including WFDB Matlab toolbox to the entry

[joachim...@gmail.com]

I am adding the mcode of the WFDB toolbox for matlab. I am calling gqrs and wqrs from my code.

When running a DRYRUN I get the following error

	Academic License

Generated *.dat file: A00001_gqrs
Generated *.hea file: A00001_gqrs
error executing: wfdb-config
java.io.IOException: Cannot run program "/home/vmuser/mcode/nativelibs/linux/bin/wfdb-config": error=13, Permission denied
	at java.lang.ProcessBuilder.start(Unknown Source)
	at org.physionet.wfdb.Wfdbexec.execToStringList(Unknown Source)
	at org.physionet.wfdb.Wfdbexec.execToStringList(Unknown Source)
Caused by: java.io.IOException: error=13, Permission denied
	at java.lang.UNIXProcess.forkAndExec(Native Method)
	at java.lang.UNIXProcess.<init>(Unknown Source)
	at java.lang.ProcessImpl.start(Unknown Source)
	... 3 more
error executing: gqrs
java.io.IOException: Cannot run program "/home/vmuser/mcode/nativelibs/linux/bin/gqrs": error=13, Permission denied
	at java.lang.ProcessBuilder.start(Unknown Source)
	at org.physionet.wfdb.Wfdbexec.execToStringList(Unknown Source)
	at org.physionet.wfdb.Wfdbexec.execToStringList(Unknown Source)
Caused by: java.io.IOException: error=13, Permission denied
	at java.lang.UNIXProcess.forkAndExec(Native Method)
	at java.lang.UNIXProcess.<init>(Unknown Source)
	at java.lang.ProcessImpl.start(Unknown Source)
	... 3 more
Struct contents reference from a non-struct array object.

Error in gqrs (line 123)
if(~isempty(strfind(err.toString,['annopen: can''t'])))

Error in challenge (line 85)
    gqrs([name '_gqrs']);

[Tomás Teijeiro Campo]

The reason is probably that the files in the 'bin' directory do not have execution permission. Try to include the next line in the 'setup.sh' script:

chmod a+x mcode/nativelibs/linux/bin/*

Regards,

Tomás

[joachim...@gmail.com]

Thanks Tomas,

That worked!

I just want to check with one of the challenge organisers (is someone read this post) that the "Possibly proprietary files" listed below are ok? There are part of the mcode from WFDB but since the server is throwing me this warning I prefer to check..

Thanks,

Joachim

---------------

Warning:

  One or more of the files submitted as part of this entry do not

  appear to have free/open-source licenses.  PhysioNet Challenge

  entries must consist entirely of free and open source software; if

  your entry is found to contain proprietary files, it will be

  disqualified from winning challenge awards.

  (This is an automated message based on the presence of certain key

  words in your entry's source code.  If these files are in fact

  freely licensed, feel free to ignore this message.  There is no need

  to re-submit your entry.)

  Possibly proprietary files (4):

mcode/nativelibs/windows/bin/curl-config

mcode/nativelibs/linux/bin/curl-config

mcode/nativelibs/linux/lib/pkgconfig/libcurl.pc

mcode/nativelibs/macosx/bin/curl-config

  Unknown binary files (389):

