For metagenomic sequence classification, I used Centrifuge, which requires sequence and taxonomy files and sequence ID to taxonomy ID mapping. Whenever I try to create Makefile and Standard, an error occurs.
time centrifuge-compress.pl tmp_p_compressed+h+v/archaea taxonomy --noDustmasker -map tmp_p_compressed+h+v/all-archaea.map \
-o reference-sequences/all-compressed-archaea.fna.tmp -t 1 -maxG 50000000 2>&1 | tee centrifuge-compress-p_compressed+h+v.log && \
mv reference-sequences/all-compressed-archaea.fna.tmp.fa reference-sequences/all-compressed-archaea.fna && mv reference-sequences/all-compressed-archaea.fna.tmp.size reference-sequences/all-compressed-archaea.size && \
mv reference-sequences/all-compressed-archaea.fna.tmp.map reference-sequences/all-compressed-archaea.map
Could not find Jellyfish.
real 0m0.041s
user 0m0.028s
sys 0m0.009s
mv: cannot stat 'reference-sequences/all-compressed-archaea.fna.tmp.fa': No such file or directory
make[1]: *** [Makefile:229: reference-sequences/all-compressed-archaea.fna] Error 1
make[1]: Leaving directory '/home/tushar/nirjhar/centrifuge/indices'
make: *** [Makefile:137: p_compressed+h+v] Error 2
I am using https://github.com/DaehwanKimLab/centrifuge repository.
Related
When I try to build system with buildroot I have problem with makin libicudata.
make[2]: Entering directory '/home/ser-builder2/buildroot/output/build/icu-64-2/source/data'
/bin/bash ../mkinstalldirs /home/ser-builder2/buildroot/output/host/x86_64-buildroot-linux-gnu/sysroot/usr/lib
LD_LIBRARY_PATH=/home/ser-builder2/buildroot/output/build/host-icu-64-2/source/stubdata:/home/ser-builder2/buildroot/output/build/host-icu-64-2/source/tools/ctestfw:/home/ser-builder2/buildroot/output/build/host-icu-64-2/source/lib:$LD_LIBRARY_PATH /home/ser-builder2/buildroot/output/build/host-icu-64-2/source/bin/pkgdata -O ../data/icupkg.inc -q -c -s /home/ser-builder2/buildroot/output/build/icu-64-2/source/data/out/build/icudt64l -d ../lib -m dll -r 64.2 -e icudt64 -T ./out/tmp -s ./out/build/icudt64l -p icudt64l -L icudata ./out/tmp/icudata.lst -I /home/ser-builder2/buildroot/output/host/x86_64-buildroot-linux-gnu/sysroot/usr/lib
pkgdata: cd ../lib/ && /usr/bin/install -c libicudata.so.64.2 /home/ser-builder2/buildroot/output/host/x86_64-buildroot-linux-gnu/sysroot/usr/lib/libicudata.so.64.2
pkgdata: cd /home/ser-builder2/buildroot/output/host/x86_64-buildroot-linux-gnu/sysroot/usr/lib && rm -f libicudata.so.64 && ln -s libicudata.so.64.2 libicudata.so.64
Segmentation fault (core dumped)
-- return status = 35584
Error creating symbolic links. Failed command: cd /home/ser-builder2/buildroot/output/host/x86_64-buildroot-linux-gnu/sysroot/usr/lib && rm -f libicudata.so.64 && ln -s libicudata.so.64.2 libicudata.so.64
Makefile:180: recipe for target 'install-local' failed
make[2]: *** [install-local] Error 1
make[2]: Leaving directory '/home/ser-builder2/buildroot/output/build/icu-64-2/source/data'
Makefile:153: recipe for target 'install-recursive' failed
make[1]: *** [install-recursive] Error 2
make[1]: Leaving directory '/home/ser-builder2/buildroot/output/build/icu-64-2/source'
package/pkg-generic.mk:278: recipe for target '/home/ser-builder2/buildroot/output/build/icu-64-2/.stamp_staging_installed' failed
make: *** [/home/ser-builder2/buildroot/output/build/icu-64-2/.stamp_staging_installed] Error 2
I don't know what to do with this. I tried to build this on another computer and everything works fine.
