Package: release.debian.org
Severity: normal
User: release.debian....@packages.debian.org
Usertags: unblock
X-Debbugs-Cc: Alois Schlögl <alois.schlo...@gmail.com>,
debian-med-packag...@lists.alioth.debian.org
Please unblock package biosig
[ Reason ]
Upstream wrote: under certain circumstances, save2gdf from biosig-tools
crashes, because of
memory corruption.
Because this bug could be a security issue, it would be great if we could
manage to fix this rather sooner than later.
see
https://alioth-lists.debian.net/pipermail/debian-med-packaging/2021-April/091120.html
[ Impact ]
biosig might become an intrusion vector due to the security issue
[ Tests ]
Unfortunately the package has only superficial tests
[ Risks ]
The package is basically a leaf package and the risk
to break anything by the attached patch is low.
[ Checklist ]
[x] all changes are documented in the d/changelog
[x] I reviewed all changes and I approve them
[x] attach debdiff against the package in testing
[ Other info ]
There was no actual bug filed by upstream who simply has sent
a patch via private mail which I forwarded to the maintainer list.
unblock biosig/2.1.2-4
diff -Nru biosig-2.1.2/debian/changelog biosig-2.1.2/debian/changelog
--- biosig-2.1.2/debian/changelog 2021-01-26 21:47:42.000000000 +0100
+++ biosig-2.1.2/debian/changelog 2021-04-15 21:04:32.000000000 +0200
@@ -1,3 +1,11 @@
+biosig (2.1.2-4) unstable; urgency=medium
+
+ * libbiosig: cherry pick some patches from upstream
+ - fix EDF-to-GDF conversion for certain files
+ - fix JSON export when SampleRate is undefined (e.g. Infinity)
+
+ -- Alois Schlögl <alois.schlo...@gmail.com> Thu, 15 Apr 2021 21:04:32 +0200
+
biosig (2.1.2-3) unstable; urgency=medium
[ Alois Schlögl ]
diff -Nru biosig-2.1.2/debian/patches/fix-edf2gdf-and-json-export.patch
biosig-2.1.2/debian/patches/fix-edf2gdf-and-json-export.patch
--- biosig-2.1.2/debian/patches/fix-edf2gdf-and-json-export.patch
1970-01-01 01:00:00.000000000 +0100
+++ biosig-2.1.2/debian/patches/fix-edf2gdf-and-json-export.patch
2021-04-15 21:04:32.000000000 +0200
@@ -0,0 +1,155 @@
+Date: Thu, 15 Apr 2021 16:11:34 +0200
+From: Alois Schlögl <alois.schlo...@gmail.com>
+Description: add missing sanity check on nmemb in fread(..,..,nmemb,..) - this
can avoid memory errors in certain files
+ under certain circumstances, save2gdf from biosig-tools crashes, because of
+ memory corruption.
+ Because this bug could be a security issue, it would be great if we could
+ manage to fix this rather sooner than later.
+
+diff --git a/biosig4c++/biosig.c b/biosig4c++/biosig.c
+index aea7260f..526a8a9b 100644
+--- a/biosig4c++/biosig.c
++++ b/biosig4c++/biosig.c
+@@ -4142,7 +4142,8 @@ else if (!strncmp(MODE,"r",1)) {
+ hdr->CHANNEL = (CHANNEL_TYPE*) realloc(hdr->CHANNEL, hdr->NS *
sizeof(CHANNEL_TYPE));