(wfdb-app-JVM7-0-9-9.jar) org/physionet/wfdb/Wfdbexec.class

(wfdb-app-JVM7-0-9-9.jar) org/physionet/wfdb/Score2013.class

(wfdb-app-JVM7-0-9-9.jar) org/physionet/wfdb/OutputReader.class

(wfdb-app-JVM7-0-9-9.jar) org/physionet/wfdb/concurrent/MapRecord.class

(wfdb-app-JVM7-0-9-9.jar) org/physionet/wfdb/concurrent/ConcurrentWfdbexec.class

(wfdb-app-JVM7-0-9-9.jar) org/physionet/wfdb/SystemSettings.class

(wfdb-app-JVM7-0-9-9.jar) org/physionet/wfdb/physiobank/PhysioNetDB.class

(wfdb-app-JVM7-0-9-9.jar) org/physionet/wfdb/physiobank/PhysioNetSignal.class

(wfdb-app-JVM7-0-9-9.jar) org/physionet/wfdb/physiobank/PhysioNetDB$1.class

(wfdb-app-JVM7-0-9-9.jar) org/physionet/wfdb/physiobank/PhysioNetRecord.class

(wfdb-app-JVM7-0-9-9.jar) org/physionet/wfdb/InputWriter.class

mcode/example/a01.fqrs

mcode/example/a01.dat

mcode/example/f1o02.ecg

mcode/example/100s.atr

mcode/example/100s.dat

mcode/example/a01.entry1

mcode/example/f1o02.dat

mcode/database/pipe/16x1.pipe/16x1

mcode/database/pipe/16x1.edr

mcode/database/pipe/16x1.wqrs

mcode/database/a01.fqrs

mcode/database/a01.dat

mcode/database/100a.atr

mcode/database/100s.atr

mcode/database/100s.dat

mcode/database/a01.entry1

mcode/nativelibs/windows/bin/makeid.exe

mcode/nativelibs/windows/bin/ann2rr.exe

mcode/nativelibs/windows/bin/fft.exe

mcode/nativelibs/windows/bin/libwfdb.dll.a

mcode/nativelibs/windows/bin/sumann.exe

mcode/nativelibs/windows/bin/stepdet.exe

mcode/nativelibs/windows/bin/sigamp.exe

mcode/nativelibs/windows/bin/memse.exe

mcode/nativelibs/windows/bin/wabp.exe

mcode/nativelibs/windows/bin/hrstats.exe

mcode/nativelibs/windows/bin/pscgen.exe

mcode/nativelibs/windows/bin/sigavg.exe

mcode/nativelibs/windows/bin/epicmp.exe

mcode/nativelibs/windows/bin/m2a.exe

mcode/nativelibs/windows/bin/mit2wav.exe

mcode/nativelibs/windows/bin/sampfreq.exe

mcode/nativelibs/windows/bin/mxm.exe

mcode/nativelibs/windows/bin/sortann.exe

mcode/nativelibs/windows/bin/pschart.exe

mcode/nativelibs/windows/bin/a2m.exe

mcode/nativelibs/windows/bin/fir.exe

mcode/nativelibs/windows/bin/rdann.exe

mcode/nativelibs/windows/bin/calsig.exe

mcode/nativelibs/windows/bin/libcurl-4.dll

mcode/nativelibs/windows/bin/edr.exe

mcode/nativelibs/windows/bin/wfdbmap.exe

mcode/nativelibs/windows/bin/libquadmath-0.dll

mcode/nativelibs/windows/bin/wrsamp.exe

mcode/nativelibs/windows/bin/libgcc_s_dw2-1.dll

mcode/nativelibs/windows/bin/gqfuse.exe

mcode/nativelibs/windows/bin/libgfortran-3.dll

mcode/nativelibs/windows/bin/wfdbwhich.exe

mcode/nativelibs/windows/bin/sqrs125.exe

mcode/nativelibs/windows/bin/gqrs.exe

mcode/nativelibs/windows/bin/mit2edf.exe

mcode/nativelibs/windows/bin/sqrs.exe

mcode/nativelibs/windows/bin/ihr.exe

mcode/nativelibs/windows/bin/md2a.exe

mcode/nativelibs/windows/bin/mfilt.exe

mcode/nativelibs/windows/bin/time2sec.exe

mcode/nativelibs/windows/bin/signum.exe

mcode/nativelibs/windows/bin/libwfdb.dll.a.10.5

mcode/nativelibs/windows/bin/rdedfann.exe

mcode/nativelibs/windows/bin/sumstats.exe

mcode/nativelibs/windows/bin/dfa.exe

mcode/nativelibs/windows/bin/log10.exe

mcode/nativelibs/windows/bin/parsescp.exe