I run into this problem too and tracked it down to the execution of pkgdata. Somehow LD_LIBRARY_PATH got screwed which causes '/usr/bin/rm' to fail. To solve it, I've modified Makefile.in and removed LD_LIBRARY_PATH=... from the invocation line.
diff -r -u a/source/Makefile.in b/source/Makefile.in
--- a/source/Makefile.in 2022-06-02 10:48:31.493046292 +0200
+++ b/source/Makefile.in 2022-06-02 11:25:57.303758900 +0200
## -258,7 +258,7 ##
#(echo 'TOOLBINDIR=$$(cross_buildroot)/bin' ;\
echo 'TOOLLIBDIR=$$(cross_buildroot)/lib' ;\
echo "INVOKE=$(LDLIBRARYPATH_ENVVAR)=$(LIBRARY_PATH_PREFIX)"'$$(TOOLLIBDIR):$$(cross_buildroot)/stubdata:$$(cross_buildroot)/tools/ctestfw:$$$$'"$(LDLIBRARYPATH_ENVVAR)" ;\
- echo "PKGDATA_INVOKE=$(LDLIBRARYPATH_ENVVAR)=$(LIBRARY_PATH_PREFIX)"'$$(cross_buildroot)/stubdata:$$(cross_buildroot)/tools/ctestfw:$$(TOOLLIBDIR):$$$$'"$(LDLIBRARYPATH_ENVVAR) " ;\
+ echo "PKGDATA_INVOKE= " ;\
echo ) >> $#
config/icucross.inc: $(top_builddir)/icudefs.mk $(top_builddir)/Makefile #platform_make_fragment#
I know that this question is quite old now, but I want to mention it if someone else will run into this.
I'm using Netbeans 11 and MSYS2 MINGW64 G++.
Here's a screenshot of my toolchains:
When I try to run a simple Hello World c++ I get the following errors:
0 [main] cppapplication_2_cygwin_try (19728) D:\Program-Workspaces\netbean
s11\CppApplication_2_Cygwin_Try\dist\Debug\MinGW_2-Windows\cppapplication_2_cygw
in_try.exe: *** fatal error - cygheap base mismatch detected - 0x180343408/0x180
347408.
This problem is probably due to using incompatible versions of the cygwin DLL.
Search for cygwin1.dll using the Windows Start->Find/Search facility
and delete all but the most recent version. The most recent version *should*
reside in x:\cygwin\bin, where 'x' is the drive on which you have
installed the cygwin distribution. Rebooting is also suggested if you
are unable to find another cygwin DLL.
In other cases like when using the CLANG++ compiler, everything compiles well with the make.exe.
Could someone help on this please?
Thanks.
EDIT: Adding the NB11 messages:
cd 'D:\Program-Workspaces\netbeans11\CppApplication_2_Cygwin_Try'
D:\Programs\msys64\usr\bin\make.exe -f Makefile CONF=Debug
"/D/Programs/msys64/usr/bin/make.exe" -f nbproject/Makefile-Debug.mk QMAKE= SUBPROJECTS= .build-conf
make[1]: Entering directory '/d/Program-Workspaces/netbeans11/CppApplication_2_Cygwin_Try'
"/D/Programs/msys64/usr/bin/make.exe" -f nbproject/Makefile-Debug.mk dist/Debug/MinGW_2-Windows/cppapplication_2_cygwin_try.exe
make[2]: Entering directory '/d/Program-Workspaces/netbeans11/CppApplication_2_Cygwin_Try'
mkdir -p build/Debug/MinGW_2-Windows
rm -f "build/Debug/MinGW_2-Windows/main.o.d"
g++ -std=c++2a -c -g -MMD -MP -MF "build/Debug/MinGW_2-Windows/main.o.d" -o build/Debug/MinGW_2-Windows/main.o main.cpp
mkdir -p dist/Debug/MinGW_2-Windows
g++ -std=c++2a -o dist/Debug/MinGW_2-Windows/cppapplication_2_cygwin_try build/Debug/MinGW_2-Windows/main.o
make[2]: Leaving directory '/d/Program-Workspaces/netbeans11/CppApplication_2_Cygwin_Try'
make[1]: Leaving directory '/d/Program-Workspaces/netbeans11/CppApplication_2_Cygwin_Try'
BUILD SUCCESSFUL (total time: 17s)
cd 'D:\Program-Workspaces\netbeans11\CppApplication_2_Cygwin_Try'
D:\Programs\msys64\usr\bin\make.exe -f Makefile CONF=Debug
"/D/Programs/msys64/usr/bin/make.exe" -f nbproject/Makefile-Debug.mk QMAKE= SUBPROJECTS= .build-conf
make[1]: Entering directory '/d/Program-Workspaces/netbeans11/CppApplication_2_Cygwin_Try'
"/D/Programs/msys64/usr/bin/make.exe" -f nbproject/Makefile-Debug.mk dist/Debug/MinGW_2-Windows/cppapplication_2_cygwin_try.exe
make[2]: Entering directory '/d/Program-Workspaces/netbeans11/CppApplication_2_Cygwin_Try'
make[2]: 'dist/Debug/MinGW_2-Windows/cppapplication_2_cygwin_try.exe' is up to date.
make[2]: Leaving directory '/d/Program-Workspaces/netbeans11/CppApplication_2_Cygwin_Try'
make[1]: Leaving directory '/d/Program-Workspaces/netbeans11/CppApplication_2_Cygwin_Try'
BUILD SUCCESSFUL (total time: 3s)
0 [main] cppapplication_2_cygwin_try (17884) D:\Program-Workspaces\netbean
s11\CppApplication_2_Cygwin_Try\dist\Debug\MinGW_2-Windows\cppapplication_2_cygw
in_try.exe: *** fatal error - cygheap base mismatch detected - 0x180343408/0x180
347408.
