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Illumina / isaac2

Aligner for sequencing data
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Compile error #1

Closed mwaldron104 closed 9 years ago

mwaldron104 commented 9 years ago

I am getting the following error when running the make command after running configure: $ make Scanning dependencies of target iSAAC_OPT [ 0%] Built target iSAAC_OPT Scanning dependencies of target isaac_bgzf [ 1%] Building CXX object c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/BgzfReader.cpp.o Linking CXX static library libisaac_bgzf.a [ 1%] Built target isaac_bgzf Scanning dependencies of target isaac_common [ 2%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/Debug.cpp.o [ 3%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/Exceptions.cpp.o [ 4%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/FileSystem.cpp.o [ 4%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/MD5Sum.cpp.o [ 5%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/Process.cpp.o [ 6%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/Program.cpp.o [ 7%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/SystemCompatibility.cpp.o /nas02/apps/isaac2-15.07.14/src/isaac2/src/c++/lib/common/SystemCompatibility.cpp: In function 'int isaac::common::linuxFallocate(int, std::size_t, std::size_t)': /nas02/apps/isaac2-15.07.14/src/isaac2/src/c++/lib/common/SystemCompatibility.cpp:162:58: error: 'fallocate' was not declared in this scope return fallocate(fd, FALLOC_FL_KEEP_SIZE, offset, len); ^ /nas02/apps/isaac2-15.07.14/src/isaac2/src/c++/lib/common/SystemCompatibility.cpp:163:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ make[2]: * [c++/lib/common/CMakeFiles/isaac_common.dir/SystemCompatibility.cpp.o] Error 1 make[1]: * [c++/lib/common/CMakeFiles/isaac_common.dir/all] Error 2 make: *\ [all] Error 2

rpetrovski commented 9 years ago

Which operating system and OS version are you trying to use?

mwaldron104 commented 9 years ago

The OS is RedHat Enterprise Linux 5.11.

I am using GCC-4.8.1 compiler.

Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill

From: rpetrovski [notifications@github.com] Sent: Wednesday, July 15, 2015 3:58 PM To: Illumina/isaac2 Cc: Waldron, Michael H Subject: Re: [isaac2] Compile error (#1)

Which operating system and OS version are you trying to use?

— Reply to this email directly or view it on GitHubhttps://github.com/Illumina/isaac2/issues/1#issuecomment-121728256.

rpetrovski commented 9 years ago

It will take some time before I can try it on rhel box. As a quick check, can you please put

include

between lines 154 and 155 of SystemCompatibility.cpp and tell me if it helped.

Roman.

mwaldron104 commented 9 years ago

I added #include between lines 154 and 155 such that it now looks like:

Before: 153 #ifdef HAVE_LINUX_FALLOC_H 154 #include <linux/falloc.h> 155 #else // #ifdef HAVE_LINUX_FALLOC_H 156 #error The header <linux/falloc.h> is required. 157 #endif // #ifdef HAVE_LINUX_FALLOC_H

After: 153 #ifdef HAVE_LINUX_FALLOC_H 154 #include <linux/falloc.h> 155 #include 156 #else // #ifdef HAVE_LINUX_FALLOC_H 157 #error The header <linux/falloc.h> is required. 158 #endif // #ifdef HAVE_LINUX_FALLOC_H

But I get the error:

[ 2%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/SystemCompatibility.cpp.o /nas02/apps/isaac2-15.07.14/src/isaac2/src/c++/lib/common/SystemCompatibility.cpp:155:9: error: #include expects "FILENAME" or

include

     ^

/nas02/apps/isaac2-15.07.14/src/isaac2/src/c++/lib/common/SystemCompatibility.cpp: In function 'int isaac::common::linuxFallocate(int, std::size_t, std::size_t)': /nas02/apps/isaac2-15.07.14/src/isaac2/src/c++/lib/common/SystemCompatibility.cpp:163:58: error: 'fallocate' was not declared in this scope return fallocate(fd, FALLOC_FL_KEEP_SIZE, offset, len); ^ /nas02/apps/isaac2-15.07.14/src/isaac2/src/c++/lib/common/SystemCompatibility.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ make[2]: * [c++/lib/common/CMakeFiles/isaac_common.dir/SystemCompatibility.cpp.o] Error 1 make[1]: * [c++/lib/common/CMakeFiles/isaac_common.dir/all] Error 2 make: *\ [all] Error 2

Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill

From: rpetrovski [notifications@github.com] Sent: Wednesday, July 15, 2015 4:59 PM To: Illumina/isaac2 Cc: Waldron, Michael H Subject: Re: [isaac2] Compile error (#1)

It will take some time before I can try it on rhel box. As a quick check, can you please put

include

between lines 154 and 155 of SystemCompatibility.cpp and tell me if it helped.

Roman.

— Reply to this email directly or view it on GitHubhttps://github.com/Illumina/isaac2/issues/1#issuecomment-121745772.

rpetrovski commented 9 years ago

Yeah, I meant #include but the github lost the file bit.

I've got the problem reproduced on CentOS 5.4. Turns out fallocate is not available in CentOS (and I guess RHEL) 5. I'm going to commit code that uses posix_fallocate instead shortly.

Roman.

rpetrovski commented 9 years ago

Just pushed the fix. Please let me know if you have any further issues.

Roman.

mwaldron104 commented 9 years ago

Successfully compiled. Thanks for the quick fix.

Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill

From: rpetrovski [notifications@github.com] Sent: Thursday, July 16, 2015 8:43 AM To: Illumina/isaac2 Cc: Waldron, Michael H Subject: Re: [isaac2] Compile error (#1)

Just pushed the fix. Please let me know if you have any further issues.

Roman.

— Reply to this email directly or view it on GitHubhttps://github.com/Illumina/isaac2/issues/1#issuecomment-121946425.

kvshams commented 8 years ago

I am using Red Hat 4.4.5-6 version (Linux version 2.6.32-220.el6.x86_64) I am getting the similar compiling error with the version (iSAAC-02.15.10.21)

make[2]: * [c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/BgzfReader.cpp.o] Error 1 make[1]: * [c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/all] Error 2 make: *\ [all] Error 2

rpetrovski commented 8 years ago

This is a different error. Please create a separate ticket and post more details for the compilation failure.

Roman.

kvshams commented 8 years ago

I have already made a new ticket but I did not get any responds yet

Thanks Shams