Compile on linux?

[jerowe]

Pinging @nizardrou

The makefile specifically references clang, which is an osx only thing. Can I do a dropin replacement for gcc?

I will try somethings from my side, but what I would really like to see from your side is a minimal docker image with pheniq installed.

[jerowe]

I created a patch to drop in gcc for clang.

Disregard this. Updated below.

[jerowe]

New patch and errors.

--- Makefile    2018-04-22 10:21:13.000000000 +0400
+++ Makefile    2018-04-22 10:40:26.000000000 +0400
@@ -30,15 +30,17 @@
 MAJOR_REVISON := 1
 MINOR_REVISON := 1

-CC              = clang++
 PREFIX          = /usr/local
 BIN_PREFIX      = $(PREFIX)/bin
 INCLUDE_PREFIX  = $(PREFIX)/include
 LIB_PREFIX      = $(PREFIX)/lib

-CFLAGS          = -std=c++11 -O3 -Wall -Wsign-compare
-LDFLAGS         =
-LIBS            = -lhts -lz -lbz2 -llzma
+CFLAGS          += -std=c++11 -O3 -Wall -Wsign-compare
+LDFLAGS         +=
+LIBS            += -lhts -lz -lbz2 -llzma
+
+CFLAGS += -I$(INCLUDE_PREFIX)
+LDFLAGS += -L$(LIB_PREFIX)

 STATIC_LIBS = \
 $(LIB_PREFIX)/libhts.a \
@@ -94,11 +96,6 @@
        override PHENIQS_VERSION := $(PHENIQS_VERSION).$(PHENIQS_GIT_VERSION)
 endif

-ifdef PREFIX
-       CFLAGS += -I$(INCLUDE_PREFIX)
-       LDFLAGS += -L$(LIB_PREFIX)
-endif
-
 all: $(PHENIQS_SOURCES) configuration.h version.h $(PHENIQS_OBJECTS)
        $(CC) $(PHENIQS_OBJECTS) $(LDFLAGS) -pthread $(LIBS) -o $(PHENIQS_EXECUTABLE)

kstring.h:281:1: warning: multi-line comment [-Wcomment]
 // #define kroundup_size_t(x) (--(x),                                       \
 ^
cc -I/opt/conda/conda-bld/pheniqs_1524379253526/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_
placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -I/opt/conda/conda-bld/pheniqs_1524379253526/_h_env_placehold
_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac
ehold_placehold_placehold_place/include/rapidjson -std=c++11 -O3 -Wall -Wsign-compare -I/usr/local/include -c -o interface.o interface.cpp
In file included from json.h:42:0,
                 from url.h:34,
                 from interface.h:37,
                 from interface.cpp:2:
kstring.h:281:1: warning: multi-line comment [-Wcomment]
 // #define kroundup_size_t(x) (--(x),                                       \
 ^
In file included from interface.cpp:4:0:
configuration.h:2:1: error: stray ‘\’ in program
 const char configuration_json[] = {\n    0x7b, 0x0a, 0x22, 0x61, 0x63, 0x74, 0x69, 0x6f, 0x6e, 0x22, 0x3a, 0x20,
 ^
configuration.h:467:5: error: stray ‘\’ in program
     0x6c, 0x61, 0x76, 0x6f, 0x72, 0x21, 0x22, 0x0a, 0x7d, 0x0a,\n};
     ^
configuration.h:2:37: error: ‘n’ was not declared in this scope
 const char configuration_json[] = {\n    0x7b, 0x0a, 0x22, 0x61, 0x63, 0x74, 0x69, 0x6f, 0x6e, 0x22, 0x3a, 0x20,
                                     ^
configuration.h:2:42: error: expected ‘}’ before numeric constant
 const char configuration_json[] = {\n    0x7b, 0x0a, 0x22, 0x61, 0x63, 0x74, 0x69, 0x6f, 0x6e, 0x22, 0x3a, 0x20,
                                          ^
configuration.h:2:42: error: expected ‘,’ or ‘;’ before numeric constant
configuration.h:467:66: error: expected declaration before ‘}’ token
     0x6c, 0x61, 0x76, 0x6f, 0x72, 0x21, 0x22, 0x0a, 0x7d, 0x0a,\n};

[jerowe]

I also created a patch to remove the '\n' characters from the configuration.h file.

--- configuration.sh    2018-04-22 10:45:53.000000000 +0400
+++ configuration.sh    2018-04-22 10:50:53.000000000 +0400
@@ -26,3 +26,5 @@

 echo "const char configuration_json[] = \
 {\n    $(cat configuration.json | sed -E 's/^ +//g' | hexdump -v -e '12/1 "0x%02x, " "\n" "    "' | sed -E 's/( 0x  ,)*$//' | grep -vE "^\s+$")\n};" >> configuration.h;
+tr '\n' ' ' < configuration.h > out.t
+mv out.t configuration.h

But then I got an error somewhere with the interface.o

[jerowe]

Ok, I have hit a wall with this. How's about we make a plan of attack.

1. Please build a minimal install example script, on linux, preferably with docker.
2. The minimal install script should remove hardcoded variables things like PREFIX, CFLAGS, INCLUDE_PATH, CC etc from the Makefile.

If you get the minimal install script working on a docker image, and give me write access to the repo, I will get a CI service setup to at least test that it builds on both linux and mac. From there I can build it as a conda package.

[jerowe]

Updates?

[moonwatcher]

Sorry, just noticed this.

clang is not an MacOS thing, its an llvm compiler that often yields faster executables than gcc, but it should all build on gcc. https://clang.llvm.org

I see you have some issues with my xxd replacement. maybe I got something wrong, can you you please post what the configuration.h file looks like? I tried to make it look similar to what xxd emits.

I will run a set of tests tomorrow to see how everything builds on gcc and make adjustments, but clang was faster in my benchmarks on linux...

[moonwatcher]

Also use g++ not gcc. I will do some testing for gcc on both MacOS and linux before the next commit but please provide some feedback about the xxd replacement script.

[jerowe]

clang is not available on the conda-forge/bioconda linux build system. Could you try for gcc? That is the path of least resistance.

On Thu, May 3, 2018 at 10:33 AM Lior Galanti notifications@github.com wrote:

Also use g++ not gcc. I will do some testing for gcc on both MacOS and linux before the next commit but please provide some feedback about the xxd replacement script.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biosails/pheniqs/issues/4#issuecomment-386202631, or mute the thread https://github.com/notifications/unsubscribe-auth/AFTFRgaGDMob0q9y8EX_OXI5nCQFbSh-ks5tuqSkgaJpZM4TevnS .

[moonwatcher]

g++ is gcc. gcc is for C code while g++ automatically links to the C++ system libraries.

https://stackoverflow.com/questions/172587/what-is-the-difference-between-g-and-gcc