CASAVA-1.8 install fails

[roko-t]

Dear all,

I've got error message during CASAVA-1.8 installation ('configure' step), but I haven't found the cause of error.

Here is error log,
-----------------
Decompressing .../CASAVA_v1.8.0/src/../redist/cmake-2.8.4.tar.gz
---------------------------------------------
CMake 2.8.4, Copyright 2000-2009 Kitware, Inc.
C compiler on this system is: /usr/local/bin/gcc
C++ compiler on this system is: /usr/local/bin/g++
Makefile processor on this system is: gmake
/usr/local/bin/g++ is GNU compiler

：
-- Looking for wcscpy
-- Looking for wcscpy - not found
-- Looking for wcslen
-- Looking for wcslen - not found
：
：
-- Check size of wchar_t
-- Check size of wchar_t - done
：
[ 13%] [ 13%] Building C object Utilities/cmlibarchive/libarchive/CMakeFiles/cmlibarchive.dir/archive_entry.c.o
Building C object Utilities/cmexpat/CMakeFiles/cmexpat.dir/xmlparse.o
・・・/CASAVA/src/CASAVA_v1.8.0-build/bootstrap/build/cmake-2.8.4/Utilities/cmlibarchive/libarchive/archive_entry.c:136: error: static declaration of 'wcscpy' follows non-static declaration
/usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.3.2/include-fixed/wchar.h:142: error: previous declaration of 'wcscpy' was here
・・・/CASAVA/src/CASAVA_v1.8.0-build/bootstrap/build/cmake-2.8.4/Utilities/cmlibarchive/libarchive/archive_entry.c:145: error: static declaration of 'wcslen' follows non-static declaration
/usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.3.2/include-fixed/wchar.h:252: error: previous declaration of 'wcslen' was here
make[2]: *** [Utilities/cmlibarchive/libarchive/CMakeFiles/cmlibarchive.dir/archive_entry.c.o] Error 1
make[1]: *** [Utilities/cmlibarchive/libarchive/CMakeFiles/cmlibarchive.dir/all] Error 2
make[1]: *** waiting unfinished job
[ 13%] Building C object Utilities/cmexpat/CMakeFiles/cmexpat.dir/xmltok.o
[ 13%] Building C object Utilities/cmexpat/CMakeFiles/cmexpat.dir/xmlrole.o
Linking C static library libcmexpat.a
[ 13%] Built target cmexpat
make: *** [all] Error 2
cmake: build failed: Terminating...
Failed to verify or install cmake
----------------


1th. because of wcscpy,wcslen are "not found".
config.h in ../CASAVA/src/CASAVA_v1.8.0-build/bootstrap/build/cmake-2.8.4/Utilities/cmlibarchive

Can anyone tell how to solve the problem?

[mgogol]

I would email [email protected] about this.

On a side note, why did they change everything in CASAVA 1.8, it's kind of annoying.

[roko-t]

Thanks,

I emailed to illumina Japan but haven't recieved a reply.
I think that this error maybe depends on the combination between CASAVA 1.8 and gcc on my environment...

[GenoMax]

On a side note, why did they change everything in CASAVA 1.8, it's kind of annoying.

To keep us on our toes

On a serious note some of the changes are useful (e.g sanger quality). People who have downstream pipelines that expect a certain folder structure are going to have the most pain though.
Last version of pipeline lasted for almost a year so a major change once a year is better than one every quarter.

[roko-t]

I think some of changes are so useful,too.
So I want to use v1.8 efficiently asap.
On the other hand, I know it takes some time and effort to master it.

[roko-t]

Cmake 2.8.4 is bundled together with the CASAVA v1.8 disribution and is automatically built.
--------------------

I set cmake 2.8.3 on my enviroment by using config option.
SO I coould install CASAVA 1.8 succesfully !!!
I'm very very happy to avoid the manual work steps(OLB + Dumultiplex + GERALD(CASAVA1.7).

[GenoMax]

Cmake 2.8.4 is bundled together with the CASAVA v1.8 disribution and is automatically built.
--------------------

I'm very very happy to avoid the manual work steps(OLB + Dumultiplex + GERALD(CASAVA1.7).

Remember that with v.1.8:
1. quality values are now in sanger format
2. sequence files generated include *all* reads (both filtered and unfiltered sequences) by default.