mcode/nativelibs/windows/bin/wqrs.exe

mcode/nativelibs/windows/bin/rr2ann.exe

mcode/nativelibs/windows/bin/bxb.exe

mcode/nativelibs/windows/bin/wfdbdesc.exe

mcode/nativelibs/windows/bin/wfdbcollate.exe

mcode/nativelibs/windows/bin/mrgann.exe

mcode/nativelibs/windows/bin/mse.exe

mcode/nativelibs/windows/bin/signame.exe

mcode/nativelibs/windows/bin/rdsamp.exe

mcode/nativelibs/windows/bin/wfdb-10.5.dll

mcode/nativelibs/windows/bin/coherence.exe

mcode/nativelibs/windows/bin/revise.exe

mcode/nativelibs/windows/bin/edf2mit.exe

mcode/nativelibs/windows/bin/ad2m.exe

mcode/nativelibs/windows/bin/readid.exe

mcode/nativelibs/windows/bin/rxr.exe

mcode/nativelibs/windows/bin/plotstm.exe

mcode/nativelibs/windows/bin/gqpost.exe

mcode/nativelibs/windows/bin/nguess.exe

mcode/nativelibs/windows/bin/ahaecg2mit.exe

mcode/nativelibs/windows/bin/nst.exe

mcode/nativelibs/windows/bin/curl.exe

mcode/nativelibs/windows/bin/visbility.exe

mcode/nativelibs/windows/bin/libwfdb.dll.a.10

mcode/nativelibs/windows/bin/ecgeval.exe

mcode/nativelibs/windows/bin/ecgpuwave.exe

mcode/nativelibs/windows/bin/tach.exe

mcode/nativelibs/windows/bin/wfdbcat.exe

mcode/nativelibs/windows/bin/wfdb-config.exe

mcode/nativelibs/windows/bin/xform.exe

mcode/nativelibs/windows/bin/corrint.exe

mcode/nativelibs/windows/bin/wfdbtime.exe

mcode/nativelibs/windows/bin/wav2mit.exe

mcode/nativelibs/windows/bin/wfdb2mat.exe

mcode/nativelibs/windows/bin/wrann.exe

mcode/nativelibs/windows/bin/wfdbsignals.exe

mcode/nativelibs/windows/bin/psfd.exe

mcode/nativelibs/windows/bin/lomb.exe

mcode/nativelibs/windows/bin/snip.exe

mcode/nativelibs/windows/bin/skewedit.exe

mcode/nativelibs/windows/lib/libquadmath-0.dll

mcode/nativelibs/windows/lib/libgcc_s_dw2-1.dll

mcode/nativelibs/windows/lib/libgfortran-3.dll

mcode/nativelibs/windows/lib/libcurl.dll.a

mcode/nativelibs/windows/database/100a.atr

mcode/nativelibs/windows/database/100s.atr

mcode/nativelibs/windows/database/100s.dat

mcode/nativelibs/linux/bin/mrgann

mcode/nativelibs/linux/bin/edr

mcode/nativelibs/linux/bin/psfd

mcode/nativelibs/linux/bin/ecgeval

mcode/nativelibs/linux/bin/mit2edf

mcode/nativelibs/linux/bin/memse

mcode/nativelibs/linux/bin/wfdbtime

mcode/nativelibs/linux/bin/mfilt

mcode/nativelibs/linux/bin/signum

mcode/nativelibs/linux/bin/ahaecg2mit

mcode/nativelibs/linux/bin/xform

mcode/nativelibs/linux/bin/signame

mcode/nativelibs/linux/bin/revise

mcode/nativelibs/linux/bin/wfdbcollate

mcode/nativelibs/linux/bin/bxb

mcode/nativelibs/linux/bin/mit2wav

mcode/nativelibs/linux/bin/ecgpuwave

mcode/nativelibs/linux/bin/hrstats

mcode/nativelibs/linux/bin/sqrs125

mcode/nativelibs/linux/bin/wabp

mcode/nativelibs/linux/bin/ad2m

mcode/nativelibs/linux/bin/md2a

mcode/nativelibs/linux/bin/nguess

mcode/nativelibs/linux/bin/m2a

mcode/nativelibs/linux/bin/sigavg

mcode/nativelibs/linux/bin/visbility

mcode/nativelibs/linux/bin/skewedit

mcode/nativelibs/linux/bin/wrsamp

mcode/nativelibs/linux/bin/heaxml

mcode/nativelibs/linux/bin/a2m

mcode/nativelibs/linux/bin/sortann

mcode/nativelibs/linux/bin/sumstats

mcode/nativelibs/linux/bin/ann2rr

