Comments (6)
And don't get trapped yourself with the the "rm -rf" zapping your patched version of make source tree:
tigmint-master $ make
make -C xml-patch-make
make[1]: Entering directory '/foo/tigmint-master/xml-patch-make'
rm -rf make-4.1
mkdir -p make-4.1
tar xvfz make-4.1.tar.gz -C make-4.1
...
from tigmint.
After you fix the previous compile error, there is one more:
gcc -g -O2 -Wl,--export-dynamic -o make ar.o arscan.o commands.o default.o dir.o expand.o file.o function.o getopt.o getopt1.o guile.o implicit.o job.o load.o loadapi.o main.o misc.o output.o read.o remake.o rule.o signame.o strcache.o variable.o version.o vpath.o hash.o xml.o remote-stub.o glob/libglob.a -ldl
/blah/x86_64-pc-linux-gnu/bin/ld: glob/libglob.a(glob.o): in function `glob_in_dir':
/foo/tigmint-master/xml-patch-make/make-4.1/make-4.1/glob/glob.c:1269: undefined reference to `__stat'
/blah/x86_64-pc-linux-gnu/bin/ld: glob/libglob.a(glob.o): in function `glob':
/foo/tigmint-master/xml-patch-make/make-4.1/make-4.1/glob/glob.c:1036: undefined reference to `__stat'
/blah/x86_64-pc-linux-gnu/bin/ld: /foo/tigmint-master/xml-patch-make/make-4.1/make-4.1/glob/glob.c:814: undefined reference to `__stat'
/blah/x86_64-pc-linux-gnu/bin/ld: /foo/tigmint-master/xml-patch-make/make-4.1/make-4.1/glob/glob.c:960: undefined reference to `__stat'
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:650: make] Error 1
make[3]: Leaving directory '/foo/tigmint-master/xml-patch-make/make-4.1/make-4.1'
from tigmint.
Hi @mmokrejs,
Just to make sure I understand - you are running the Makefile
in the main repo? (ie. executing
make`)?
To be honest, this is a file that Shaun (original developer of Tigmint, who has since moved on) generated around the time that we were working on the manuscript, and I've never even looked at it myself! I believe he used it for testing, but we have since integrated tests into our CI.
I'm personally inclined to just move it out of the main directory to a subdirectory so it isn't confusing for users because I don't really think it's necessary (Ie. I've deleted it on my end and everything still works fine). Would that be OK with you, or did you want to use it for a particular purpose?
from tigmint.
Yes, I execute main in the top-level directory, which recurses into ./xml-patch-make/make-4.1/make-4.1/
eventually. The issue we have too new glibc on the cluster. I assume it may be easier to update the xml-make
patch to apply over more recent make
sources. Or even better, try to get the changes accepted by upstream. But, if the xml-make is not necessary, I do not mind it to be deleted. But certainly it got executed for mme one:
tigmint-master$ patch -p1 < make-4.2.1.patch
...
patch -p1 < d77ffeda4fc5d25b47f778563e6b7842dfef317d.patch # well this one does not apply anymore
...
tigmint-master$ make
...
gcc -g -O2 -Wl,--export-dynamic -o make ar.o arscan.o commands.o default.o dir.o expand.o file.o function.o getopt.o getopt1.o guile.o implicit.o job.o load.o loadapi.o main.o misc.o output.o read.o remake.o rule.o signame.o strcache.o variable.o version.o vpath.o hash.o remote-stub.o glob/libglob.a -ldl
make[4]: Entering directory '/foo/tigmint-master/xml-patch-make/make-4.1/make-4.1'
/usr/bin/mkdir -p '/foo/tigmint-master/xml-patch-make/make-4.1/make-4.1/../bin'
/usr/bin/install -c make '/foo/tigmint-master/xml-patch-make/make-4.1/make-4.1/../bin/./xml-make4.1'
/usr/bin/mkdir -p '/foo/tigmint-master/xml-patch-make/make-4.1/make-4.1/../include'
/usr/bin/install -c -m 644 gnumake.h '/foo/tigmint-master/xml-patch-make/make-4.1/make-4.1/../include'
/usr/bin/mkdir -p '/foo/tigmint-master/xml-patch-make/make-4.1/make-4.1/../share/man/man1'
/usr/bin/install -c -m 644 'make.1' '/foo/tigmint-master/xml-patch-make/make-4.1/make-4.1/../share/man/man1/xml-make4.1.1'
make[4]: Leaving directory '/foo/tigmint-master/xml-patch-make/make-4.1/make-4.1'
make[3]: Leaving directory '/foo/tigmint-master/xml-patch-make/make-4.1/make-4.1'
make[2]: Leaving directory '/foo/tigmint-master/xml-patch-make/make-4.1/make-4.1'
make[1]: Leaving directory '/foo/tigmint-master/xml-patch-make'
xml-patch-make/make-4.1/make-4.1/make --xml tigmint-make.xml -f bin/tigmint-make all
xml-patch-make/make-4.1/make-4.1/make: unrecognized option '--xml'
Usage: make [options] [target] ...