[oliviera]

Dear roko-t
I encounter the same problem that you do to install casava1.8
Could you share with me how you did configure cmake, thats would help a lot

Cheers

[oliviera]

Hi again,
I simply reinstall the newest version of cmake 2.8.5. Should be ok now.
Cheers
olia

[argyjbao]

CASAVA 1.8.2 install fail

Dear buddy,
I also got error when installing CASAVA 1.8.2.
When I configure, it said:
========================================================
cmake version "cmake version 2.8.4" is already installed at /hd4/app/miseq/CASAVA_v1.8.2_Build/bootstrap/bin/cmake
nothing to be done
Using installed /hd4/app/miseq/CASAVA_v1.8.2_Build/bootstrap/bin/cmake
-- install prefix: /hd4/app/miseq/CASAVA/v1.8.2
-- install exec prefix: .
-- install bin dir: ./bin
-- install lib dir: ./lib/CASAVA-1.8.2
-- install libexec dir: ./libexec/CASAVA-1.8.2
-- install include dir: include/CASAVA-1.8.2
-- install data dir: share/CASAVA-1.8.2
-- install doc dir: doc/CASAVA-1.8.2
-- install man dir: man
-- Verifying target directories access
-- Creating external tools in subdirectory opt
-- Found ZLIB header: /usr/local/include/zlib.h
-- Found ZLIB library: /usr/local/lib/libz.so
-- gzip compression supported
-- Found BZIP2 header: /usr/include/bzlib.h
-- Found BZIP2 library: /usr/lib64/libbz2.so
-- bzip2 compression supported
-- Found PTHREAD header: /usr/include/pthread.h
-- Found PTHREAD library: /usr/lib64/libpthread.so
-- pthread supported
-- using compiler: gcc version 4.1.2
-- Adding the c++ library subdirectory: blt_util
-- Adding the c++ library subdirectory: blt_common
-- Adding the c++ library subdirectory: blt
-- Adding the c++ library subdirectory: starling
-- Adding the c++ library subdirectory: common
-- Adding the c++ library subdirectory: io
-- Adding the c++ library subdirectory: alignment
-- Adding the c++ library subdirectory: basecalling
-- Adding the c++ library subdirectory: assembly
-- Adding the c++ library subdirectory: variance
-- Adding the c++ library subdirectory: applications
-- Adding the c++ library subdirectory: demultiplex
-- Adding the c++ library subdirectory: statistics
-- Adding the c++ library subdirectory: SamMD
-- Adding the c++ library subdirectory: SamMD2Export
-- Adding the c++ library subdirectory: eland_ms
-- Adding the c++ library subdirectory: kagu
-- Adding the c++ library subdirectory: smallRna
-- Adding the c++ program subdirectory: bin
-- Adding the c++ program subdirectory: Alignment
-- Adding the c++ program subdirectory: BaseCalls
-- Adding the c++ program subdirectory: PostAlignment
-- Adding the c++ program subdirectory: Demultiplex
-- Adding the c++ program subdirectory: SmallRna
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Doxygen: DOXYGEN_EXECUTABLE-NOTFOUND. Dot: DOXYGEN_DOT_EXECUTABLE-NOTFOUND.
-- Adding the verifyBoost dynamic link binary checker: verifyBoost
-- Found PTHREAD header: /usr/include/pthread.h
-- Found PTHREAD library: /usr/lib64/libpthread.so
-- pthread supported
-- Configuring done
-- Generating done
-- Build files have been written to: /hd4/app/miseq/CASAVA_v1.8.2_Build
The build directory /hd4/app/miseq/CASAVA_v1.8.2_Build was configured successfully

Type make at the top level of the root directory to build CASAVA
==================================================

However, when I make, it has the error messages:
==================================================

Scanning dependencies of target CASAVA_CODE_MIN
[ 0%] Extracting the CodeMin headers and examples
[ 1%] Built target CASAVA_CODE_MIN
[ 1%] Built target CASAVA_SAMTOOLS
[ 1%] Building illumina_samtools_extensions
/hd4/app/miseq/CASAVA_v1.8.2_Build/opt/samtools-0.1.8/libbam.a(bam_import.o): In function `__bam_get_lines':
/hd4/app/miseq/CASAVA_v1.8.2_Build/opt/samtools-0.1.8/bam_import.c:76: undefined reference to `gzopen64'
/hd4/app/miseq/CASAVA_v1.8.2_Build/opt/samtools-0.1.8/libbam.a(bam_import.o): In function `sam_open':
/hd4/app/miseq/CASAVA_v1.8.2_Build/opt/samtools-0.1.8/bam_import.c:442: undefined reference to `gzopen64'
/hd4/app/miseq/CASAVA_v1.8.2_Build/opt/samtools-0.1.8/libbam.a(bam_import.o): In function `sam_header_read2':
/hd4/app/miseq/CASAVA_v1.8.2_Build/opt/samtools-0.1.8/bam_import.c:126: undefined reference to `gzopen64'
collect2: ld 返回 1
make[3]: *** [bam_cat] 错误 1
make[2]: *** [opt/CMakeFiles/CASAVA_ILMNSAMTOOLS] 错误 2
make[1]: *** [opt/CMakeFiles/CASAVA_ILMNSAMTOOLS.dir/all] 错误 2
make: *** [all] 错误 2
=======================================================

Thanks in advance!
Jessie

[oliviera]

Hi Jessie,
In your case I also find the error Doxygen not found. Not sure what it is but the compilation fail probably because of this error. Install Doxygen first on your system and then compile again. http://www.stack.nl/~dimitri/doxygen/download.html

Cheers

[tahamasoodi]

You need to install all the prerequisites as mentioned in the user guide before installing CASAVA.

