g'\'' > fasta.d' ; \ fi ; if [ -e delcher.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc delcher.cc \ | sed '\''s/delcher\\.o[ :]*/& delcher.d/g'\'' > delcher.d' ; \ fi ; @@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e delcher.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/delcher.o delcher.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" delcher.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ fasta.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e fasta.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/fasta.o fasta.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" fasta.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ gene.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e gene.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/gene.o gene.cc ; \ else \ BUILDSTDERR: /cm/cmtools: warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: gene.cc: In member function 'bool PWM_t::Read(FILE*)': BUILDSTDERR: gene.cc:318:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 318 | fscanf (fp, "%d", & width); BUILDSTDERR: | ~~~~~~~^~~~~~~~~~~~~~~~~~~ BUILDSTDERR: gene.cc:331:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 331 | fscanf (fp, "%s", tag); // skip tag in first column BUILDSTDERR: | ~~~~~~~^~~~~~~~~~~~~~~ BUILDSTDERR: gene.cc:334:17: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 334 | fscanf (fp, "%lf", & x); BUILDSTDERR: | ~~~~~~~^~~~~~~~~~~~~~~~ BUILDSTDERR: gene.cc: In function 'int Read_String(FILE*, char*&, long int&, char*, int)': BUILDSTDERR: gene.cc:847:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 847 | fgets (Line, MAX_LINE, fp); BUILDSTDERR: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: ar: creating /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a BUILDSTDERR: make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: icm.cc: In member function 'void Fixed_Length_ICM_t::read(const char*)': BUILDSTDERR: icm.cc:1489:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 1489 | fread (line, sizeof (char), ID_STRING_LEN, fp); // skip the text header line BUILDSTDERR: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: icm.cc:1517:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 1517 | fread (permutation, sizeof (int), length, fp); BUILDSTDERR: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition /bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" gene.o ; \ fi ; ################### libGLMcommon.a ##################### a - delcher.o a - fasta.o a - gene.o make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Common' ##### Making Directory /builddir/build/BUILD/glimmer3.02/src/ICM all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/ICM' if [ -e score-fixed.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc score-fixed.cc \ | sed '\''s/score-fixed\\.o[ :]*/& score-fixed.d/g'\'' > score-fixed.d' ; \ fi ; if [ -e build-fixed.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc build-fixed.cc \ | sed '\''s/build-fixed\\.o[ :]*/& build-fixed.d/g'\'' > build-fixed.d' ; \ fi ; if [ -e build-icm.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc build-icm.cc \ | sed '\''s/build-icm\\.o[ :]*/& build-icm.d/g'\'' > build-icm.d' ; \ fi ; if [ -e icm.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc icm.cc \ | sed '\''s/icm\\.o[ :]*/& icm.d/g'\'' > icm.d' ; \ fi ; @@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e icm.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/icm.o icm.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" icm.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ build-icm.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e build-icm.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/build-icm.o build-icm.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" build-icm.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ build-fixed.cc @@@@@@@@@@@@@@@@@@@@@ BUILDSTDERR: if [ -e build-fixed.cc ] : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: ar: creating /builddir/build/BUILD/glimmer3.02/lib/libGLMicm.a ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/build-fixed.o build-fixed.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" build-fixed.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ score-fixed.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e score-fixed.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/score-fixed.o score-fixed.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" score-fixed.o ; \ fi ; ################### libGLMicm.a ##################### a - icm.o a - build-icm.o a - build-fixed.o a - score-fixed.o ++++++++++++++++++++ build-icm ++++++++++++++++++++++ if [ -z "build-icm.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/build-icm -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-icm.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ -lGLMicm ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/build-icm; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/build-icm -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-icm.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ -lGLMicm ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/build-icm; fi; \ fi ; ++++++++++++++++++++ build-fixed ++++++++++++++++++++++ if [ -z "build-fixed.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/build-fixed -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-fixed.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ -lGLMicm ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/build-fixed; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/build-fixed -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-fixed.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ -lGLMicm ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/build-fixed; fi; \ fi ; ++++++++++++++++++++ score-fixed ++++++++++++++++++++++ if [ -z "score-fixed.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/score-fixed -g -lm \ BUILDSTDERR: -L/builddir/build/BUILD/glimmer3make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: anomaly.cc: In function 'int main(int, char**)': BUILDSTDERR: anomaly.cc:82:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] BUILDSTDERR: 82 | if (Start < End && End - Start <= Len / 2 || Start - End > Len / 2) BUILDSTDERR: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ .02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib score-fixed.