mcode/nativelibs/linux/bin/pscgen

mcode/nativelibs/linux/bin/gqfuse

mcode/nativelibs/linux/bin/wrann

mcode/nativelibs/linux/bin/wfdb-config

mcode/nativelibs/linux/bin/xmlann

mcode/nativelibs/linux/bin/mse

mcode/nativelibs/linux/bin/xmlhea

mcode/nativelibs/linux/bin/fft

mcode/nativelibs/linux/bin/makeid

mcode/nativelibs/linux/bin/wav2mit

mcode/nativelibs/linux/bin/time2sec

mcode/nativelibs/linux/bin/tach

mcode/nativelibs/linux/bin/sampfreq

mcode/nativelibs/linux/bin/lomb

mcode/nativelibs/linux/bin/pschart

mcode/nativelibs/linux/bin/parsescp

mcode/nativelibs/linux/bin/fir

mcode/nativelibs/linux/bin/curl

mcode/nativelibs/linux/bin/nst

mcode/nativelibs/linux/bin/snip

mcode/nativelibs/linux/bin/stepdet

mcode/nativelibs/linux/bin/wfdbsignals

mcode/nativelibs/linux/bin/readid

mcode/nativelibs/linux/bin/gqrs

mcode/nativelibs/linux/bin/gqpost

mcode/nativelibs/linux/bin/epicmp

mcode/nativelibs/linux/bin/wqrs

mcode/nativelibs/linux/bin/wfdbmap

mcode/nativelibs/linux/bin/wfdb2mat

mcode/nativelibs/linux/bin/mxm

mcode/nativelibs/linux/bin/wfdbwhich

mcode/nativelibs/linux/bin/corrint

mcode/nativelibs/linux/bin/annxml

mcode/nativelibs/linux/bin/rxr

mcode/nativelibs/linux/bin/wfdbcat

mcode/nativelibs/linux/bin/wfdbdesc

mcode/nativelibs/linux/bin/sumann

mcode/nativelibs/linux/bin/rdsamp

mcode/nativelibs/linux/bin/coherence

mcode/nativelibs/linux/bin/edf2mit

mcode/nativelibs/linux/bin/calsig

mcode/nativelibs/linux/bin/rr2ann

mcode/nativelibs/linux/bin/ihr

mcode/nativelibs/linux/bin/rdann

mcode/nativelibs/linux/bin/plotstm

mcode/nativelibs/linux/bin/rdedfann

mcode/nativelibs/linux/bin/dfa

mcode/nativelibs/linux/bin/log10

mcode/nativelibs/linux/bin/sqrs

mcode/nativelibs/linux/bin/sigamp

mcode/nativelibs/linux/lib/libwfdb.so

mcode/nativelibs/linux/lib/libquadmath.so.0

mcode/nativelibs/linux/lib/libwfdb.so.10.5

mcode/nativelibs/linux/lib/libgfortran.so.3

mcode/nativelibs/linux/lib/libwfdb.so.10

mcode/nativelibs/linux/lib64/libwfdb.so.10.5

mcode/nativelibs/linux/lib64/libwfdb.so.10

mcode/nativelibs/macosx/bin/mrgann

mcode/nativelibs/macosx/bin/edr

mcode/nativelibs/macosx/bin/psfd

mcode/nativelibs/macosx/bin/ecgeval

mcode/nativelibs/macosx/bin/mit2edf

mcode/nativelibs/macosx/bin/memse

mcode/nativelibs/macosx/bin/wfdbtime

mcode/nativelibs/macosx/bin/mfilt

mcode/nativelibs/macosx/bin/signum

mcode/nativelibs/macosx/bin/ahaecg2mit

mcode/nativelibs/macosx/bin/xform

mcode/nativelibs/macosx/bin/signame

mcode/nativelibs/macosx/bin/revise

mcode/nativelibs/macosx/bin/wfdbcollate

mcode/nativelibs/macosx/bin/bxb

mcode/nativelibs/macosx/bin/mit2wav

mcode/nativelibs/macosx/bin/patchann

mcode/nativelibs/macosx/bin/ecgpuwave

mcode/nativelibs/macosx/bin/hrstats

mcode/nativelibs/macosx/bin/sqrs125

mcode/nativelibs/macosx/bin/wabp

mcode/nativelibs/macosx/bin/libquadmath.0.dylib

mcode/nativelibs/macosx/bin/libgfortran.dylib

mcode/nativelibs/macosx/bin/ad2m

mcode/nativelibs/macosx/bin/md2a

mcode/nativelibs/macosx/bin/nguess

mcode/nativelibs/macosx/bin/m2a

mcode/nativelibs/macosx/bin/sigavg

mcode/nativelibs/macosx/bin/visbility