+ hdr->AS.Header = (uint8_t*) realloc(Header1,hdr->HeadLen);
+ char *Header2 = (char*)hdr->AS.Header+256;
+- count += ifread(hdr->AS.Header+count, 1, hdr->HeadLen-count,
hdr);
++ if (hdr->HeadLen > count)
++ count += ifread(hdr->AS.Header+count, 1,
hdr->HeadLen-count, hdr);
+
+ if (count < hdr->HeadLen) {
+ biosigERROR(hdr, B4C_INCOMPLETE_FILE, "reading
BDF/EDF variable header failed");
+@@ -4275,7 +4276,7 @@ else if (!strncmp(MODE,"r",1)) {
+ if (Dur==0.0 && FLAG_BUGGY_NEUROLOGGER_EDF) Dur =
hdr->SPR/496.0;
+ hdr->SampleRate = hdr->SPR/Dur;
+
+- if (VERBOSE_LEVEL>8) fprintf(stdout,"[EDF 220] #=%i
SPR=%i\n",(int)iftell(hdr),(int)hdr->SPR);
++ if (VERBOSE_LEVEL>8) fprintf(stdout,"[EDF 220] #=%i SPR=%i
Dur=%g\n",(int)iftell(hdr),(int)hdr->SPR, Dur);
+
+ if (hdr->NRec <= 0) {
+ struct stat FileBuf;
+@@ -4547,7 +4548,8 @@ if (VERBOSE_LEVEL>7) fprintf(stdout,"EDF+
event\n\ts1:\t<%s>\n\ts2:\t<%s>\n\ts3:
+ hdr->HeadLen += 4;
+ // read header up to nLenght and nID of foreign data section
+ hdr->AS.Header = (uint8_t*) realloc(hdr->AS.Header,
hdr->HeadLen);
+- count += ifread(Header1+count, 1, hdr->HeadLen-count,
hdr);
++ if (hdr->HeadLen > count)
++ count += ifread(Header1+count, 1, hdr->HeadLen-count,
hdr);
+ uint32_t POS = hdr->HeadLen;
+ // read "foreign data section" and "per channel data types
section"
+ hdr->HeadLen += leu16p(hdr->AS.Header + hdr->HeadLen-4) - 4;
+@@ -4555,7 +4557,8 @@ if (VERBOSE_LEVEL>7) fprintf(stdout,"EDF+
event\n\ts1:\t<%s>\n\ts2:\t<%s>\n\ts3:
+ // read "foreign data section" and "per channel data types
section"
+ hdr->HeadLen += 4*hdr->NS;
+ hdr->AS.Header = (uint8_t*)realloc(Header1, hdr->HeadLen+8);
+- count += ifread(Header1+POS, 1, hdr->HeadLen-POS, hdr);
++ if (hdr->HeadLen > POS)
++ count += ifread(Header1+POS, 1, hdr->HeadLen-POS, hdr);
+
+ if (VERBOSE_LEVEL>7) fprintf(stdout,"%s (line %i) %s %i/%i
%i/%i %i/%i %i/%i %i/%i \n", \
+ __FILE__, __LINE__, __func__, \
+@@ -5596,7 +5599,8 @@ fprintf(stdout,"ACQ EVENT: %i POS: %i\n",k,POS);
+
+ hdr->HeadLen = 1024;
+ hdr->AS.Header = (uint8_t*)realloc(hdr->AS.Header,
hdr->HeadLen);
+- count +=
ifread(hdr->AS.Header+count,1,hdr->HeadLen-count,hdr);
++ if (hdr->HeadLen > count)
++ count += ifread(hdr->AS.Header+count, 1,
hdr->HeadLen-count, hdr);
+ hdr->NS = leu16p(hdr->AS.Header+2);
+ hdr->NRec = leu32p(hdr->AS.Header+6);
+ hdr->SPR = leu32p(hdr->AS.Header+10);
+@@ -7451,7 +7455,8 @@ if (VERBOSE_LEVEL > 7) fprintf(stdout,"biosig/%s (line
%d): #%d label <%s>\n", _
+
+ /* read file */
+ hdr->AS.Header =
(uint8_t*)realloc(hdr->AS.Header,hdr->HeadLen+1);
+- count += ifread(hdr->AS.Header+count,1,hdr->HeadLen-count,hdr);
++ if (hdr->HeadLen > count)
++ count += ifread(hdr->AS.Header+count, 1,
hdr->HeadLen-count, hdr);
+ hdr->AS.Header[count]=0;
+
+ }
+@@ -14075,7 +14080,8 @@ if (VERBOSE_LEVEL>7) fprintf(stdout,
"asprintf_hdr2json: sz=%i\n", (int)sz);