This problem is probably due to using incompatible versions of the cygwin DLL.
Search for cygwin1.dll using the Windows Start->Find/Search facility
and delete all but the most recent version. The most recent version *should*
reside in x:\cygwin\bin, where 'x' is the drive on which you have
installed the cygwin distribution. Rebooting is also suggested if you
are unable to find another cygwin DLL.
RUN FAILED (exit value 127, total time: 1s)
I want to install Jasper on my rpi. It is currently running Raspbian. I am following instructions on the Jasper installation page, but when I try to install openfst and run sudo make install I get an error:
Making install in src
make[1]: Entering directory `/home/pi/openfst-1.3.3/src'
Making install in include
make[2]: Entering directory `/home/pi/openfst-1.3.3/src/include'
make[3]: Entering directory `/home/pi/openfst-1.3.3/src/include'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/include" || /bin/mkdir -p "/usr/local/include"
/bin/mkdir -p '/usr/local/include/fst'
/usr/bin/install -c -m 644 fst/arc.h fst/determinize.h fst/intersect.h fst/queue.h fst/statesort.h fst/arcfilter.h fst/dfs-visit.h fst/invert.h fst/randequivalent.h fst/string-weight.h fst/difference.h fst/lexicographic-weight.h fst/randgen.h fst/symbol-table.h fst/arcsort.h fst/encode.h fst/lock.h fst/random-weight.h fst/synchronize.h fst/epsnormalize.h fst/log.h fst/rational.h fst/test-properties.h fst/cache.h fst/equal.h fst/arc-map.h fst/map.h fst/register.h fst/topsort.h fst/closure.h fst/equivalent.h fst/matcher.h fst/matcher-fst.h fst/relabel.h fst/union-find.h fst/compact-fst.h fst/expanded-fst.h fst/minimize.h fst/replace.h fst/union.h '/usr/local/include/fst'
/bin/mkdir -p '/usr/local/include/fst'
/usr/bin/install -c -m 644 fst/compat.h fst/factor-weight.h fst/state-map.h fst/mutable-fst.h fst/reverse.h fst/util.h fst/complement.h fst/flags.h fst/partition.h fst/reweight.h fst/vector-fst.h fst/compose-filter.h fst/float-weight.h fst/product-weight.h fst/rmepsilon.h fst/verify.h fst/compose.h fst/fst-decl.h fst/project.h fst/rmfinalepsilon.h fst/visit.h fst/concat.h fst/fst.h fst/properties.h fst/shortest-distance.h fst/weight.h fst/connect.h fst/fstlib.h fst/prune.h fst/shortest-path.h fst/const-fst.h fst/heap.h fst/push.h fst/state-table.h fst/slist.h fst/pair-weight.h fst/config.h fst/tuple-weight.h fst/power-weight.h fst/lookahead-matcher.h '/usr/local/include/fst'
/bin/mkdir -p '/usr/local/include/fst/script'
/usr/bin/install -c -m 644 fst/script/arcsort.h fst/script/arg-packs.h fst/script/closure.h fst/script/compile-impl.h fst/script/compile.h fst/script/compose.h fst/script/concat.h fst/script/connect.h fst/script/convert.h fst/script/decode.h fst/script/determinize.h fst/script/difference.h fst/script/disambiguate.h fst/script/draw-impl.h fst/script/draw.h fst/script/encode.h fst/script/epsnormalize.h fst/script/equal.h fst/script/equivalent.h fst/script/fst-class.h fst/script/fstscript.h fst/script/info-impl.h fst/script/info.h fst/script/intersect.h fst/script/invert.h fst/script/map.h fst/script/minimize.h fst/script/print-impl.h fst/script/print.h fst/script/project.h fst/script/prune.h fst/script/push.h fst/script/randequivalent.h fst/script/randgen.h fst/script/register.h fst/script/relabel.h fst/script/replace.h fst/script/reverse.h fst/script/reweight.h fst/script/rmepsilon.h '/usr/local/include/fst/script'
/bin/mkdir -p '/usr/local/include/fst'