[argyjbao]

Thank you, oliviera and tahamasoodi,
I am sorry for the late report. I installed CASAVA 1.8 successfully.
At first, I installed Doxygen and other packages, then you need make some changes when making CASAVA:

1. in CASAVA build directory, change the options in file /opt/samtools-0.1.8/Makefile:
option in LIBCURSES: -lcurses -> -lncurses (because ncurse was installed);
option in CFLAGS: add "-fPIC -L/usr/local/lib";
2. in CASAVA source directory, CASAVA_v1.8.2/redist/illumina_samtools_extensions-1.0.0.tar.gz, edit the file "makefile" by adding "-fPIC -L/usr/local/lib" in CFLAGS;
3. in CASAVA build directory, edit the file CASAVA_v1.8.2_Build/c++/bin/CMakeFiles/CASAVA.dir/flags.make by adding "-fPIC -L/usr/local/lib" in CXX_FLAGS.

Then the installation should be OK!

[JdeBruin]

I do hope someone can help me with this I am trying to install Casava 1.8.2 on a Red Hat Server. I have installed all the requirements as stated in the guide.

I get the following error:

[root@manager CASAVA_v1.8.2-build]# make
[ 0%] Building the SAM/BAM library and tools
bam_tview.c:418:2: warning: #warning "No curses library is available; tview is disabled."
libbam.a(bam_import.o): In function `__bam_get_lines':
/root/apps/tmp/CASAVA_v1.8.2-build/opt/samtools-0.1.8/bam_import.c:76: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `sam_open':
/root/apps/tmp/CASAVA_v1.8.2-build/opt/samtools-0.1.8/bam_import.c:442: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `sam_header_read2':
/root/apps/tmp/CASAVA_v1.8.2-build/opt/samtools-0.1.8/bam_import.c:126: undefined reference to `gzopen64'
collect2: ld returned 1 exit status
make[3]: *** [samtools] Error 1
make[2]: *** [opt/samtools-0.1.8/libbam.a] Error 2
make[1]: *** [opt/CMakeFiles/CASAVA_SAMTOOLS.dir/all] Error 2
make: *** [all] Error 2

after which I done the following as suggested:

1. in CASAVA build directory, change the options in file /opt/samtools-0.1.8/Makefile:
option in LIBCURSES: -lcurses -> -lncurses (because ncurse was installed);
option in CFLAGS: add "-fPIC -L/usr/local/lib";
2. in CASAVA source directory, CASAVA_v1.8.2/redist/illumina_samtools_extensions-1.0.0.tar.gz, edit the file "makefile" by adding "-fPIC -L/usr/local/lib" in CFLAGS;
3. in CASAVA build directory, edit the file CASAVA_v1.8.2_Build/c++/bin/CMakeFiles/CASAVA.dir/flags.make by adding "-fPIC -L/usr/local/lib" in CXX_FLAGS.

I am still getting the same error.

I believe this is a zlib issue so this is my zlib install installed with rpm:

[root@manager CASAVA_v1.8.2-build]# rpm -qi zlib
Name : zlib Relocations: (not relocatable)
Version : 1.2.3 Vendor: Red Hat, Inc.
Release : 27.el6 Build Date: Wed Aug 10 10:38:10 2011
Install Date: Thu Aug 2 08:33:41 2012 Build Host: x86-001.build.bos.redhat.com
Group : System Environment/Libraries Source RPM: zlib-1.2.3-27.el6.src.rpm
Size : 152225 License: zlib and Boost
Signature : RSA/8, Mon Sep 26 08:44:23 2011, Key ID 199e2f91fd431d51
Packager : Red Hat, Inc. <http://bugzilla.redhat.com/bugzilla>
URL : http://www.gzip.org/zlib/
Summary : The zlib compression and decompression library
Description :
Zlib is a general-purpose, patent-free, lossless data compression
library which is used by many different programs.
Name : zlib Relocations: (not relocatable)
Version : 1.2.3 Vendor: Red Hat, Inc.
Release : 27.el6 Build Date: Wed Aug 10 10:38:10 2011
Install Date: Fri Feb 8 09:03:08 2013 Build Host: x86-007.build.bos.redhat.com
Group : System Environment/Libraries Source RPM: zlib-1.2.3-27.el6.src.rpm
Size : 139037 License: zlib and Boost
Signature : RSA/8, Mon Sep 26 08:44:28 2011, Key ID 199e2f91fd431d51
Packager : Red Hat, Inc. <http://bugzilla.redhat.com/bugzilla>
URL : http://www.gzip.org/zlib/
Summary : The zlib compression and decompression library


Any help would be wonderfull!!

[GenoMax]

Have you copied the "libbam.a" into /usr/local/lib or set LD_LIBRARY_PATH ro include the location of that file?

This appears to be a RHEL 6.x system.