+ c += sprintf(STR, "\t\"NumberOfRecords\"\t: %i,\n",(int)hdr->NRec);
+ c += sprintf(STR, "\t\"SamplesPerRecords\"\t: %i,\n",(int)hdr->SPR);
+ c += sprintf(STR, "\t\"NumberOfSamples\"\t:
%i,\n",(int)(hdr->NRec*hdr->SPR));
+- if (!isnan(hdr->SampleRate)) c += sprintf(STR, "\t\"Samplingrate\"\t:
%f,\n",hdr->SampleRate);
++ if ((0.0 <= hdr->SampleRate) && (hdr->SampleRate < INFINITY))
++ c += sprintf(STR, "\t\"Samplingrate\"\t:
%f,\n",hdr->SampleRate);
+ snprintf_gdfdatetime(tmp, 40, hdr->T0);
+ c += sprintf(STR, "\t\"StartOfRecording\"\t: \"%s\",\n",tmp);
+ c += sprintf(STR, "\t\"TimezoneMinutesEastOfUTC\"\t: %i,\n",
hdr->tzmin);
+@@ -14143,15 +14149,16 @@ if (VERBOSE_LEVEL>7) fprintf(stdout,
"asprintf_hdr2json: count=%i\n", (int)c);
+ c += sprintf(STR,"\n\t\t{\n");
+ c += sprintf(STR,"\t\t\"ChannelNumber\"\t: %i,\n", (int)k+1);
+ c += sprintf(STR,"\t\t\"Label\"\t: \"%s\",\n", hc->Label);
++ double fs = hdr->SampleRate * hc->SPR/hdr->SPR;
++ if ((0.0 <= fs) && (fs < INFINITY)) c += sprintf(STR,
"\t\t\"Samplingrate\"\t: %f,\n", fs);
+ if ( hc->Transducer && strlen(hc->Transducer) ) c +=
sprintf(STR,"\t\t\"Transducer\"\t: \"%s\",\n", hc->Transducer);
+- c += sprintf(STR,"\t\t\"PhysicalUnit\"\t: \"%s\",\n",
PhysDim3(hc->PhysDimCode));
+ if (!isnan(hc->PhysMax)) c +=
sprintf(STR,"\t\t\"PhysicalMaximum\"\t: %g,\n", hc->PhysMax);
+ if (!isnan(hc->PhysMin)) c +=
sprintf(STR,"\t\t\"PhysicalMinimum\"\t: %g,\n", hc->PhysMin);
+ if (!isnan(hc->DigMax)) c +=
sprintf(STR,"\t\t\"DigitalMaximum\"\t: %f,\n", hc->DigMax);
+ if (!isnan(hc->DigMin)) c +=
sprintf(STR,"\t\t\"DigitalMinimum\"\t: %f,\n", hc->DigMin);
+ if (!isnan(hc->Cal)) c += sprintf(STR,"\t\t\"scaling\"\t:
%g,\n", hc->Cal);
+ if (!isnan(hc->Off)) c += sprintf(STR,"\t\t\"offset\"\t:
%g,\n", hc->Off);
+- if (!isnan(hc->TOffset)) c += sprintf(STR,"\t\t\"TimeDelay\"\t:
%g,\n", hc->TOffset);
++ if (!isnan(hc->TOffset)) c += sprintf(STR,"\t\t\"TimeDelay\"\t:
%g", hc->TOffset);
+ uint8_t flag = (0 < hc->LowPass && hc->LowPass<INFINITY) | ((0
< hc->HighPass && hc->HighPass<INFINITY)<<1) | ((0 < hc->Notch &&
hc->Notch<INFINITY)<<2);
+ if (flag) {
+ c += sprintf(STR, "\t\t\"Filter\" : {\n");
+@@ -14168,8 +14175,7 @@ if (VERBOSE_LEVEL>7) fprintf(stdout,
"asprintf_hdr2json: count=%i\n", (int)c);
+ if (!isnan(hc->fZ)) c += sprintf(STR, "\t\t\"fZ\"\t:
%g,\n", hc->fZ);
+ break;
+ }
+- double fs = hdr->SampleRate * hc->SPR/hdr->SPR;
+- if (!isnan(fs)) c += sprintf(STR, "\t\t\"Samplingrate\"\t: %f",
fs);
++ c += sprintf(STR,"\t\t\"PhysicalUnit\"\t: \"%s\"",
PhysDim3(hc->PhysDimCode));
+ c += sprintf(STR, "\n\t\t}"); // end-of-CHANNEL
+ }
+ c += sprintf(STR, "\n\t]"); // end-of-CHANNELS
+@@ -14272,7 +14278,8 @@ int fprintf_hdr2json(FILE *fid, HDRTYPE* hdr)
+ fprintf(fid,"\t\"NumberOfRecords\"\t: %i,\n",(int)hdr->NRec);