Options:
-b, -m Ignored for compatibility.
-B, --always-make Unconditionally make all targets.
-C DIRECTORY, --directory=DIRECTORY
Change to DIRECTORY before doing anything.
-d Print lots of debugging information.
--debug[=FLAGS] Print various types of debugging information.
-e, --environment-overrides
Environment variables override makefiles.
--eval=STRING Evaluate STRING as a makefile statement.
-f FILE, --file=FILE, --makefile=FILE
Read FILE as a makefile.
-h, --help Print this message and exit.
-i, --ignore-errors Ignore errors from recipes.
-I DIRECTORY, --include-dir=DIRECTORY
Search DIRECTORY for included makefiles.
-j [N], --jobs[=N] Allow N jobs at once; infinite jobs with no arg.
-k, --keep-going Keep going when some targets can't be made.
-l [N], --load-average[=N], --max-load[=N]
Don't start multiple jobs unless load is below N.
-L, --check-symlink-times Use the latest mtime between symlinks and target.
-n, --just-print, --dry-run, --recon
Don't actually run any recipe; just print them.
-o FILE, --old-file=FILE, --assume-old=FILE
Consider FILE to be very old and don't remake it.
-O[TYPE], --output-sync[=TYPE]
Synchronize output of parallel jobs by TYPE.
-p, --print-data-base Print make's internal database.
-q, --question Run no recipe; exit status says if up to date.
-r, --no-builtin-rules Disable the built-in implicit rules.
-R, --no-builtin-variables Disable the built-in variable settings.
-s, --silent, --quiet Don't echo recipes.
-S, --no-keep-going, --stop
Turns off -k.
-t, --touch Touch targets instead of remaking them.
--trace Print tracing information.
-v, --version Print the version number of make and exit.
-w, --print-directory Print the current directory.
--no-print-directory Turn off -w, even if it was turned on implicitly.
-W FILE, --what-if=FILE, --new-file=FILE, --assume-new=FILE
Consider FILE to be infinitely new.
--warn-undefined-variables Warn when an undefined variable is referenced.
This program built for x86_64-unknown-linux-gnu
Report bugs to <[email protected]>
make: *** [Makefile:68: tigmint-make.xml] Error 2
tigmint-master$
I know all these Makefiles
resemble those in abyss
. Even zsh
bug I reported after @sjackman added the timing feature while not documenting the new dependency. I was lazy to look up the old thread. ;-)
from tigmint.
Thanks for the feedback, @mmokrejs! I did just go ahead and move that Makefile to tests
so it's not in the top-level directory and hopefully won't cause confusion. Like I mentioned, I never used it myself! I'd suggest using our test demos at tests/test_installation
if you want some data to test installations.
from tigmint.
Closing - moved Makefile in question to tests
directory to avoid it causing confusion.
from tigmint.
Related Issues (20)
- About samtools invalid option in tigmint-make arcs mode HOT 4
- pre-alignment HOT 2
- Forward+reverse + long reads HOT 4
- yet another "make: *** No rule to make target" issue HOT 5
- Feature has length = 0, Skipping - followed by empty output from tigmint-long HOT 9
- Understanding tigmint-long outputs HOT 3
- tigmint compilation issue HOT 2
- _sqlite3.cpython-310-x86_64-linux-gnu.so: undefined symbol: sqlite3_trace_v2
- Error : no progress of scaffolding running HOT 5
- tigmint-long error HOT 1
- Respect $TMPDIR as anticipated by sort tool HOT 1
- samtools sort may be replaced by bamsort which scales better HOT 2
- pigz may be better replaced by bgzip HOT 2
- tigmint-make ignores $PATH and is supposed to be run from unpacked source tree instead HOT 3
- README does not list all dependencies HOT 2
- Does bin/tigmint_estimate_dist.py really work with FASTA files as well? HOT 5
- src/long-to-linked-pe v1.0: Using more than 6 threads does not scale, reverting to 6. HOT 5
- tigmint_molecule_paf.py: TypeError: expected string or bytes-like object HOT 11
- tigmint-make: minimap2 is being called with -y argument HOT 3
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from tigmint.