pugz 0.8.0

[tseemann]

• Have you followed the guidelines for contributing?
• Have you checked that there aren't other open pull requests for the same formula update/change?
• Have you built your formula locally with brew install --build-from-source FORMULA, where FORMULA is the name of the formula you're submitting?
• Does your build pass brew audit --strict FORMULA (after doing brew install FORMULA)?

---

[tseemann]

/usr/bin/ld: /tmp/ccNbQPgH.ltrans0.ltrans.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5'
/lib/x86_64-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
Makefile:192: recipe for target 'gunzip' failed
make: *** [gunzip] Error 1

I assume this in OpenMP related; will depend on gcc and see.

[tseemann]

Now with make V=1:
I notice the -lrt in the final link?

ar cr libdeflate.a 
CC="g++-5" CFLAGS=" -std=c++14 -I. -Icommon -lpthread -Iexternal/type_safe/include -Iexternal/type_safe/external/debug_assert -Wall -Wundef -Wrestrict -Wnull-dereference -Wuseless-cast -Wshadow -Weffc++ -Wpedantic -Wvla -O4 -flto -march=native -mtune=native -g -D_POSIX_C_SOURCE=200809L -D_FILE_OFFSET_BITS=64 -DHAVE_CONFIG_H" programs/detect.sh > programs/config.h
g++-5 -o programs/gunzip.o -c  -std=c++14 -I. -Icommon -lpthread -Iexternal/type_safe/include -Iexternal/type_safe/external/debug_assert -Wall -Wundef -Wrestrict -Wnull-dereference -Wuseless-cast -Wshadow -Weffc++ -Wpedantic -Wvla -O4 -flto -march=native -mtune=native -g -D_POSIX_C_SOURCE=200809L -D_FILE_OFFSET_BITS=64 -DHAVE_CONFIG_H programs/gunzip.cpp
g++-5 -o programs/prog_util.o -c  -std=c++14 -I. -Icommon -lpthread -Iexternal/type_safe/include -Iexternal/type_safe/external/debug_assert -Wall -Wundef -Wrestrict -Wnull-dereference -Wuseless-cast -Wshadow -Weffc++ -Wpedantic -Wvla -O4 -flto -march=native -mtune=native -g -D_POSIX_C_SOURCE=200809L -D_FILE_OFFSET_BITS=64 -DHAVE_CONFIG_H programs/prog_util.cpp
g++-5 -o programs/tgetopt.o -c  -std=c++14 -I. -Icommon -lpthread -Iexternal/type_safe/include -Iexternal/type_safe/external/debug_assert -Wall -Wundef -Wrestrict -Wnull-dereference -Wuseless-cast -Wshadow -Weffc++ -Wpedantic -Wvla -O4 -flto -march=native -mtune=native -g -D_POSIX_C_SOURCE=200809L -D_FILE_OFFSET_BITS=64 -DHAVE_CONFIG_H programs/tgetopt.cpp
g++-5 -o gunzip   -std=c++14 -I. -Icommon -lpthread -Iexternal/type_safe/include -Iexternal/type_safe/external/debug_assert -Wall -Wundef -Wrestrict -Wnull-dereference -Wuseless-cast -Wshadow -Weffc++ -Wpedantic -Wvla -O4 -flto -march=native -mtune=native -g -D_POSIX_C_SOURCE=200809L -D_FILE_OFFSET_BITS=64 -DHAVE_CONFIG_H programs/gunzip.o programs/prog_util.o programs/tgetopt.o libdeflate.a -lrt
/usr/bin/ld: /tmp/cclubzas.ltrans0.ltrans.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5'
/lib/x86_64-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status

[sjackman]

g++-5 -o gunzip   -std=c++14 -I. -Icommon -lpthread -Iexternal/type_safe/include -Iexternal/type_safe/external/debug_assert -Wall -Wundef -Wrestrict -Wnull-dereference -Wuseless-cast -Wshadow -Weffc++ -Wpedantic -Wvla -O4 -flto -march=native -mtune=native -g -D_POSIX_C_SOURCE=200809L -D_FILE_OFFSET_BITS=64 -DHAVE_CONFIG_H programs/gunzip.o programs/prog_util.o programs/tgetopt.o libdeflate.a -lrt

The -lpthread is in the wrong location on this command line. All the -l options need to occur after the object files programs/gunzip.o programs/prog_util.o programs/tgetopt.o where the -lrt is currently found.