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ -lGLMicm ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/score-fixed; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/score-fixed -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib score-fixed.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ -lGLMicm ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/score-fixed; fi; \ fi ; make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/ICM' ##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Glimmer all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Glimmer' if [ -e test.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc test.cc \ | sed '\''s/test\\.o[ :]*/& test.d/g'\'' > test.d' ; \ fi ; if [ -e long-orfs.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc long-orfs.cc \ | sed '\''s/long-orfs\\.o[ :]*/& long-orfs.d/g'\'' > long-orfs.d' ; \ fi ; if [ -e glimmer3.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc glimmer3.cc \ | sed '\''s/glimmer3\\.o[ :]*/& glimmer3.d/g'\'' > glimmer3.d' ; \ fi ; if [ -e anomaly.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc anomaly.cc \ | sed '\''s/anomaly\\.o[ :]*/& anomaly.d/g'\'' > anomaly.d' ; \ fi ; @@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e anomaly.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/anomaly.o anomaly.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" anomaly.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ glimmer3.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e glimmer3.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ BUILDSTDERR: -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.: warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: glimmer3.cc: In function 'void Score_Orfs(std::vector&, std::vector&, FILE*)': BUILDSTDERR: glimmer3.cc:2861:20: warning: variable 'max_rate' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 2861 | double max, max_rate; BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: glimmer3.cc:2867:23: warning: variable 'max_j' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 2867 | int fr, frame, max_j, orf_start, frame_score; BUILDSTDERR: | ^~~~~ BUILDSTDERR: glimmer3.cc: In function 'void Read_Entropy_Profiles(const char*, bool&)': BUILDSTDERR: glimmer3.cc:2608:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 2608 | fgets (line, MAX_LINE, fp); // skip header line BUILDSTDERR: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: glimmer3.cc: In function 'void Score_Orfs(std::vector&, std::vector&, FILE*)': BUILDSTDERR: glimmer3.cc:3010:26: warning: 'first_score' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 3010 | gene_score = 100.0 * best_score / (best_j - 2); BUILDSTDERR: | ~~~~~~^~~~~~~~~~~~ BUILDSTDERR: glimmer3.cc: In function 'int main(int, char**)': BUILDSTDERR: glimmer3.cc:3441:32: warning: 'rev_start' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 3441 | gene . Set_Gene_Len (rev_start - p -> pos); BUILDSTDERR: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: glimmer3.cc:3412:21: note: 'rev_start' was declared here BUILDSTDERR: 3412 | int f, i, j, n, rev_start; BUILDSTDERR: | ^~~~~~~~~ BUILDSTDERR: glimmer3.cc:3442:29: warning: 'prev_score' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 3442 | gene . Set_Score (prev_score - p -> score); BUILDSTDERR: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: glimmer3.cc:3411:12: note: 'prev_score' was declared here BUILDSTDERR: 3411 | double prev_score; BUILDSTDERR: | ^~~~~~~~~~ BUILDSTDERR: glimmer3.cc:940:43: warning: 'orf_stop' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 940 | orf . Set_Orf_Len (i - orf_stop - 4); BUILDSTDERR: | ~~^~~~~~~~~~ BUILDSTDERR: glimmer3.cc:907:24: note: 'orf_stop' was declared here BUILDSTDERR: 907 | int which, orf_stop; BUILDSTDERR: | ^~~~~~~~ BUILDSTDERR: glimmer3.cc:896:12: warning: 'ignore_ct' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 896 | if (ignore_sub >= ignore_ct) BUILDSTDERR: | ^~ BUILDSTDERR: glimmer3.cc:830:9: note: 'ignore_ct' was declared here BUILDSTDERR: 830 | int ignore_ct; BUILDSTDERR: | ^~~~~~~~~ BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: long-orfs.cc: In function 'void Find_Orfs(std::vector&)': BUILDSTDERR: long-orfs.cc:585:9: warning: variable 'first_fwd_stop' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 585 | int first_fwd_stop [3] = {0}; BUILDSTDERR: | ^~~~~~~~~~~~~~ BUILDSTDERR: long-orfs.cc: In function 'void Read_Entropy_Profiles(const char*, bool&)': BUILDSTDERR: long-orfs.cc:1317:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 1317 | fgets (line, MAX_LINE, fp); // skip header line BUILDSTDERR: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: long-orfs.cc: In function 'int main(int, char**)': BUILDSTDERR: long-orfs.cc:655:12: warning: 'ignore_ct' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 655 | if (ignore_sub >= ignore_ct) BUILDSTDERR: | ^~ BUILDSTDERR: long-orfs.cc:590:9: note: 'ignore_ct' was declared here BUILDSTDERR: 590 | int ignore_ct; BUILDSTDERR: | ^~~~~~~~~ BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition 02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/glimmer3.o glimmer3.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" glimmer3.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ long-orfs.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e long-orfs.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/long-orfs.o long-orfs.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" long-orfs.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ test.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e test.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/test.o test.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" test.o ; \ fi ; ++++++++++++++++++++ anomaly ++++++++++++++++++++++ if [ -z "anomaly.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/anomaly -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib anomaly.