mcode/nativelibs/macosx/bin/skewedit

mcode/nativelibs/macosx/bin/wrsamp

mcode/nativelibs/macosx/bin/heaxml

mcode/nativelibs/macosx/bin/a2m

mcode/nativelibs/macosx/bin/sortann

mcode/nativelibs/macosx/bin/sumstats

mcode/nativelibs/macosx/bin/ann2rr

mcode/nativelibs/macosx/bin/pscgen

mcode/nativelibs/macosx/bin/libwfdb.10.5.24.dylib

mcode/nativelibs/macosx/bin/gqfuse

mcode/nativelibs/macosx/bin/wrann

mcode/nativelibs/macosx/bin/wfdb-config

mcode/nativelibs/macosx/bin/libwfdb.10.dylib

mcode/nativelibs/macosx/bin/xmlann

mcode/nativelibs/macosx/bin/mse

mcode/nativelibs/macosx/bin/xmlhea

mcode/nativelibs/macosx/bin/fft

mcode/nativelibs/macosx/bin/makeid

mcode/nativelibs/macosx/bin/wav2mit

mcode/nativelibs/macosx/bin/time2sec

mcode/nativelibs/macosx/bin/libwfdb.dylib

mcode/nativelibs/macosx/bin/tach

mcode/nativelibs/macosx/bin/sampfreq

mcode/nativelibs/macosx/bin/lomb

mcode/nativelibs/macosx/bin/pschart

mcode/nativelibs/macosx/bin/parsescp

mcode/nativelibs/macosx/bin/fir

mcode/nativelibs/macosx/bin/curl

mcode/nativelibs/macosx/bin/nst

mcode/nativelibs/macosx/bin/snip

mcode/nativelibs/macosx/bin/stepdet

mcode/nativelibs/macosx/bin/wfdbsignals

mcode/nativelibs/macosx/bin/readid

mcode/nativelibs/macosx/bin/libcurl.dylib

mcode/nativelibs/macosx/bin/gqrs

mcode/nativelibs/macosx/bin/gqpost

mcode/nativelibs/macosx/bin/epicmp

mcode/nativelibs/macosx/bin/wqrs

mcode/nativelibs/macosx/bin/wfdbmap

mcode/nativelibs/macosx/bin/wfdb2mat

mcode/nativelibs/macosx/bin/mxm

mcode/nativelibs/macosx/bin/wfdbwhich

mcode/nativelibs/macosx/bin/corrint

mcode/nativelibs/macosx/bin/annxml

mcode/nativelibs/macosx/bin/rxr

mcode/nativelibs/macosx/bin/wfdbcat

mcode/nativelibs/macosx/bin/wfdbdesc

mcode/nativelibs/macosx/bin/sumann

mcode/nativelibs/macosx/bin/rdsamp

mcode/nativelibs/macosx/bin/coherence

mcode/nativelibs/macosx/bin/edf2mit

mcode/nativelibs/macosx/bin/libgfortran.3.dylib

mcode/nativelibs/macosx/bin/calsig

mcode/nativelibs/macosx/bin/libcurl.4.dylib

mcode/nativelibs/macosx/bin/rr2ann

mcode/nativelibs/macosx/bin/ihr

mcode/nativelibs/macosx/bin/rdann

mcode/nativelibs/macosx/bin/plotstm

mcode/nativelibs/macosx/bin/rdedfann

mcode/nativelibs/macosx/bin/dfa

mcode/nativelibs/macosx/bin/log10

mcode/nativelibs/macosx/bin/sqrs

mcode/nativelibs/macosx/bin/sigamp

mcode/nativelibs/custom/bin/mrgann

mcode/nativelibs/custom/bin/ecgeval

mcode/nativelibs/custom/bin/mit2edf

mcode/nativelibs/custom/bin/memse

mcode/nativelibs/custom/bin/wfdbtime

mcode/nativelibs/custom/bin/mfilt

mcode/nativelibs/custom/bin/signum

mcode/nativelibs/custom/bin/ahaecg2mit

mcode/nativelibs/custom/bin/xform

mcode/nativelibs/custom/bin/signame

mcode/nativelibs/custom/bin/revise

mcode/nativelibs/custom/bin/wfdbcollate

mcode/nativelibs/custom/bin/bxb

mcode/nativelibs/custom/bin/mit2wav

mcode/nativelibs/custom/bin/hrstats

mcode/nativelibs/custom/bin/sqrs125

mcode/nativelibs/custom/bin/wabp

mcode/nativelibs/custom/bin/ad2m

mcode/nativelibs/custom/bin/md2a

mcode/nativelibs/custom/bin/nguess

mcode/nativelibs/custom/bin/m2a

mcode/nativelibs/custom/bin/sigavg

mcode/nativelibs/custom/bin/skewedit