[sjackman]

A hack fix for now would be either

inreplace "Makefile", "-lpthread", "-pthread"

or

inreplace "Makefile", "-lrt", "-lpthread -lrt"

[sjackman]

It'd be good to report this bug upstream. It should be easily reproducible on any Ubuntu system.

[tseemann]

@tseemann reported upstream, added hack w/ note - thank you!

[tseemann]

Fails on macos now:

==> make V=1
ar cr libdeflate.a 
CC="g++-9" CFLAGS=" -std=c++14 -I. -Icommon -lpthread -Iexternal/type_safe/include -Iexternal/type_safe/external/debug_assert -Wall -Wundef -Wrestrict -Wnull-dereference -Wuseless-cast -Wshadow -Weffc++ -Wpedantic -Wvla -O4 -flto -march=native -mtune=native -g -D_POSIX_C_SOURCE=200809L -D_FILE_OFFSET_BITS=64 -DHAVE_CONFIG_H" programs/detect.sh > programs/config.h
ar: no archive members specified
usage:  ar -d [-TLsv] archive file ...
	ar -m [-TLsv] archive file ...
	ar -m [-abiTLsv] position archive file ...
	ar -p [-TLsv] archive [file ...]
	ar -q [-cTLsv] archive file ...
	ar -r [-cuTLsv] archive file ...
	ar -r [-abciuTLsv] position archive file ...
	ar -t [-TLsv] archive [file ...]
	ar -x [-ouTLsv] archive [file ...]
make: *** [libdeflate.a] Error 1
make: *** Waiting for unfinished jobs....

[Piezoid]

The (empty) static lib is now disabled on master.
Link argument order should also be fixed.

Imho, it is a bit early for a distributed release. But at least this will allow to sort out bugs on macos.

I didn't try at all to build on macos, nor do I have the hardware to do so.
The linux specific syscalls (non posix madvises) should be disabled by the preprocessor.

Edit: I think I got this pass in CircleCI

diff --git a/Formula/pugz.rb b/Formula/pugz.rb
index 2b4d60e..94c54c3 100644
--- a/Formula/pugz.rb
+++ b/Formula/pugz.rb
@@ -1,19 +1,12 @@
 class Pugz < Formula
   desc "Truly parallel gzip decompression"
   homepage "https://github.com/Piezoid/pugz"
-  url "https://github.com/Piezoid/pugz/archive/recombseq19-demo.tar.gz"
+  url "https://github.com/Piezoid/pugz/archive/97be6839c48878b498112933655506800af3b8e2.tar.gz"
   version "0.8.0"
-  sha256 "1005519d7ea80c4f59593b0e9bd2e9337c02a2b5c52dfe1732c16f75e4eeecb3"
-
-  depends_on "gcc" if OS.mac? # for openmp
-
-  fails_with :clang # needs openmp
+  sha256 "e0ec4763a9aa64d7ebf333ec333ba72ebfc5797c051a56fd9dd1ce6fca040dc8"
 
   def install
-    # https://github.com/Piezoid/pugz/issues/10
-    inreplace "Makefile", "-lrt", "-lpthread -lrt"
-
-    system "make", "V=1"
+    system "make", "asserts=0", "V=1"
     bin.install "gunzip" => "pugz"
     pkgshare.install "example"
     doc.install "paper/paper.pdf"

Not sure why you put a requirement on gcc for openmp, pugz uses plain pthread and compile fine with clang on linux.
Tell me if I should make a 0.8.1 release.

[sjackman]

Thanks for your help, Maël!

Imho, it is a bit early for a distributed release. But at least this will allow to sort out bugs on macos.

In your opinion, should we close this PR, and wait for a stable release?

[tseemann]

I would just add caveats section about stability; but i will defer to you

[sjackman]

Not sure why you put a requirement on gcc for openmp, pugz uses plain pthread and compile fine with clang on linux.

@tseemann Could you please remove the gcc dependency and fails_with :clang?

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.