/usr/bin/install -c -m 644 fst/types.h fst/add-on.h fst/label-reachable.h fst/accumulator.h fst/interval-set.h fst/state-reachable.h fst/lookahead-filter.h fst/generic-register.h fst/edit-fst.h fst/replace-util.h fst/icu.h fst/string.h fst/signed-log-weight.h fst/sparse-tuple-weight.h fst/sparse-power-weight.h fst/expectation-weight.h fst/symbol-table-ops.h fst/bi-table.h fst/mapped-file.h '/usr/local/include/fst'
/bin/mkdir -p '/usr/local/include/fst/extensions/pdt'
/usr/bin/install -c -m 644 fst/extensions/pdt/collection.h fst/extensions/pdt/compose.h fst/extensions/pdt/expand.h fst/extensions/pdt/info.h fst/extensions/pdt/paren.h fst/extensions/pdt/pdt.h fst/extensions/pdt/pdtlib.h fst/extensions/pdt/pdtscript.h fst/extensions/pdt/replace.h fst/extensions/pdt/reverse.h fst/extensions/pdt/shortest-path.h '/usr/local/include/fst/extensions/pdt'
/bin/mkdir -p '/usr/local/include/fst/extensions/far'
/usr/bin/install -c -m 644 fst/extensions/far/compile-strings.h fst/extensions/far/create.h fst/extensions/far/equal.h fst/extensions/far/extract.h fst/extensions/far/far.h fst/extensions/far/farlib.h fst/extensions/far/farscript.h fst/extensions/far/info.h fst/extensions/far/main.h fst/extensions/far/print-strings.h fst/extensions/far/stlist.h fst/extensions/far/sttable.h '/usr/local/include/fst/extensions/far'
/bin/mkdir -p '/usr/local/include/fst/script'
/usr/bin/install -c -m 644 fst/script/script-impl.h fst/script/shortest-distance.h fst/script/shortest-path.h fst/script/symbols.h fst/script/synchronize.h fst/script/text-io.h fst/script/topsort.h fst/script/union.h fst/script/weight-class.h fst/script/fstscript-decl.h fst/script/verify.h '/usr/local/include/fst/script'
make[3]: Leaving directory `/home/pi/openfst-1.3.3/src/include'
make[2]: Leaving directory `/home/pi/openfst-1.3.3/src/include'
Making install in lib
make[2]: Entering directory `/home/pi/openfst-1.3.3/src/lib'
make[3]: Entering directory `/home/pi/openfst-1.3.3/src/lib'
test -z "/usr/local/lib" || /bin/mkdir -p "/usr/local/lib"
/bin/bash ../../libtool --mode=install /usr/bin/install -c libfst.la '/usr/local/lib'
libtool: install: /usr/bin/install -c .libs/libfst.so.1.0.0 /usr/local/lib/libfst.so.1.0.0
libtool: install: (cd /usr/local/lib && { ln -s -f libfst.so.1.0.0 libfst.so.1 || { rm -f libfst.so.1 && ln -s libfst.so.1.0.0 libfst.so.1; }; })
libtool: install: (cd /usr/local/lib && { ln -s -f libfst.so.1.0.0 libfst.so || { rm -f libfst.so && ln -s libfst.so.1.0.0 libfst.so; }; })
libtool: install: /usr/bin/install -c .libs/libfst.lai /usr/local/lib/libfst.la
libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin" ldconfig -n /usr/local/lib
----------------------------------------------------------------------
Libraries have been installed in:
/usr/local/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/pi/openfst-1.3.3/src/lib'
make[2]: Leaving directory `/home/pi/openfst-1.3.3/src/lib'
Making install in script
make[2]: Entering directory `/home/pi/openfst-1.3.3/src/script'
/bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I./../include -g -O2 -MT push.lo -MD -MP -MF .deps/push.Tpo -c -o push.lo push.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I./../include -g -O2 -MT push.lo -MD -MP -MF .deps/push.Tpo -c push.cc -fPIC -DPIC -o .libs/push.o
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.6/README.Bugs> for instructions.
make[2]: *** [push.lo] Error 1
make[2]: Leaving directory `/home/pi/openfst-1.3.3/src/script'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/pi/openfst-1.3.3/src'
make: *** [install-recursive] Error 1
Can anyone help?
Thanks for all suggestions!
I found the solution to the problem! I changed my swap size to 500 and it worked! I thought I had already changed it, but apparently you need to restart the rpi (of course) and I forgot to.