mcode/nativelibs/custom/bin/wrsamp

mcode/nativelibs/custom/bin/heaxml

mcode/nativelibs/custom/bin/a2m

mcode/nativelibs/custom/bin/sortann

mcode/nativelibs/custom/bin/sumstats

mcode/nativelibs/custom/bin/ann2rr

mcode/nativelibs/custom/bin/pscgen

mcode/nativelibs/custom/bin/gqfuse

mcode/nativelibs/custom/bin/wrann

mcode/nativelibs/custom/bin/wfdb-config

mcode/nativelibs/custom/bin/xmlann

mcode/nativelibs/custom/bin/xmlhea

mcode/nativelibs/custom/bin/fft

mcode/nativelibs/custom/bin/makeid

mcode/nativelibs/custom/bin/wav2mit

mcode/nativelibs/custom/bin/time2sec

mcode/nativelibs/custom/bin/tach

mcode/nativelibs/custom/bin/sampfreq

mcode/nativelibs/custom/bin/lomb

mcode/nativelibs/custom/bin/pschart

mcode/nativelibs/custom/bin/fir

mcode/nativelibs/custom/bin/nst

mcode/nativelibs/custom/bin/snip

mcode/nativelibs/custom/bin/wfdbsignals

mcode/nativelibs/custom/bin/readid

mcode/nativelibs/custom/bin/gqrs

mcode/nativelibs/custom/bin/gqpost

mcode/nativelibs/custom/bin/epicmp

mcode/nativelibs/custom/bin/wqrs

mcode/nativelibs/custom/bin/wfdbmap

mcode/nativelibs/custom/bin/wfdb2mat

mcode/nativelibs/custom/bin/mxm

mcode/nativelibs/custom/bin/wfdbwhich

mcode/nativelibs/custom/bin/annxml

mcode/nativelibs/custom/bin/rxr

mcode/nativelibs/custom/bin/wfdbcat

mcode/nativelibs/custom/bin/wfdbdesc

mcode/nativelibs/custom/bin/sumann

mcode/nativelibs/custom/bin/rdsamp

mcode/nativelibs/custom/bin/coherence

mcode/nativelibs/custom/bin/edf2mit

mcode/nativelibs/custom/bin/calsig

mcode/nativelibs/custom/bin/rr2ann

mcode/nativelibs/custom/bin/ihr

mcode/nativelibs/custom/bin/rdann

mcode/nativelibs/custom/bin/plotstm

mcode/nativelibs/custom/bin/rdedfann

mcode/nativelibs/custom/bin/log10

mcode/nativelibs/custom/bin/sqrs

mcode/nativelibs/custom/bin/sigamp

mcode/nativelibs/custom/lib/libwfdb.so.10.5

mcode/nativelibs/custom/lib/libwfdb.so.10

(wfdb-app-JVM6-0-9-9.jar) org/physionet/wfdb/Wfdbexec.class

(wfdb-app-JVM6-0-9-9.jar) org/physionet/wfdb/Score2013.class

(wfdb-app-JVM6-0-9-9.jar) org/physionet/wfdb/OutputReader.class

(wfdb-app-JVM6-0-9-9.jar) org/physionet/wfdb/concurrent/MapRecord.class

(wfdb-app-JVM6-0-9-9.jar) org/physionet/wfdb/concurrent/ConcurrentWfdbexec.class

(wfdb-app-JVM6-0-9-9.jar) org/physionet/wfdb/SystemSettings.class

(wfdb-app-JVM6-0-9-9.jar) org/physionet/wfdb/physiobank/PhysioNetDB.class

(wfdb-app-JVM6-0-9-9.jar) org/physionet/wfdb/physiobank/PhysioNetSignal.class

(wfdb-app-JVM6-0-9-9.jar) org/physionet/wfdb/physiobank/PhysioNetDB$1.class

(wfdb-app-JVM6-0-9-9.jar) org/physionet/wfdb/physiobank/PhysioNetRecord.class

(wfdb-app-JVM6-0-9-9.jar) org/physionet/wfdb/InputWriter.class

[Benjamin Moody]

On 3/21/17, joachim...@gmail.com <joachim...@gmail.com> wrote:
> Thanks Tomas,
>
> That worked!
>
> I just want to check with one of the challenge organisers (is someone read
> this post) that the "Possibly proprietary files" listed below are ok? There
>
> are part of the mcode from WFDB but since the server is throwing me this
> warning I prefer to check..
>
> Thanks,
> Joachim

This is okay, for the WFDB Toolbox we have allowed this in the past.