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/anomaly; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/anomaly -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib anomaly.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/anomaly; fi; \ fi ; ++++++++++++++++++++ glimmer3 ++++++++++++++++++++++ if [ -z "glimmer3.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/glimmer3 -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib glimmer3.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a /builddir/build/BUILD/glimmer3.02/lib/libGLMicm.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/glimmer3; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/glimmer3 -g -lm \ BUILDSTDERR: -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib glimmer3.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a /builddir/build/BUILD/glimmer3.02/lib/libGLMicm.amake[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/glimmer3; fi; \ fi ; ++++++++++++++++++++ long-orfs ++++++++++++++++++++++ if [ -z "long-orfs.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/long-orfs -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib long-orfs.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/long-orfs; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/long-orfs -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib long-orfs.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/long-orfs; fi; \ fi ; ++++++++++++++++++++ test ++++++++++++++++++++++ if [ -z "test.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/test -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib test.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/test; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/test -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib test.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/test; fi; \ fi ; make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Glimmer' ##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Util all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Util' if [ -e window-acgt.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc window-acgt.cc \ | sed '\''s/window-acgt\\.o[ :]*/& window-acgt.d/g'\'' > window-acgt.d' ; \ fi ; if [ -e uncovered.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc uncovered.cc \ | sed '\''s/uncovered\\.o[ :]*/& uncovered.d/g'\'' > uncovered.d' ; \ fi ; if [ -e start-codon-distrib.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc start-codon-distrib.cc \ | sed '\''s/start-codon-distrib\\.o[ :]*/& start-codon-distrib.d/g'\'' > start-codon-distrib.d' ; \ fi ; if [ -e multi-extract.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc multi-extract.cc \ | sed '\''s/multi-extract\\.o[ :]*/& multi-extract.d/g'\'' > multi-extract.d' ; \ fi ; if [ -e extract.cc ] ; then \ BUILDSTDERR: /bin/sh -ec 'g++ -M -I/builddirmake[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: entropy-score.cc: In function 'int main(int, char**)': BUILDSTDERR: entropy-score.cc:157:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: 157 | if (line [n - 1] == '\n'); BUILDSTDERR: | ^~ BUILDSTDERR: entropy-score.cc:158:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: 158 | line [n - 1] = '\0'; BUILDSTDERR: | ^~~~ BUILDSTDERR: entropy-score.cc: In function 'void Read_Entropy_Profiles(const char*, bool&)': BUILDSTDERR: entropy-score.cc:327:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 327 | fgets (line, MAX_LINE, fp); // skip header line BUILDSTDERR: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc extract.cc \ | sed '\''s/extract\\.o[ :]*/& extract.d/g'\'' > extract.d' ; \ fi ; if [ -e entropy-score.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc entropy-score.cc \ | sed '\''s/entropy-score\\.o[ :]*/& entropy-score.d/g'\'' > entropy-score.d' ; \ fi ; if [ -e entropy-profile.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc entropy-profile.cc \ | sed '\''s/entropy-profile\\.o[ :]*/& entropy-profile.d/g'\'' > entropy-profile.d' ; \ fi ; @@@@@@@@@@@@@@@@@@@ entropy-profile.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e entropy-profile.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/entropy-profile.o entropy-profile.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" entropy-profile.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ entropy-score.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e entropy-score.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/entropy-score.o entropy-score.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" entropy-score.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ extract.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e extract.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/extract.o extract.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" extract.o ; \ BUILDSTDERR: fi : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition BUILDSTDERR: : warning: "__cplusplus" redefined BUILDSTDERR: : note: this is the location of the previous definition ; @@@@@@@@@@@@@@@@@@@ multi-extract.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e multi-extract.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/multi-extract.o multi-extract.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" multi-extract.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ start-codon-distrib.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e start-codon-distrib.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/start-codon-distrib.o start-codon-distrib.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" start-codon-distrib.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ uncovered.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e uncovered.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/uncovered.o uncovered.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" uncovered.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ window-acgt.cc @@@@@@@@@@@@@@@@@@@@@ if [ -e window-acgt.cc ] ; then \ g++ -D__cplusplus -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c \ -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/window-acgt.o window-acgt.