I'm trying to get Netbeans up and running so I can start a Fortran project. I've downloaded the binaries and installed the plugins to the best of my knowledge. When I try to compile my hello world I get this error:
"/usr/bin/make" -f nbproject/Makefile-Debug.mk QMAKE= SUBPROJECTS= .build-conf
"/usr/bin/make" -f nbproject/Makefile-Debug.mk dist/Debug/GNU-MacOSX/convection
mkdir -p build/Debug/GNU-MacOSX
gfortran -c -g -o build/Debug/GNU-MacOSX/main.o main.f
gfortran: error trying to exec 'f951': execvp: No such file or directory
make[2]: *** [build/Debug/GNU-MacOSX/main.o] Error 1
make[1]: *** [.build-conf] Error 2
make: *** [.build-impl] Error 2
BUILD FAILED (exit value 2, total time: 111ms)
Any thoughts?
EDIT: I'm using Mac OSX 10.8.5
EDIT 2: I've been messing around for awhile now and now the error is slightly different:
"/usr/bin/make" -f nbproject/Makefile-Debug.mk QMAKE= SUBPROJECTS= .build-conf
"/usr/bin/make" -f nbproject/Makefile-Debug.mk dist/Debug/GNU-MacOSX/convection
mkdir -p build/Debug/GNU-MacOSX
gfortran -c -g -o build/Debug/GNU-MacOSX/main.o main.f
make[2]: gfortran: No such file or directory
make[2]: *** [build/Debug/GNU-MacOSX/main.o] Error 1
make[1]: *** [.build-conf] Error 2
make: *** [.build-impl] Error 2
BUILD FAILED (exit value 2, total time: 127ms)
EDIT 3: And just for fun, here is the output from a successful build that I was able to do in Ubuntu:
"/usr/bin/make" -f nbproject/Makefile-Debug.mk QMAKE= SUBPROJECTS= .build-conf
make[1]: Entering directory `/home/hannah/NetBeansProjects/test'
"/usr/bin/make" -f nbproject/Makefile-Debug.mk dist/Debug/GNU-Linux-x86/test
make[2]: Entering directory `/home/hannah/NetBeansProjects/test'
make[2]: `dist/Debug/GNU-Linux-x86/test' is up to date.
make[2]: Leaving directory `/home/hannah/NetBeansProjects/test'
make[1]: Leaving directory `/home/hannah/NetBeansProjects/test'
BUILD SUCCESSFUL (total time: 92ms)
I had the same problem on 10.9. I needed to make a new gfortran link in my /usr/bin (Base directory). After that it worked fine. If I had it in usr/local/bin,..or any other path it didn't work.
Here is a link to someone else's solution to this problem. gfortran is unable to find f951.
http://ubuntuforums.org/showthread.php?t=1164394
I think I found the solution here: http://eftrunk.blogspot.com/2011/11/how-to-fix-error-trying-to-exec-f951.html
Will report back if it works or not.
I am trying to build Emacs on 64-bit Windows 7 using Cyqwin:
Emacs 23.3 or 23.4
CYGWIN_NT-6.1-WOW64 1.7.11(0.260/5/3) 2012-02-24 14:05 i686 Cygwin
Some info from ./configure log:
What compiler should emacs be built with?
gcc -g -O2 -Wdeclarati
What operating system and machine description files should Emacs use?
`s/cygwin.h' and `m/intel386.h'
I am able to create Makefile without problems. However, if I run make procedure, it is building for couple of minutes then, in certain point, it gets stuck for 2 minutes and then produces error:
Makefile:149: recipe for target `autoloads' failed
make[2]: *** [autoloads] Interrupt
Makefile:198: recipe for target `/cygdrive/c/emacs-23.3/src/../lisp/loaddefs.el' failed
make[1]: *** [/cygdrive/c/emacs-23.3/src/../lisp/loaddefs.el] Interrupt
Makefile:339: recipe for target `src' failed
make: *** [src] Interrupt
In both cases (Emacs 23.3 and 23.4) Makefile:149 referes to the same part of a makefile in Emacs\lisp folder:
149 autoloads: $(LOADDEFS) doit
150 , chmod +w $(lisp)/ps-print.el $(lisp)/emulation/tpu-edt.el \
151 $(lisp)/emacs-lisp/cl-loaddefs.el $(lisp)/mail/rmail.el \
152 $(lisp)/dired.el $(lisp)/ibuffer.el
153 wd=$(lisp); $(setwins_almost); \
154 echo Directories: $$wins; \
155 $(emacs) -l autoload --eval '(setq generated-autoload-file "$(lisp)/loaddefs.el")' -f batch-update-autoloads $$wins
in version 23.3. the building gets stuck while generating autoloads for *.el files:
Generating autoloads for progmodes/cc-mode.el...
Generating autoloads for progmodes/cc-mode.el...done
Generating autoloads for progmodes/cc-styles.el...
Generating autoloads for progmodes/cc-styles.el...done
Generating autoloads for progmodes/cc-vars.el...