In any case, I have added the packages to the repository so you can
install the Toolbox (and WFDB itself) via dependencies.txt. Add these
lines:

wfdb-app-toolbox=0.9.9+src-0~pn1
wfdb=10.5.25~pre2-0~pn1
libwfdb10=10.5.25~pre2-0~pn1
ecgpuwave=1.3.3-0~pn1

If using Octave your program will also need to do a 'pkg load wfdb'.

Benjamin

[joachim...@gmail.com]

Thanks Benjamin,
That worked well,

Best,

Joachim

[Aleksandr Dubrovin]

I am adding the mcode of the WFDB Toolbox for Matlab. 

When running an EXAMPLE I get the following error

Either couldn't read from the template file or couldn't write to the OutputStream.

java.io.IOException: Cannot run program "E:\ECGdatabase\ptb-diagnostic-ecg-database-1.0.0\wfdb-app-toolbox-0-10-0\mcode\nativelibs\windows\bin\visbility": CreateProcess error=2, Не удается найти указанный файл

at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

at org.physionet.wfdb.Wfdbexec.execWithStandardInput(Unknown Source)

at org.physionet.wfdb.Wfdbexec.execWithStandardInput(Unknown Source)

Caused by: java.io.IOException: CreateProcess error=2, Не удается найти указанный файл

at java.lang.ProcessImpl.create(Native Method)

at java.lang.ProcessImpl.<init>(ProcessImpl.java:386)

at java.lang.ProcessImpl.start(ProcessImpl.java:137)

at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

... 2 more

Error using visgraph (line 82)

Java exception occurred:

java.lang.NullPointerException

at org.physionet.wfdb.Wfdbexec.execWithStandardInput(Unknown Source)

at org.physionet.wfdb.Wfdbexec.execWithStandardInput(Unknown Source)

Error in untitled (line 20)

[k,logP]=visgraph(out);

[PhysioNet Challenge]

Dear Aleksander,

The PhysioNet Challenges are part of the PhysioNet resource which is managed by three separate research groups that reflect the three specific aims of the grant for PhysioNet:

1. The Laboratory for Computational Physiology (LCP) at MIT - which runs the physionet.org website to distribute data and resources such as open source software. It maintains the software, and in particular the WFDB libraries to access the data.
2. The ReyLab at Harvard - which develops computational software and other open-source resources and research posted though physionet.org.
3. Biomedical Informatics (BMI) at Emory - which runs the Challenges and physionetchallenges.org. It does not support code or data access other than that directly provided for the current Challenge by the Challenge Organizers.
   

All libraries and code provided on physionet.org are supported by the LCP, which can be reached directly for support on contact [AT] physionet.org. For example, https://archive.physionet.org/physiotools/matlab/wfdb-app-matlab/faq.shtml should describe your error with the WFDB toolbox, but if it does address your question, then please email contact [at] physionet.org for direct support.

Previous Challenges are not generally supported, but requests will be considered, particularly if resources are available. Test data from previous Challenges will never be released to prevent overfitting on the test data. Submission of open-source code to be re-run on past Challenge data will be considered if the requestor can provide resources to assist in this. Unfortunately, the funding from the NIH and our generous sponsors cannot match the large number of time-consuming requests that we receive.

Similarly, the PhysioNet Challenges partner with Computing in Cardiology (CinC), which administers the annual CinC conference. Information for CinC authors can be found at https://www.cinc.org/inf_authors/ and the websites for each year’s conference.

Best,

Matt

(On behalf of the Challenge team.)

https://physionetchallenges.org/
https://physionet.org/

Please post questions and comments in the forum. However, if your question reveals information about your entry, then please email challenge at physionet.org. We may post parts of our reply publicly if we feel that all Challengers should benefit from it. We will not answer emails about the Challenge to any other address. This email is maintained by a group. Please do not email us individually.