This was originally filed against Fedora 17, but is still reproducing in Fedora 18.  I've updated the bug to reflect this.

Versions of components on Fedora 18 that produce the problem:

sound-juicer-3.5.0-2
libmusicbrainz5-5.0.1-5
libdiscid-0.2.2-7
gstreamer1-1.0.7-1
gstreamer1-plugins-base-1.0.7-1
gstreamer1-plugins-good

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Still reproducing in Fedora 20 - updating version field.

Versions of components on Fedora 20 that produce the problem:

sound-juicer-3.5.0-5.fc20.x86_64
libmusicbrainz5-5.0.1-8.fc20.x86_64
libdiscid-0.2.2-9.fc20.x86_64
gstreamer1-1.2.2-1.fc20.x86_64
gstreamer1-1.2.2-1.fc20.i686
gstreamer1-plugins-base-1.2.2-1.fc20.x86_64
gstreamer1-plugins-good-1.2.2-2.fc20.x86_64

I've spent some time on this one. When it's done encoding the file, libflac calls update_metadata() in src/libFLAC/stream_encoder.c which tries to seek at the beginning of the encoded file to rewrite the STREAMINFO header with the computed md5 checksum.
This calls gst_flac_enc_seek_callback() which starts by doing:

    /* try to seek to the beginning of the output */
    query = gst_query_new_seeking (GST_FORMAT_BYTES);
    if (gst_pad_query (peerpad, query)) {
      GstFormat format;

      gst_query_parse_seeking (query, &format, &seekable, NULL, NULL);
      if (format != GST_FORMAT_BYTES)
        seekable = FALSE;
    } else {
      GST_LOG_OBJECT (flacenc, "SEEKING query not handled");
    }
    gst_query_unref (query);

sound-juicer is using giosink, which does not handle SEEKING queries:

static gboolean
gst_gio_base_sink_query (GstBaseSink * bsink, GstQuery * query)
{
  GstGioBaseSink *sink = GST_GIO_BASE_SINK (bsink);
  GstFormat format;

  switch (GST_QUERY_TYPE (query)) {
    case GST_QUERY_POSITION:
      gst_query_parse_position (query, &format, NULL);
      switch (format) {
        case GST_FORMAT_BYTES:
        case GST_FORMAT_DEFAULT:
          gst_query_set_position (query, GST_FORMAT_BYTES, sink->position);
          return TRUE;
        default:
          return FALSE;
      }
    case GST_QUERY_FORMATS:
      gst_query_set_formats (query, 2, GST_FORMAT_DEFAULT, GST_FORMAT_BYTES);
      return TRUE;
    case GST_QUERY_URI:
      if (GST_IS_URI_HANDLER (sink)) {
        gchar *uri;

        uri = gst_uri_handler_get_uri (GST_URI_HANDLER (sink));
        gst_query_set_uri (query, uri);
        g_free (uri);
        return TRUE;
      }
      return FALSE;
    default:
      return GST_BASE_SINK_CLASS (parent_class)->query (bsink, query);
  }
}


Compare with filesink which has in its gst_file_sink_query() method:

    case GST_QUERY_SEEKING:
      gst_query_parse_seeking (query, &format, NULL, NULL, NULL);
      if (format == GST_FORMAT_BYTES || format == GST_FORMAT_DEFAULT) {
        gst_query_set_seeking (query, GST_FORMAT_BYTES, self->seekable, 0, -1);
      } else {
        gst_query_set_seeking (query, format, FALSE, 0, -1);
      }
      res = TRUE;
      break;

However, switching sound-juicer to using filesink is not enough to get the flac signature to be written :( 

gst-launch-1.0 filesrc ! flacparse ! flacdec !  flacenc !filesink does the right thing though, so I guess this is a bug related to flacenc being wrapped inside an encodebin. gst debug log has flacenc 
gstflacenc.c:974:gst_flac_enc_seek_callback: Seek to 26 succeeded
gstflacenc.c:1154:gst_flac_enc_write_callback:<flacenc1> Fixing up headers at pos=26, size=16

but this does not seem to translate to an updated header in the encoded flac file :(

I've been able to reproduce this using (from gstreamer source)
 
gst-plugins-base/tests/examples/encoding -f audio/x-flac -a audio/x-flac  -o /home/teuf/output.flac file:///home/teuf/11k16bitpcm.wav

(wav file came from http://www.nch.com.au/acm/11k16bitpcm.wav linked from https://en.wikipedia.org/wiki/WAV but any random file should do the trick).

After that (metaflac comes with the 'flac' package)
$ metaflac --list --block-number=0 /home/teuf/output.flac
METADATA block #0
  type: 0 (STREAMINFO)
  is last: false
  length: 34
  minimum blocksize: 4608 samples
  maximum blocksize: 4608 samples
  minimum framesize: 0 bytes
  maximum framesize: 0 bytes
  sample_rate: 11025 Hz
  channels: 1
  bits-per-sample: 16
  total samples: 0
  MD5 signature: 00000000000000000000000000000000


If instead I do things manually with:
gst-launch-1.0 filesrc location=/home/teuf/11k16bitpcm.wav ! wavparse !  flacenc ! filesink location=/home/teuf/output.flac


$ metaflac --list --block-number=0 /home/teuf/output.flac
METADATA block #0
  type: 0 (STREAMINFO)
  is last: false
  length: 34
  minimum blocksize: 4608 samples
  maximum blocksize: 4608 samples
  minimum framesize: 214 bytes
  maximum framesize: 7700 bytes
  sample_rate: 11025 Hz
  channels: 1
  bits-per-sample: 16
  total samples: 152267
  MD5 signature: 7ad725dd59f9d1f4bf6d50cf80aee75d

I'll file a gstreamer bug for this tomorrow.

Christophe,

Excellent code sleuthing.  All the best.

(In reply to Christophe Fergeau from comment #6)
> sound-juicer is using giosink, which does not handle SEEKING queries:
> [...] 
> Compare with filesink which has in its gst_file_sink_query() method:
> [...] 
> However, switching sound-juicer to using filesink is not enough to get the
> flac signature to be written :( 
> 

Rather than hardcoding the output sink, we probably can let gstreamer pick the 'best' one for us through:

 sink = gst_element_make_from_uri (GST_URI_SINK, outputuri, "sink", NULL);

It seems to be picking filesink for local files, and hopefully will use a different sink for non file:// URIs.

This message is a reminder that Fedora 20 is nearing its end of life.
Approximately 4 (four) weeks from now Fedora will stop maintaining
and issuing updates for Fedora 20. It is Fedora's policy to close all
bug reports from releases that are no longer maintained. At that time
this bug will be closed as EOL if it remains open with a Fedora  'version'
of '20'.

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plan to fix it in a currently maintained version, simply change the 'version' 
to a later Fedora version.

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able to fix it before Fedora 20 is end of life. If you would still like 
to see this bug fixed and are able to reproduce it against a later version 
of Fedora, you are encouraged  change the 'version' to a later Fedora 
version prior this bug is closed as described in the policy above.

Although we aim to fix as many bugs as possible during every release's 
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more recent Fedora release includes newer upstream software that fixes 
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