LASTZ installation

[as1438]

Hey,

I am trying to install LASTZ version 1.03.02 on my 64-bit Linux desktop. I have extracted the files in appropriate directory, edited the make‑include.mak file to specify a particular directory and included this directory in my $PATH. Now when i cd into the /src folder and run make, i get this error --

cd src && make lastz lastz_D
make[1]: Entering directory `/usr/local/bin/lastz/src'
gcc -c -O3 -Wall -Wextra -Werror -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DVERSION_MAJOR="\"1"\" -DVERSION_MINOR="\"03"\"
-DVERSION_SUBMINOR="\"02"\" -DREVISION_DATE="\"20110719"\"
-DSUBVERSION_REV="\"1567:1570"\" -Dscore_type=\'I\' lastz.c -o lastz.o
lastz.c: In function ‘main’:
lastz.c:507:9: error: variable ‘freeTargetRev’ set but not used
[-Werror=unused-but-set-variable]
lastz.c: In function ‘start_one_strand’:
lastz.c:2197:9: error: variable ‘base****’ set but not used
[-Werror=unused-but-set-variable]
lastz.c: In function ‘parse_options’:
lastz.c:6473:9: error: variable ‘seq1Filename’ set but not used
[-Werror=unused-but-set-variable]
cc1: all warnings being treated as errors

make[1]: *** [lastz.o] Error 1
make[1]: Leaving directory `/usr/local/bin/lastz/src'
make: *** [build_lastz] Error 2

Can anyone help me figure out why i am getting this error and how to fix it?

Thanks a lot.

[scami]

may be....

Hi there,

today I experienced the same your problem. I sorted it out in the following way:

1) Open the Makefile file within the src directory with a text editor
2) Delete the word -Werror at the line 31 . Save and quit
3) Repeat the make / make install procedure

I obtained the executables files in the bin folder

hope it helps.....

regards

[DFJ111]

^^ This worked for me. Thanks!

[yekaixiong]

This worked for me too! But I am just curious why "-Werror" would cause the problem.

[Bob-Harris]

This worked for me too! But I am just curious why "-Werror" would cause the problem.

Sorry for this very late reply. I haven't been on seqanswers until today.

Werror tells the compiler to treat all warnings as errors. Turning this off is the easiest solution, but then you are left to scratch your head wondering whether the reported warning is benign or not. In this case it is.

I enabled Werror in the distribution because my intent is lastz should build without any warnings. The problem arises when newer versions of the compiler get better at detecting suspicious coding practices. In the cases reported at the start of this thread, the suspicious code is some variables that had been used during debugging which I neglected to remove. I believe I removed them in a later version; I will check.

There is a paragraph in the readme about this (but it probably wasn't in the 1.03.02 readme):

http://www.bx.psu.edu/~rsharris/lastz/newer/README.lastz-1.03.54.html#install

1.03.02 is a couple years old. The latest version is 1.03.54 which can be found at the bottom of this page:

http://www.bx.psu.edu/~rsharris/lastz/newer

Bob H
(lastz author)

[GenoMax]

@Bob H: Good to have you on the list.

Is it possible to change the wording on the main page for LASTZ (http://www.bx.psu.edu/~rsharris/lastz/) for the Newer versions. The "not officially released" part probably keeps people from trying the latest version of the software.

[Bob-Harris]

The "not officially released" part probably keeps people from trying the latest version of the software.

Agreed.

The problem has been that the text of the readme file has lagged the new features added over the past 4 years. As features have been added, they've been added to the readme, but I haven't had the time to review the rest of the document to make sure everything it says is correct (with regard to newer features). I think most of the issue would be things the readme says the program can't do, but which it now can.

Bob H

[madhubioinfo]

i have installed the lastz-distrib-1.02.00 version and as said in the manual i did make , make install then i tried make test there also i dint get any output without any error it returned but when i try to run my sequences on it shows the following error lastz-distrib-1.02.00/bin/lastz: No match i went and checked my bin directory lastz file is there still am confused why such an error?

[GenoMax]

i have installed the lastz-distrib-1.02.00 version and as said in the manual i did make , make install then i tried make test there also i dint get any output without any error it returned but when i try to run my sequences on it shows the following error lastz-distrib-1.02.00/bin/lastz: No match i went and checked my bin directory lastz file is there still am confused why such an error?

If lastz is in "bin" then you may need to add execute permissions to the file. You can do it as follows (if you are in the directory with lastz file):

$ chmod u+x lastz

This command should print help for lastz if the compilation was proper.

$ ./lastz

[madhubioinfo]

i have given the permisions to the executable lastz file also if i type ./lastz showing the help i tried this also, still the same error is displaying

[GenoMax]

Can you provide the full command line you are using (you can remove specific file paths/server names)?

[madhubioinfo]

lastz-distrib-1.02.00/test_data/fake_apple.fa [multiple] /lastz-distrib-1.02.00/test_data/fake_orange_reads.fa --format=sam --output=test.sam

[GenoMax]

lastz-distrib-1.02.00/test_data/fake_apple.fa [multiple] /lastz-distrib-1.02.00/test_data/fake_orange_reads.fa --format=sam --output=test.sam

I am not sure what [multiple] refers to in the command line above but the following works for me:

$ lastz /path_to/lastz-distrib-1.02.00/test_data/fake_apple.fa /path_to/lastz-distrib-1.02.00/test_data/fake_orange_reads.fa --format=sam --output=test.sam

[Bob-Harris]

it shows the following error lastz-distrib-1.02.00/bin/lastz: No match

Sorry for not replying sooner. I've been out of town and I did not have my account info for seqanswers.

The "no match" report is not from lastz (that text doesn't appear anywhere in the program). It is something the shell is reporting. I had a similar report a couple years ago but unfortunately I forget exactly what the cause was. Does your PATH environment variable contain the directory the lastz executable is in?

lastz-distrib-1.02.00/test_data/fake_apple.fa [multiple] /lastz-distrib-1.02.00/test_data/fake_orange_reads.fa --format=sam --output=test.sam

One problem in this command line is the blank space before [multiple]. This needs to be attached to the file name, without spaces. But I don't think that's what is causing the what you are reporting (lastz will report this differently).

[Bob-Harris]

The "no match" report is not from lastz (that text doesn't appear anywhere in the program). It is something the shell is reporting. I had a similar report a couple years ago but unfortunately I forget exactly what the cause was.

I have found the prior report of this, from 2011. I was never able to determine the cause. We came up with a workaround which I will describe below.

First, though, can you run the following commands and tell me what the responses are?

which lastz
ls -al `which lastz`

The first of those commands should tell you whether your shell is trying to run the same lastz that you think it is.

The second command will tell you whether there might be something wrong with the file. For example if its size is zero. On my machine the lastz executable's file size is about 500K.

Do you know what shell you are using? I've only used bash.

The workaround that the previous user ended up using was to put his command in a text file, set the text file as an executable, and run that. Not ideal, and I don't have a clue why that way would work but not from the command line (maybe different shells?). It's out of my area of expertise.