PHLAWD not compiling

Alexander Davila

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Sep 28, 2012, 1:16:37 PM9/28/12

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I have gotten to ./configure but when I try to do the make command I get this error:

<Sequence> >&)in genedb.o

...

ld: symbol(s) not found for architecture x86_64

collect2: ld returned 1 exit status

make: *** [PHLAWD] Error 1

I am installing on a MBP running Mountain Lion (OSX 10.8.2).

I also had to bypass the Makefile edit for MAFFT because I kept getting this error:

gcc -Denablemultithread -O3 -c io.c

In file included from mltaln.h:278,

from io.c:1:

dp.h:7: error: thread-local storage not supported for this target

dp.h:8: error: thread-local storage not supported for this target

dp.h:9: error: thread-local storage not supported for this target

dp.h:10: error: thread-local storage not supported for this target

In file included from io.c:1:

mltaln.h:287: error: thread-local storage not supported for this target

mltaln.h:288: error: thread-local storage not supported for this target

mltaln.h:289: error: thread-local storage not supported for this target

mltaln.h:290: error: thread-local storage not supported for this target

make: *** [io.o] Error 1

any help would be greatly appreciated

Cody Hinchliff

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Sep 29, 2012, 2:06:37 AM9/29/12

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Are you using the mac makefile? The following command successfully builds for me under 10.8.2 with X Code 4.5.

make -f Makefile.MAC

Alexander Davila

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Oct 2, 2012, 2:10:28 PM10/2/12

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That solved it. Cheers

Javi IgA

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Oct 19, 2015, 11:20:27 AM10/19/15

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Hi PHLAWD users,

I ran into a similar issue trying to install PHLAWD on Mac OS X 10.10.3. Both compiling from source (makefile.MAC) and trying homebrew give the same error:

"ld: symbol(s) not found for architecture x86_64

collect2: error: ld returned 1 exit status"

Anyone might have any suggestions please?

Cheers,

Javi

Stephen Smith

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Oct 19, 2015, 11:21:55 AM10/19/15

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OK, interesting. Yeah, I doubt much testing has gone on for 10.10 since it is so new. I can explore some of this and potentially update the Makefile.MAC

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Javi IgA

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Oct 19, 2015, 11:53:02 AM10/19/15

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Thanks for the speedy reply. That'd be excellent!

Stephen Smith

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Oct 27, 2015, 1:48:29 PM10/27/15

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Hi Javi
So I have had better luck using these compilers http://hpc.sourceforge.net. I would install the one that fits your machine and go from there.

Joseph Brown

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Nov 11, 2015, 4:05:34 PM11/11/15

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PHLAWD Mac people (wait, is that redundant? ;P ),

I believe I've got installation working for mac (10.11.1). I have been using the compilers that Stephen recommended (http://hpc.sourceforge.net). When you clone, switch to the branch "mac". Here is what should do ya (assumes all dependencies (MAFFT, MUSCLE, quicktree, and sqlite3) are installed; I installed all of these from source, not using homebrew):

git clone g...@github.com:blackrim/phlawd.git

cd phlawd

git checkout mac

cd src

autoconf

./configure

make

sudo make install

HTH.

JWB

Message has been deleted

Rafael Molina Venegas

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Mar 12, 2017, 7:39:49 AM3/12/17

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Hi,

I am trying to install PHLAWD on Mac Sierra 10.12 following the Joseph guideline (thanks!). However, I got the following error message:

ld: library not found for -lsqlitewrapped

I have read somewhere that the sqlite3 library is installed by default on Sierra, but I do not know about sqlitewrapped... I wonder how did you go around this? (you did not mention the sqlitewrapped library in your post)

Thank you in advance,

Rafa

robert...@gmail.com

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Mar 28, 2018, 10:04:41 AM3/28/18

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