MIT-LCP / MIT-LCP/physionet

HRV Make Install error

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Description

Hello,

I am trying to install HRV on an HPC cluster using centos7.

make install error:

$  make install
cc -O -o rrlist rrlist.c -lwfdb
rrlist.c:25:23: fatal error: wfdb/wfdb.h: No such file or directory
 #include <wfdb/wfdb.h>
                       ^
compilation terminated.
make: *** [rrlist] Error 1

The path I have it installing to is: /opt/ohpc/pub/apps/HRV/test

After editing this path in the Makefile I run make install.
Makefile:

#                                       Last revised:   Aug 4 2009 (by GBM)
# 'make' description file for the HRV Toolkit

# The WFDB library must be installed before the HRV Toolkit can be compiled.
# Get the WFDB software from http://physionet.org/physiotools/wfdb.shtml .

# The HRV Toolkit will be installed in BINDIR (by default, /usr/bin). If you
# change it, make sure that your PATH includes BINDIR.
BINDIR=/opt/ohpc/pub/apps/HRV/test

# These scripts need a POSIX shell (e.g., sh or bash) in order to run.
SCRIPTS = get_hrv plt_rrs

# These binaries are compiled by 'make all'.
ALL = filt filtnn hours pwr rrlist seconds statnn

# 'make install' copies the HRV toolkit's scripts and binaries to BINDIR.
install:        all
        cp -p $(SCRIPTS) $(ALL) $(BINDIR)

all:            $(ALL)

# 'make bin-tarball' creates a tarball of binaries.
bin-tarball:    all
        mkdir HRV
        cp -p $(SCRIPTS) $(ALL) Usages HRV
        tar cfvz HRV-`arch`-`uname`.tar.gz HRV
        rm -rf HRV

# 'make clean' removes old copies of the executables.
clean:
        rm -f $(ALL)

filt :          filt.c
        $(CC) -O -o $@ filt.c

filtnn :        filtnn.c
        $(CC) -O -o $@ filtnn.c

hours :         hours.c
        $(CC) -O -o $@ hours.c

pwr :           pwr.c
        $(CC) -O -o $@ pwr.c

rrlist :        rrlist.c
        $(CC) -O -o $@ rrlist.c -lwfdb

seconds :       seconds.c
        $(CC) -O -o $@ seconds.c

statnn :        statnn.c
        $(CC) -O -o $@ statnn.c -lm

Loaded modules

Currently Loaded Modules:
  1) autotools   2) prun/1.3   3) gnu8/8.3.0   4) openmpi3/3.1.4   5) ohpc   6) plt/2.5a   7) expat-2.2.9-gcc-10.2.0-jnq5tcr   8) wfdb/10.6.2

Paths:

echo $PATH
/opt/ohpc/pub/apps/wfdb/10.6.2/bin:/opt/ohpc/pub/apps/wfdb/10.6.2/lib:/opt/ohpc/pub/apps/wfdb/10.6.2:/opt/ohpc/pub/spack/opt/spack/linux-centos7-sandybridge/gcc-10.2.0/expat-2.2.9-jnq5tcra4f2nxcegt6l4hhcqffnlah6l/bin:/opt/ohpc/pub/apps/plt/2.5a/bin:/opt/ohpc/pub/apps/plt/2.5a:/opt/ohpc/pub/spack/bin:/opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/bin:/opt/ohpc/pub/compiler/gcc/8.3.0/bin:/opt/ohpc/pub/utils/prun/1.3:/opt/ohpc/pub/utils/autotools/bin:/opt/ohpc/pub/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/user/.local/bin:/home/user/bin
$ echo $LD_LIBRARY_PATH
/opt/ohpc/pub/apps/wfdb/10.6.2/lib/
$ echo $INCLUDE
/opt/ohpc/pub/apps/wfdb/10.6.2/include/

Module file for wfdb

cat 10.6.2 
#%Module1.0#######################################################################
## cmgui modulefile
##
proc ModulesHelp { } {

        puts stderr "\tAdds WFDB to Koko"
}

module-whatis   "Adds WFDB to Koko."

set              application       wfdb/10.6.2
set              root              /opt/ohpc/pub/apps/$application

setenv     LD_LIBRARY_PATH   /opt/ohpc/pub/apps/wfdb/10.6.2/lib/
#setenv     LD_LIBRARY_PATH   $root/lib/libwfdb.so.10
#setenv     LIBRARY_PATH   $root/lib/libwfdb.so.10
setenv     INCLUDE   /opt/ohpc/pub/apps/wfdb/10.6.2/include/



#prepend-path      INCLUDE           /opt/ohpc/pub/apps/wfdb/10.6.2/include/wfdb/
prepend-path      PATH              $root
prepend-path      PATH              $root/lib
prepend-path      PATH              $root/bin
#prepend-path      PATH              /opt/ohpc/pub/apps/wfdb/10.6.2/include/

wfdb.h is here:

ls /opt/ohpc/pub/apps/wfdb/10.6.2/include/wfdb/
ecgcodes.h  ecgmap.h  wfdbf.c  wfdb.h  wfdblib.h

Please help, thanks!

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the Makefile's rrlist target and the installed wfdb.h path shown under /opt/ohpc/pub/apps/wfdb/10.6.2/include/wfdb/. Check how the compiler is expected to locate that header when running make install on CentOS 7. Done means the toolkit builds and make install copies the listed scripts and binaries into BINDIR.

Written by the indexing model from the issue text.

Assessment

Tech stack
c, centos
Domain
build-system, operating-systems
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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