Generating autoloads for progmodes/cc-vars.el...done
Generating autoloads for international/ccl.el...
Makefile:149: recipe for target `autoloads' failed
make[2]: *** [autoloads] Interrupt
in verison 23.4 the building gets stuck while saving loaddefs:
make[2]: Entering directory `/cygdrive/c/emacs-23.4/lisp'
chmod +w /cygdrive/c/emacs-23.4/lisp/ps-print.el /cygdrive/c/emacs-23.4/lisp/emulation/tpu-edt.el \
/cygdrive/c/emacs-23.4/lisp/emacs-lisp/cl-loaddefs.el /cygdrive/c/emacs-23.4/lisp/mail/rmail.el \
/cygdrive/c/emacs-23.4/lisp/dired.el /cygdrive/c/emacs-23.4/lisp/ibuffer.el
wd=/cygdrive/c/emacs-23.4/lisp; subdirs=`(cd $wd; find . -type d -print)`; for file in $subdirs; do case $file in */Old | */RCS | */CVS | */CVS/* | */.* | */.*/* | */=* | */obsolete | */term ) ;; *) wins="$wins $wd/$file" ;; esac; done ; \
echo Directories: $wins; \
EMACSLOADPATH=/cygdrive/c/emacs-23.4/lisp LC_ALL=C ../src/bootstrap-emacs.exe -batch --no-site-file --multibyte -l autoload --eval '(setq generated-autoload-file "/cygdrive/c/emacs-23.4/lisp/loaddefs.el")' -f batch-update-autoloads $wins
Directories: /cygdrive/c/emacs-23.4/lisp/. /cygdrive/c/emacs-23.4/lisp/./calc /cygdrive/c/emacs-23.4/lisp/./calendar /cygdrive/c/emacs-23.4/lisp/./cedet /cygdrive/c/emacs-23.4/lisp/./cedet/ede /cygdrive/c/emacs-23.4/lisp/./cedet/semantic /cygdrive/c/emacs-23.4/lisp/./cedet/semantic/analyze /cygdrive/c/emacs-23.4/lisp/./cedet/semantic/bovine /cygdrive/c/emacs-23.4/lisp/./cedet/semantic/decorate/cygdrive/c/emacs-23.4/lisp/./cedet/semantic/symref /cygdrive/c/emacs-23.4/lisp/./cedet/semantic/wisent /cygdrive/c/emacs-23.4/lisp/./cedet/srecode /cygdrive/c/emacs-23.4/lisp/./emacs-lisp /cygdrive/c/emacs-23.4/lisp/./emulation /cygdrive/c/emacs-23.4/lisp/./erc /cygdrive/c/emacs-23.4/lisp/./eshell /cygdrive/c/emacs-23.4/lisp/./gnus /cygdrive/c/emacs-23.4/lisp/./international /cygdrive/c/emacs-23.4/lisp/./language /cygdrive/c/emacs-23.4/lisp/./mail /cygdrive/c/emacs-23.4/lisp/./mh-e /cygdrive/c/emacs-23.4/lisp/./net /cygdrive/c/emacs-23.4/lisp/./nxml /cygdrive/c/emacs-23.4/lisp/./org /cygdrive/c/emacs-23.4/lisp/./play /cygdrive/c/emacs-23.4/lisp/./progmodes /cygdrive/c/emacs-23.4/lisp/./textmodes /cygdrive/c/emacs-23.4/lisp/./url
Saving file /cygdrive/c/emacs-23.4/lisp/loaddefs.el...
Makefile:149: recipe for target `autoloads' failed
make[2]: *** [autoloads] Interrupt
Does anyone have a clue how can I fix this bug? Wrong C compiler ? Change Makefile? Use 'make' with some parameter?
Thank you for any help or reference.