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer3.02/obj" window-acgt.o ; \ fi ; ++++++++++++++++++++ entropy-profile ++++++++++++++++++++++ if [ -z "entropy-profile.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/entropy-profile -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-profile.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/entropy-profile; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/entropy-profile -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-profile.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/entropy-profile; fi; \ fi ; ++++++++++++++++++++ entropy-score ++++++++++++++++++++++ if [ -z "entropy-score.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/entropy-score -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-score.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/entropy-score; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/entropy-score -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-score.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/entropy-score; fi; \ fi ; ++++++++++++++++++++ extract ++++++++++++++++++++++ if [ -z "extract.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/extract -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib extract.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/extract; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/extract -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib extract.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/extract; fi; \ fi ; ++++++++++++++++++++ multi-extract ++++++++++++++++++++++ if [ -z "multi-extract.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/multi-extract -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib multi-extract.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/multi-extract; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/multi-extract -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib multi-extract.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/multi-extract; fi; \ fi ; ++++++++++++++++++++ start-codon-distrib ++++++++++++++++++++++ if [ -z "start-codon-distrib.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/start-codon-distrib -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib start-codon-distrib.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ BUILDSTDERR: true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/start-codon-distmake[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rib; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/start-codon-distrib -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib start-codon-distrib.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/start-codon-distrib; fi; \ fi ; ++++++++++++++++++++ uncovered ++++++++++++++++++++++ if [ -z "uncovered.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/uncovered -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib uncovered.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/uncovered; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/uncovered -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib uncovered.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/uncovered; fi; \ fi ; ++++++++++++++++++++ window-acgt ++++++++++++++++++++++ if [ -z "window-acgt.o" ] ; then \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if cc -o /builddir/build/BUILD/glimmer3.02/bin/window-acgt -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib window-acgt.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/window-acgt; fi; \ else \ cd /builddir/build/BUILD/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer3.02/bin/window-acgt -g -lm \ -L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib window-acgt.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/window-acgt; fi; \ fi ; make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Util' * Make Target is all ##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Common all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Common' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Common' ##### Making Directory /builddir/build/BUILD/glimmer3.02/src/ICM all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/ICM' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/ICM' ##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Glimmer all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Glimmer' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Glimmer' ##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Util all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Util' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Util' * Make Target is all ##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Common all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Common' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Common' ##### Making Directory /builddir/build/BUILD/glimmer3.02/src/ICM all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/ICM' make[1]: Nothing to be done for 'all'. BUILDSTDERR: make[1]: Leaving directory '/builddir/build/BUImake[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 LD/glimmer3.02/src/ICM' ##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Glimmer all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Glimmer' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Glimmer' ##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Util all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Util' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Util' make: Leaving directory '/builddir/build/BUILD/glimmer3.02/src' Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.yQ8S4f + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64 BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64 + cd glimmer3.02 + rm -rf /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64 + mkdir -p /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3 + mkdir -p /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/share/glimmer3 + mkdir -p /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/bin + install -m 755 scripts/g3-from-scratch.csh scripts/g3-from-training.csh scripts/g3-iterated.csh /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64//usr/bin + install -m 755 bin/anomaly bin/build-fixed bin/build-icm bin/entropy-profile bin/entropy-score bin/extract bin/glimmer3 bin/long-orfs bin/multi-extract bin/score-fixed bin/start-codon-distrib bin/uncovered bin/window-acgt /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3 + install -m 755 scripts/get-motif-counts.awk scripts/glim-diff.awk scripts/match-list-col.awk scripts/not-acgt.awk scripts/upstream-coords.awk /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/share/glimmer3 + ln -s ../libexec/glimmer3/glimmer3 /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64//usr/bin/glimmer3 + /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 3.02b-13.fc31 --unique-debug-suffix -3.02b-13.fc31.riscv64 --unique-debug-src-base glimmer-3.02b-13.fc31.