+ fprintf(fid,"\t\"SamplesPerRecords\"\t: %i,\n",(int)hdr->SPR);
+ fprintf(fid,"\t\"NumberOfSamples\"\t: %i,\n",(int)(hdr->NRec*hdr->SPR));
+- if (!isnan(hdr->SampleRate)) fprintf(fid,"\t\"Samplingrate\"\t:
%f,\n",hdr->SampleRate);
++ if ((0.0 <= hdr->SampleRate) && (hdr->SampleRate < INFINITY))
++ fprintf(fid,"\t\"Samplingrate\"\t: %f,\n", hdr->SampleRate);
+
+ snprintf_gdfdatetime(tmp, 40, hdr->T0);
+ fprintf(fid,"\t\"StartOfRecording\"\t: \"%s\",\n",tmp);
+@@ -14330,8 +14337,9 @@ int fprintf_hdr2json(FILE *fid, HDRTYPE* hdr)
+ fprintf(fid,"\n\t\t{\n");
+ fprintf(fid,"\t\t\"ChannelNumber\"\t: %i,\n", (int)k+1);
+ fprintf(fid,"\t\t\"Label\"\t: \"%s\",\n", hc->Label);
++ double fs = hdr->SampleRate * hc->SPR/hdr->SPR;
++ if ((0.0 <= fs) && (fs < INFINITY))
fprintf(fid,"\t\t\"Samplingrate\"\t: %f,\n", fs);
+ if ( hc->Transducer && strlen(hc->Transducer) )
fprintf(fid,"\t\t\"Transducer\"\t: \"%s\",\n", hc->Transducer);
+- fprintf(fid,"\t\t\"PhysicalUnit\"\t: \"%s\",\n",
PhysDim3(hc->PhysDimCode));
+ if (!isnan(hc->PhysMax))
fprintf(fid,"\t\t\"PhysicalMaximum\"\t: %g,\n", hc->PhysMax);
+ if (!isnan(hc->PhysMin))
fprintf(fid,"\t\t\"PhysicalMinimum\"\t: %g,\n", hc->PhysMin);
+ if (!isnan(hc->DigMax)) fprintf(fid,"\t\t\"DigitalMaximum\"\t:
%f,\n", hc->DigMax);
+@@ -14355,8 +14363,7 @@ int fprintf_hdr2json(FILE *fid, HDRTYPE* hdr)
+ if (!isnan(hc->fZ)) fprintf(fid,"\t\t\"fZ\"\t: %g,\n",
hc->fZ);
+ break;
+ }
+- double fs = hdr->SampleRate * hc->SPR/hdr->SPR;
+- if (!isnan(fs)) fprintf(fid,"\t\t\"Samplingrate\"\t: %f", fs);
// no comma at the end because its the last element
++ fprintf(fid,"\t\t\"PhysicalUnit\"\t: \"%s\"",
PhysDim3(hc->PhysDimCode)); // no comma at the end because its the last
element
+ fprintf(fid,"\n\t\t}"); // end-of-CHANNEL
+ }
+ fprintf(fid,"\n\t]"); // end-of-CHANNELS
+diff --git a/biosig4c++/t210/sopen_heka_read.c
b/biosig4c++/t210/sopen_heka_read.c
+index 5fac494c..f00d1321 100644
+--- a/biosig4c++/t210/sopen_heka_read.c
++++ b/biosig4c++/t210/sopen_heka_read.c
+@@ -150,7 +150,8 @@ void sopen_heka(HDRTYPE* hdr, FILE *itx) {
+ struct stat FileBuf;
+ stat(hdr->FileName,&FileBuf);
+ hdr->AS.Header = (uint8_t*)realloc(hdr->AS.Header,
FileBuf.st_size);
+- count += ifread(hdr->AS.Header+count, 1, 1024-count, hdr);
++ if (count < 1024)
++ count += ifread(hdr->AS.Header+count, 1, 1024-count,
hdr);
+ hdr->HeadLen = count;
+
+ hdr->FILE.LittleEndian = *(uint8_t*)(hdr->AS.Header+52) > 0;
diff -Nru biosig-2.1.2/debian/patches/series biosig-2.1.2/debian/patches/series
--- biosig-2.1.2/debian/patches/series 2021-01-26 21:47:42.000000000 +0100
+++ biosig-2.1.2/debian/patches/series 2021-04-15 21:04:32.000000000 +0200
@@ -7,3 +7,4 @@
install_strip.patch
sopen-add-support-for-timezone-information-in-GDF-files.patch
fix-edfannot-issue-eeglab93.patch
+fix-edf2gdf-and-json-export.patch