************PART2************
Ok, so here is the continuing according to your advices:
1#
make autoloads
is not possible as it is because this sub-part is in the sub-makefile so it will produce error:
$ make autoloads
chmod +w /cygdrive/c/emacs-23.4/lisp/ps-print.el /cygdrive/c/emacs-23.4/lisp/emulation/tpu-edt.el \
/cygdrive/c/emacs-23.4/lisp/emacs-lisp/cl-loaddefs.el /cygdrive/c/emacs-23.4/lisps/mail/rmail.el \
/cygdrive/c/emacs-23.4/lisp/dired.el /cygdrive/c/emacs-23.4/lisp/ibuffer.el
wd=/cygdrive/c/emacs-23.4/lisp; subdirs=`(cd $wd; find . -type d -print)`; for file in $subdirs; do case $file in */Old | */RCS | */CVS | */CVS/* | */.* | */.*/* | */=* | */obsolete | */term ) ;; *) wins="$wins $wd/$file" ;; esac; done; \
echo Directories: $wins; \
EMACSLOADPATH=/cygdrive/c/emacs-23.4/lisp LC_ALL=C ../src/emacs -batch --no-site-file --multibyte -l autoload --eval '(setq generated-autoload-file "/cygdrive/c/emacs-23.4/lisp/loaddefs.el")' -f batch-update-autoloads $wins
Directories: /cygdrive/c/emacs-23.4/lisp/. /cygdrive/c/emacs-23.4/lisp/./calc /cygdrive/c/emacs-23.4/lisp/./calendar /cygdrive/c/emacs-23.4/lisp/./cedet /cygdrive/c/emacs-23.4/lisp/./cedet/ede /cygdrive/c/emacs-23.4/lisp/./cedet/semantic /cygdrive/c/emacs-23.4/lisp/./cedet/semantic/analyze /cygdrive/c/emacs-23.4/lisp/./cedet/semantic/bovine /cygdrive/c/emacs-23.4/lisp/./cedet/semantic/decorate /cygdrive/c/emacs-23.4/lisp/./cedet/semantic/symref /cygdrive/c/emacs-23.4/lisp/./cedet/semantic/wisent /cygdrive/c/emacs-23.4/lisp/./cedet/srecode /cygdrive/c/emacs-23.4/lisp/./emacs-lisp /cygdrive/c/emacs-23.4/lisp/./emulation /cygdrive/c/emacs-23.4/lisp/./erc /cygdrive/c/emacs-23.4/lisp/./eshell /cygdrive/c/emacs-23.4/lisp/./gnus /cygdrive/c/emacs-23.4/lisp/./international /cygdrive/c/emacs-23.4/lisp/./language /cygdrive/c/emacs-23.4/lisp/./mail /cygdrive/c/emacs-23.4/lisp/./mh-e /cygdrive/c/emacs-23.4/lisp/./net /cygdrive/c/emacs-23.4/lisp/./nxml /cygdrive/c/emacs-23.4/lisp/./org /cygdrive/c/emacs-23.4/lisp/./play /cygdrive/c/emacs-23.4/lisp/./progmodes /cygdrive/c/emacs-23.4/lisp/./textmodes /cygdrive/c/emacs-23.4/lisp/./url
/bin/sh: line 2: ../src/emacs: No such file or directory
Makefile:149: recipe for target `autoloads' failed
make: *** [autoloads] Error 127
If I am doing something wrong, please correct me.
2#
removing $(LOADDEFS) doit in deed does not change the result
3#
To run just the first part
autoloads:
chmod +w $(lisp)/ps-print.el $(lisp)/emulation/tpu-edt.el \
$(lisp)/emacs-lisp/cl-loaddefs.el $(lisp)/mail/rmail.el \
$(lisp)/dired.el $(lisp)/ibuffer.el
resolves in no error within autoloads,
however after 20 sec it froze for a while and produces another error
(description of this problem is bellow)
4#
To run the second part only:
autoloads:
wd=$(lisp); $(setwins_almost); \
echo Directories: $$wins; \
$(emacs) -l autoload --eval '(setq generated-autoload-file "$(lisp)/loaddefs.el")' -f batch-update-autoloads $$wins
creshed with origin error
5#
to run autoloads as in 3# also with
wd=$(lisp);
autoloads without error, later same error as in 3#
6#
run autoloads with wd=$(lisp);$(setwins_almost);
autoloads without error, later same error as in 3#
7#
add also line
echo Directories: $$wins;
autoloads without error, later same error as in 3#
8#
add also line
$(emacs) -l autoload --eval '(setq generated-autoload-file "$(lisp)/loaddefs.el")' -f batch-update-autoloads $$wins
the origin error, of course
DESCRIPTION of 2nd ERROR (part 3#):
make[2]: Entering directory `/cygdrive/c/emacs-23.4/lisp'
Compiling /cygdrive/c/emacs-23.4/src/../lisp/abbrev.el
>>Error occurred processing /cygdrive/c/emacs-23.4/src/../lisp/abbrev.el: Symbol's value as variabl e is void ((warning-series))
Makefile:1478: recipe for target `compile-onefile' failed
make[2]: *** [compile-onefile] Error 1
make[2]: Leaving directory `/cygdrive/c/emacs-23.4/lisp'
Makefile:195: recipe for target `/cygdrive/c/emacs-23.4/src/../lisp/abbrev.elc' failed
make[1]: *** [/cygdrive/c/emacs-23.4/src/../lisp/abbrev.elc] Error 2
make[1]: Leaving directory `/cygdrive/c/emacs-23.4/src'
