make: *** [fastq-mcf] Error 1

[GoogleCodeExporter]

What is the expected output? What do you see instead?
Attached a word file...problem during make

What version of the product are you using? On what operating system?
ea-utils.1.1.2-537. installed on windows7

Please provide any additional information

Original issue reported on code.google.com by koirob...@googlemail.com on 3 Jun 2013 at 12:49

Attachments:

• [ea-utils make install.docx](https://storage.googleapis.com/google-code-attachments/ea-utils/issue-18/comment-0/ea-utils make install.docx)

[GoogleCodeExporter]

OK, I make a mingw port.   Not too many changes were needed.    You'll need to 
get release 621.

Original comment by earone...@gmail.com on 3 Jun 2013 at 1:16

[GoogleCodeExporter]

(let me know if this works so i can close the ticket)

Original comment by earone...@gmail.com on 3 Jun 2013 at 5:50

[GoogleCodeExporter]

Sorry I am a lit bit confused how do I get the 621 . In your repository all the 
Makefile, fastaq-lib.h, fastaq-lib.cpp & the sparseconfig.h are the modified 
files that I need.
After some fooling around realised can't copy paste or wget them need them 
through svn but not sure what to do. I did a svn checkout for all these 4files 
and in the modifications it shows modified version 621 for these 4 files but 
when I ran the "CC=g++ PREFIX=/usr/local make install" it is still giving me 
error and I guess the same error as earlier 

Original comment by koirob...@googlemail.com on 4 Jun 2013 at 6:03

Attachments:

• ea-error.docx

[GoogleCodeExporter]

the big issue is that the windows socket library needs to be linked in.   The 
Makefile checks to see if you're on Windows by looking at the $OS variable and 
then changing the linking variables (I am trying to avoid dealing with 
"configure" for some reason). Also, the other code now checks for windows.   I 
successfully compiled all but "varcall" on mingw using windows 7.   

when you ran svn checkout... did you compile FROM the checked-out directory... 
or did you move things around first?   try just "checkout ... make"

Original comment by earone...@gmail.com on 4 Jun 2013 at 6:08

[GoogleCodeExporter]

i could just upload the windows binaries.

Original comment by earone...@gmail.com on 4 Jun 2013 at 6:09

[GoogleCodeExporter]

I am unable to figure out what I am doing wrong. so I have my 
ea-utilis.1.1.2-537 folder with all my files in there. I have downloaded 
svntortoise. 
I right click and go to svn checkout and it opens a new window .in the new 
window in url "http://ea-utils.googlecode.com/svn/trunk/clipper/Makefile" in 
the checkout directory "C:\Users\ea-utilis.1.1.2-537" checkout depth-fully 
recursive, and selected head revision.
This shows the makefile with an red ! on the Makefile . I opened the diff file 
and it shows working base revision 621 (the script file with the modified 
codes) and the working copy with "ID-520....."(the older copy).
Please let me know if I am doing something wrong....

Original comment by koirob...@googlemail.com on 6 Jun 2013 at 6:28

[GoogleCodeExporter]

1. Did you try the precompiled executables?  I uploaded them.... not sure if 
you need libs to use them.

2. I don't know tortise, I just paste the command line Google gives you to 
checkout.   

3. The Makefile should have this in it:
ifeq ($(OS),Windows_NT)
    $(CC) $(CFLAGS) samtools/*.o -lz -lpthread -lws2_32 fastq-lib.cpp $< -o $@
else
    $(CC) $(CFLAGS) samtools/*.o -lz -lpthread fastq-lib.cpp $< -o $@
endif

Original comment by earone...@gmail.com on 6 Jun 2013 at 6:35

[GoogleCodeExporter]

where are the precompiled executables....I just saw the svn directory with the 
4 modified files in version 621.
this time in my ea-utils folder I deleted these 4 files and did the checkout 
for all these 4 files. I checked the makefile and it has the above lines in it.
I ran the following code and got this error
$ cd C:/Users/bashi/ea-utils.1.1.2-537

"$ CC=g++ PREFIX=/usr/local make install
g++ -O3 -I.  fastq-lib.cpp -o fastq-mcf fastq-mcf.c
fastq-mcf.c: In function 'int main(int, char**)':
fastq-mcf.c:193:39: error: 'SVNREV' was not declared in this scope
make: *** [fastq-mcf] Error 1"

Original comment by koirob...@googlemail.com on 6 Jun 2013 at 7:02

[GoogleCodeExporter]

I added them to https://code.google.com/p/ea-utils/downloads

Original comment by earone...@gmail.com on 6 Jun 2013 at 7:12

[GoogleCodeExporter]

Yes I have downloaded them and they are running......Thank you for the help and 
support.

Original comment by koirob...@googlemail.com on 7 Jun 2013 at 8:48

[GoogleCodeExporter]

Original comment by earone...@gmail.com on 7 Jun 2013 at 12:13

• Changed state: Done
• Added labels: Type-Other
• Removed labels: Type-Defect

[GoogleCodeExporter]

[deleted comment]

[GoogleCodeExporter]

0 $ pwd
/share/apps/qiime_software/qiime-deploy/failed_packages/ea-utils.1.1.2-537
1 $ make
g++ -O3 -I.  fastq-lib.cpp tidx/tidx-lib.cpp -o varcall varcall.cpp -lgsl 
-lgslcblas
In file included from tidx/tidx-lib.cpp:14:
tidx/fastq-lib.h:1: error: expected unqualified-id before ‘.’ token
In file included from tidx/tidx-lib.cpp:16:
tidx/tidx.h:21: error: ‘annot’ was not declared in this scope
tidx/tidx.h:21: error: template argument 1 is invalid
tidx/tidx.h:21: error: template argument 2 is invalid
tidx/tidx.h:21: error: template argument 2 is invalid
tidx/tidx.h:21: error: template argument 5 is invalid
...

2 $ uname -a
Linux majorbio_cluster.com 2.6.32-220.13.1.el6.x86_64 #1 SMP Tue Apr 17 
23:56:34 BST 2012 x86_64 x86_64 x86_64 GNU/Linux
3 $ g++ --version
g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
4 $ help
.....................

Original comment by boboi...@gmail.com on 23 Jan 2014 at 8:03