NITRC: BXH/XCEDE Tools: help

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help > running on NITRC-CE

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running on NITRC-CE

I'm having a heckuva time getting executables running on a NITRC-CE:

$ ./bxh_xcede_tools-1.10.7-lsb30.x86_64/bin/dicom2bxh
-bash: ./bxh_xcede_tools-1.10.7-lsb30.x86_64/bin/dicom2bxh: No such file or directory

$ ./bxh_xcede_tools-1.10.7-lsb31.i386/bin/dicom2bxh
-bash: ./bxh_xcede_tools-1.10.7-lsb31.i386/bin/dicom2bxh: No such file or directory

The executables certainly exist:

$ ls -l ./bxh_xcede_tools-1.10.7-lsb30.x86_64/bin/dicom2bxh
lrwxrwxrwx 1 ch ch 9 Jan 11 2013 ./bxh_xcede_tools-1.10.7-lsb30.x86_64/bin/dicom2bxh -> bxhabsorb

$ ls -l ./bxh_xcede_tools-1.10.7-lsb30.x86_64/bin/bxhabsorb
-rwxr-xr-x 1 ch ch 3187976 Jan 11 2013 ./bxh_xcede_tools-1.10.7-lsb30.x86_64/bin/bxhabsorb

and all the libraries are there:

$ ldd ./bxh_xcede_tools-1.10.7-lsb30.x86_64/bin/dicom2bxh
linux-vdso.so.1 => (0x00007fff423ef000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f86fdb42000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f86fd92b000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f86fd70d000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f86fd509000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f86fd209000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f86fcff2000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f86fcc33000)
/lib64/ld-lsb-x86-64.so.3 => /lib64/ld-linux-x86-64.so.2 (0x00007f86fde65000)

The machine is 64-bit:

$ uname -a
Linux nitrcce 3.2.0-49-virtual #75-Ubuntu SMP Tue Jun 18 17:59:38 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

so I installed ia32-libs, but I get the same problem.

So I downloaded the source and am trying to compile (tags/RELEASE_1_10_9). After some library and header wrangling, I end up with the following, which looks like a code issue rather than a supporting libraries/files issue:

g++ -c -o bxh_dicom.o -DXMLH_VERSIONSTR="\"BXH utilities (1.10.9)\"" -I. -g -O2 -pthread -I/usr/include/libxml2 -I/usr/include/libxml2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libxml2 -I/usr/include/libgdome -I/usr/include/dcmtk/dcmdata -I/usr/include/dcmtk/ofstd -I/usr/include/dcmtk/config -I. -DBIAC=1 -DHAVE_CONFIG_H ./bxh_dicom.cpp
In file included from ./bxh_dicom.cpp:44:0:
./dcistrmfb.h:234:18: error: conflicting return type specified for ‘virtual Uint32 DcmInputFileBufferedStream::tell() const’
/usr/include/dcmtk/dcmdata/dcistrma.h:196:24: error: overriding ‘virtual offile_off_t DcmInputStream::tell() const’
./dcistrmfb.h:245:27: error: cannot declare field ‘DcmInputFileBufferedStream::producer_’ to be of abstract type ‘DcmFileBufferedProducer’
./dcistrmfb.h:48:7: note: because the following virtual functions are pure within ‘DcmFileBufferedProducer’:
/usr/include/dcmtk/dcmdata/dcistrma.h:67:18: note: virtual bool DcmProducer::eos()
/usr/include/dcmtk/dcmdata/dcistrma.h:76:24: note: virtual offile_off_t DcmProducer::avail()
/usr/include/dcmtk/dcmdata/dcistrma.h:83:24: note: virtual offile_off_t DcmProducer::read(void*, offile_off_t)
/usr/include/dcmtk/dcmdata/dcistrma.h:89:24: note: virtual offile_off_t DcmProducer::skip(offile_off_t)
/usr/include/dcmtk/dcmdata/dcistrma.h:95:16: note: virtual void DcmProducer::putback(offile_off_t)
./bxh_dicom.cpp: In function ‘int bxh_DICOM_readFilesStart(BXHDocPtr, int, const char**, int, int, const char*, int, int, void**)’:
./bxh_dicom.cpp:1056:16: error: ‘class DcmObject’ has no member named ‘error’
./bxh_dicom.cpp: In function ‘int bxh_DICOM_readFilesCont(BXHDocPtr, const char*, void**)’:
./bxh_dicom.cpp:2047:4: error: ‘DCM_ManufacturersModelName’ was not declared in this scope
./bxh_dicom.cpp:2082:4: error: ‘DCM_AcquisitionDatetime’ was not declared in this scope
./bxh_dicom.cpp:2102:4: error: ‘DCM_LargestMonochromePixelValue’ was not declared in this scope
./bxh_dicom.cpp:2677:16: error: ‘class DcmObject’ has no member named ‘error’
./bxh_dicom.cpp:2679:78: error: ‘class DcmDataset’ has no member named ‘error’
./bxh_dicom.cpp:2981:130: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat]
./bxh_dicom.cpp:3072:197: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat]
make[1]: *** [bxh_dicom.o] Error 1
make[1]: Leaving directory `/home/ch/build/bxh_xcede_tools/tags/RELEASE_1_10_9/bxh_xcede_tools/libsrc'
make: *** [libsrc] Error 2

So I'm at a loss on both approaches. Any suggestions?

Thanks,
c

running on NITRC-CE

I'll try this out myself on NITRC-CE and see if I can figure it out...

running on NITRC-CE

I believe the solution is to install the lsb-core package:

apt-get install lsb-core

but that doesn't seem to work on my NITRC-CE instance because it can't
find the dependencies. Are the repositories on the NITRC-CE instance set
up correctly?

RE: running on NITRC-CE

That did the trick for me, thanks! (Have you considered packaging bxh_xcede_tools for NeuroDebian?)

So what's the error you get when you try to install lsb-core?

RE: running on NITRC-CE

I will look into neurodebian!

Here is the error message:

gadde@nitrcce:~$ sudo apt-get install lsb-core
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
lsb-core : Depends: libc6-i386 but it is not going to be installed
Depends: lib32z1 but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

RE: running on NITRC-CE

Thanks -- an apt-get update should fix that (if you're doing more than just helping me solve my problem :) ).

Thanks, Syam!