Makefile:339: recipe for target `src' failed
make: *** [src] Error 2
before that a lot of *.el files are compiled
part of the Makefile in lisp/
# The src/Makefile.in has its own set of dependencies and when they decide
# that one Lisp file needs to be re-compiled, we had better recompile it as
# well, otherwise every subsequent make will again call us, until we finally
# end up deciding that yes, the file deserves recompilation.
# One option is to try and reproduce exactly the same dependencies here as
# we have in src/Makefile.in, but it turns out to be painful
# (e.g. src/Makefile.in may have a dependency for ../lisp/foo.elc where we
# only know of $(lisp)/foo.elc). So instead we provide a direct way for
# src/Makefile.in to rebuild a particular Lisp file, no questions asked.
# Use byte-compile-refresh-preloaded to try and work around some of
# the most common problems of not bootstrapping from a clean state.
1477 compile-onefile:
1478 #echo Compiling $(THEFILE)
1479 ## Use byte-compile-refresh-preloaded to try and work around some of
1480 ## the most common bootstrapping problems.
1481 #$(emacs) -l bytecomp -f byte-compile-refresh-preloaded $(BYTE_COMPILE_EXTRA_FLAGS) -f batch-byte-compile $(THEFILE)
There is a list of ELC files in Makefile:
## Explicitly list the .elc files, for the sake of parallel builds.
## http://lists.gnu.org/archive/html/bug-gnu-emacs/2008-05/msg00016.html
## This can probably be done more elegantly, but needs to be portable.
ELCFILES = \
$(lisp)/abbrev.elc \
$(lisp)/abbrevlist.elc \
$(lisp)/add-log.elc \
$(lisp)/align.elc \
$(lisp)/allout.elc \
$(lisp)/ansi-color.elc \
$(lisp)/apropos.elc \
$(lisp)/arc-mode.elc \
...
$(lisp)/info.elc \
$(lisp)/informat.elc \
$(lisp)/international/ccl.elc \
$(lisp)/international/characters.elc \
$(lisp)/international/fontset.elc \
$(lisp)/international/isearch-x.elc \
The Makefile somewhy recreates *.el files maybe from *.elc files, however all *.el files are already there. OK now I have two errors insted of one : )(if there are not connected of course)
Thank you again.
Generated makefiles are notoriously hard to maintain and troubleshoot, but we can try. The rule in question has two prerequisites and two commands, the second composed of four shell commands strung together:
autoloads: $(LOADDEFS) doit
chmod +w $(lisp)/ps-print.el $(lisp)/emulation/tpu-edt.el \
$(lisp)/emacs-lisp/cl-loaddefs.el $(lisp)/mail/rmail.el \
$(lisp)/dired.el $(lisp)/ibuffer.el
wd=$(lisp); $(setwins_almost); \
echo Directories: $$wins; \
$(emacs) -l autoload --eval '(setq generated-autoload-file "$(lisp)/loaddefs.el")' -f batch-update-autoloads $$wins
First I would try make autoloads. If that gives the same error, we can proceed, otherwise post the results.
Then remove the prerequisites ($(LOADDEFS) doit), since they should be idempotent and have no effect of the operation of this rule (unless the makefile is really convoluted) and try again.
Then split the command into smaller commands and try one by one. First
autoloads:
chmod +w $(lisp)/ps-print.el $(lisp)/emulation/tpu-edt.el \
$(lisp)/emacs-lisp/cl-loaddefs.el $(lisp)/mail/rmail.el \
$(lisp)/dired.el $(lisp)/ibuffer.el
This should give no error. If it does then probably one of those files is missing; post the results. If not then try the second command without the first:
autoloads:
wd=$(lisp); $(setwins_almost); \
echo Directories: $$wins; \
$(emacs) -l autoload --eval '(setq generated-autoload-file "$(lisp)/loaddefs.el")' -f batch-update-autoloads $$wins
I expect this will give the same error as originally; if not, just put the first command back in and proceed.
Now break down the second command. We can't omit the early parts, since the later parts depend on them, so first try
autoloads:
wd=$(lisp);
That should work, unless lisp is something weird (yeah, yeah, I know). Then
autoloads:
wd=$(lisp); $(setwins_almost);
I'll bet that's where it fails, but if not, continue:
autoloads:
wd=$(lisp); $(setwins_almost); \
echo Directories: $$wins;
That should work. Then
autoloads:
wd=$(lisp); $(setwins_almost); \
echo Directories: $$wins; \
$(emacs) -l autoload --eval '(setq generated-autoload-file "$(lisp)/loaddefs.el")' -f batch-update-autoloads $$wins
will almost certainly fail.
That's enough for a first pass. Tell us the results and we'll proceed.
I'd recommend you try with the Emacs-24 pretest instead, and if that fails, report it as a bug.