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/glimmer3.02 BUILDSTDERR: 748 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/entropy-profile explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/anomaly explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/build-fixed explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/build-icm extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/entropy-profile extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/anomaly extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/build-fixed extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/build-icm explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/entropy-score explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/extract extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/entropy-score extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/extract explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/glimmer3 explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/long-orfs extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/glimmer3 extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/long-orfs explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/multi-extract extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/multi-extract explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/score-fixed extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/score-fixed explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/start-codon-distrib extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/start-codon-distrib explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/uncovered extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/uncovered explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/window-acgt extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/libexec/glimmer3/window-acgt original debug info size: 7436kB, size after compression: 5216kB /usr/lib/rpm/sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match. mangling shebang in /usr/bin/g3-from-scratch.csh from /bin/csh to #!/usr/bin/csh mangling shebang in /usr/bin/g3-from-training.csh from /bin/csh to #!/usr/bin/csh mangling shebang in /usr/bin/g3-iterated.csh from /bin/csh to #!/usr/bin/csh mangling shebang in /usr/share/glimmer3/match-list-col.awk from /bin/awk -f to #!/usr/bin/awk -f mangling shebang in /usr/share/glimmer3/get-motif-counts.awk from /bin/awk -f to #!/usr/bin/awk -f mangling shebang in /usr/share/glimmer3/not-acgt.awk from /bin/awk -f to #!/usr/bin/awk -f mangling shebang in /usr/share/glimmer3/glim-diff.awk from /bin/awk -f to #!/usr/bin/awk -f mangling shebang in /usr/share/glimmer3/upstream-coords.awk from /bin/awk -f to #!/usr/bin/awk -f Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.mSWDWh Processing files: glimmer-3.02b-13.fc31.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Z4R6Ti + umask 022 + cd /builddir/build/BUILD + cd glimmer3.02 + DOCDIR=/builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/share/doc/glimmer + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/share/doc/glimmer + cp -pr LICENSE /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/share/doc/glimmer + cp -pr glim302notes.pdf /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/share/doc/glimmer + cp -pr sample-run /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64/usr/share/doc/glimmer + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Provides: glimmer = 3.02b-13.fc31 glimmer(riscv-64) = 3.02b-13.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/awk /usr/bin/csh ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.4)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH) Processing files: glimmer-debugsource-3.02b-13.fc31.riscv64 Provides: glimmer-debugsource = 3.02b-13.fc31 glimmer-debugsource(riscv-64) = 3.02b-13.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: glimmer-debuginfo-3.02b-13.fc31.riscv64 Provides: debuginfo(build-id) = 0008ad541a2d2a09f04d3d068ccecc472f6516b1 debuginfo(build-id) = 035b7d83783e927bf472b02bf8dbef2373257d7d debuginfo(build-id) = 04691d0a80ec3e1c8cea6d0917f3ec8027385c59 debuginfo(build-id) = 13a2a4dba6d74a494994062dad757b005dd4b3b4 debuginfo(build-id) = 18b2f66c8242bb59fa50d3323e328f5c7ee91be1 debuginfo(build-id) = 4cbd82c180f2da7f246e654ecd9843fe982b41d4 debuginfo(build-id) = 5609b22d631a2c1b5867969207773413e628f7bf debuginfo(build-id) = 7056a104f5a2eacd299c367f141aa5bcd87d95a6 debuginfo(build-id) = 790591158862653bd33d5acc522de9023aefdc57 debuginfo(build-id) = b38c98717095cd1067150c2e5e4e524cb2e171b8 debuginfo(build-id) = d252acd3087fbca3e54748f7a1152526218610e3 debuginfo(build-id) = daec95221c787b57e174a5e658a765928186ae6d debuginfo(build-id) = db51c62317c979d696c79a9e1700425d4d168974 glimmer-debuginfo = 3.02b-13.fc31 glimmer-debuginfo(riscv-64) = 3.02b-13.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: glimmer-debugsource(riscv-64) = 3.02b-13.fc31 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64 Wrote: /builddir/build/RPMS/glimmer-debugsource-3.02b-13.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/glimmer-debuginfo-3.02b-13.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/glimmer-3.02b-13.fc31.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.NGyQ6f + umask 022 + cd /builddir/build/BUILD + cd glimmer3.02 + /usr/bin/rm -rf /builddir/build/BUILDROOT/glimmer-3.02b-13.fc31.riscv64 + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Child return code was: 0