[PATCH] gnu: bedtools: Update to 2.24.0.

[PATCH] gnu: bedtools: Update to 2.24.0.

[Ben Woodcroft]

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There was some discussion of this on the bio-packaging list re changes 
in usage with Ricardo, but I think it breaks any dependent packages.
http://lists.open-bio.org/pipermail/bio-packaging/2015-July/000113.html

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From 3fd0b0c655c5f4f4317636f05d8242e2de9ae075 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Fri, 24 Jul 2015 23:11:31 +1000
Subject: [PATCH] gnu: bedtools: Update to 2.24.0.

* gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 78cd3ce..9cd661b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -148,7 +148,7 @@ computational cluster.")
 (define-public bedtools
   (package
     (name "bedtools")
-    (version "2.22.0")
+    (version "2.24.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
@@ -156,7 +156,7 @@ computational cluster.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl"))))
+                "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))))
     (build-system gnu-build-system)
     (native-inputs `(("python" ,python-2)))
     (inputs `(("samtools" ,samtools)
-- 
2.4.3

Re: [PATCH] gnu: bedtools: Update to 2.24.0.

[Ricardo Wurmus]

Ben Woodcroft <b.woodcroft@uq.edu.au> writes:

> There was some discussion of this on the bio-packaging list re changes 
> in usage with Ricardo, but I think it breaks any dependent packages.
> http://lists.open-bio.org/pipermail/bio-packaging/2015-July/000113.html

Did you mean “I *don’t* think it breaks any dependent packages”?
Because that’s what I think :)

Only ‘pybedtools’ uses the ‘bedtools’ package, and only ‘clipper’ uses
‘pybedtools’.  ‘pybedtools’ is unlikely to be affected by a change in
command line behaviour.

~~ Ricardo

Re: [PATCH] gnu: bedtools: Update to 2.24.0.

[Ben Woodcroft]

On 25/07/15 01:11, Ricardo Wurmus wrote:
> Ben Woodcroft <b.woodcroft@uq.edu.au> writes:
>
>> There was some discussion of this on the bio-packaging list re changes
>> in usage with Ricardo, but I think it breaks any dependent packages.
>> http://lists.open-bio.org/pipermail/bio-packaging/2015-July/000113.html
> Did you mean “I *don’t* think it breaks any dependent packages”?
> Because that’s what I think :)
Yeh sorry was half asleep watching Le Tour.
> Only ‘pybedtools’ uses the ‘bedtools’ package, and only ‘clipper’ uses
> ‘pybedtools’.  ‘pybedtools’ is unlikely to be affected by a change in
> command line behaviour.
I built these two packages locally without incident.

ben

Re: [PATCH] gnu: bedtools: Update to 2.24.0.

[Mark H Weaver]

Ben Woodcroft <b.woodcroft@uq.edu.au> writes:

> From 3fd0b0c655c5f4f4317636f05d8242e2de9ae075 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrustben@gmail.com>
> Date: Fri, 24 Jul 2015 23:11:31 +1000
> Subject: [PATCH] gnu: bedtools: Update to 2.24.0.

Pushed, thanks!

     Mark

Re: [PATCH] gnu: bedtools: Update to 2.24.0.

[Andreas Enge]

Hello,

unfortunately, it seems to fail in 32 bit (i686 and mips):
   http://hydra.gnu.org/eval/105733#tabs-new
   
with lots of messages of the kind
   In file included from ../../utils//general/BedtoolsTypes.h:20:0,
                 from ContextBase.h:21,
                 from ContextIntersect.h:11,
                 from ContextIntersect.cpp:8:
../../utils//general/QuickString.h:41:15: error: ‘QuickString& QuickString::operator=(size_t)’ cannot be overloaded
  QuickString &operator = (size_t);

Andreas

Re: [PATCH] gnu: bedtools: Update to 2.24.0.

[Ben Woodcroft]

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On 25/07/15 19:02, Andreas Enge wrote:
> Hello,
>
> unfortunately, it seems to fail in 32 bit (i686 and mips):
>     http://hydra.gnu.org/eval/105733#tabs-new
>     
> with lots of messages of the kind
>     In file included from ../../utils//general/BedtoolsTypes.h:20:0,
>                   from ContextBase.h:21,
>                   from ContextIntersect.h:11,
>                   from ContextIntersect.cpp:8:
> ../../utils//general/QuickString.h:41:15: error: ‘QuickString& QuickString::operator=(size_t)’ cannot be overloaded
>    QuickString &operator = (size_t);
Helpfully this is fixed in upstream though it hasn't yet made it to a 
release. Attached is a new patch that hopefully will help.

ben

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From 47519e0145298c00e4bfa672d92b9f700d12f5ad Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 25 Jul 2015 22:54:19 +1000
Subject: [PATCH] gnu: bedtools: Update to 2.24.0.

* gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0.
---
 gnu/packages/bioinformatics.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 78cd3ce..738d559 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -148,7 +148,7 @@ computational cluster.")
 (define-public bedtools
   (package
     (name "bedtools")
-    (version "2.22.0")
+    (version "2.24.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
@@ -156,7 +156,10 @@ computational cluster.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl"))))
+                "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))
+              ;; Fixed in upstream, see
+              ;; https://github.com/arq5x/bedtools2/issues/271
+              (patches (list (search-patch "bedtools-32bit-compilation.patch")))))
     (build-system gnu-build-system)
     (native-inputs `(("python" ,python-2)))
     (inputs `(("samtools" ,samtools)
-- 
2.4.3

Re: [PATCH] gnu: bedtools: Update to 2.24.0.

[Ben Woodcroft]

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On 25/07/15 22:57, Ben Woodcroft wrote:
> gnu: bedtools: Update to 2.24.0.
>
> * gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0.

Sorry try this instead.

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From 8220fe64f34a77a2307c9f0caca69decaf9f7b61 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 25 Jul 2015 22:58:08 +1000
Subject: [PATCH] gnu: bedtools: Update to 2.24.0.

* gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0.
---
 gnu/packages/bioinformatics.scm                    |   7 +-
 .../patches/bedtools-32bit-compilation.patch       | 168 +++++++++++++++++++++
 2 files changed, 173 insertions(+), 2 deletions(-)
 create mode 100644 gnu/packages/patches/bedtools-32bit-compilation.patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 78cd3ce..738d559 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -148,7 +148,7 @@ computational cluster.")
 (define-public bedtools
   (package
     (name "bedtools")
-    (version "2.22.0")
+    (version "2.24.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
@@ -156,7 +156,10 @@ computational cluster.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl"))))
+                "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))
+              ;; Fixed in upstream, see
+              ;; https://github.com/arq5x/bedtools2/issues/271
+              (patches (list (search-patch "bedtools-32bit-compilation.patch")))))
     (build-system gnu-build-system)
     (native-inputs `(("python" ,python-2)))
     (inputs `(("samtools" ,samtools)
diff --git a/gnu/packages/patches/bedtools-32bit-compilation.patch b/gnu/packages/patches/bedtools-32bit-compilation.patch
new file mode 100644
index 0000000..0a4e710
--- /dev/null
+++ b/gnu/packages/patches/bedtools-32bit-compilation.patch
@@ -0,0 +1,168 @@
+From b47dbefcb57f8e6c4fe397f64346338620740b71 Mon Sep 17 00:00:00 2001
+From: arq5x <arq5x@virginia.edu>
+Date: Wed, 15 Jul 2015 15:15:23 -0600
+Subject: [PATCH] settle on uint32_t signature for QuickString. Resolves #267
+ and #271?
+
+---
+ src/coverageFile/coverageFile.cpp | 24 ++++++++++++------------
+ src/utils/general/QuickString.cpp | 27 ++++++++++++++-------------
+ src/utils/general/QuickString.h   |  6 +++---
+ 3 files changed, 29 insertions(+), 28 deletions(-)
+
+diff --git a/src/coverageFile/coverageFile.cpp b/src/coverageFile/coverageFile.cpp
+index 859cfdc..0fb544b 100644
+--- a/src/coverageFile/coverageFile.cpp
++++ b/src/coverageFile/coverageFile.cpp
+@@ -83,11 +83,11 @@ void CoverageFile::giveFinalReport(RecordOutputMgr *outputMgr) {
+ 		float depthPct = (float)basesAtDepth / (float)_totalQueryLen;
+ 
+ 		_finalOutput = "all\t";
+-		_finalOutput.append(depth);
++		_finalOutput.append(static_cast<uint32_t>(depth));
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(basesAtDepth);
++		_finalOutput.append(static_cast<uint32_t>(basesAtDepth));
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(_totalQueryLen);
++		_finalOutput.append(static_cast<uint32_t>(_totalQueryLen));
+ 		_finalOutput.append("\t");
+ 		format(depthPct);
+ 
+@@ -138,7 +138,7 @@ size_t CoverageFile::countBasesAtDepth(size_t depth) {
+ 
+ void CoverageFile::doCounts(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
+ {
+-	_finalOutput = hits.size();
++	_finalOutput = static_cast<uint32_t>(hits.size());
+ 	outputMgr->printRecord(hits.getKey(), _finalOutput);
+ }
+ 
+@@ -147,9 +147,9 @@ void CoverageFile::doPerBase(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
+ 	//loop through all bases in query, printing full record and metrics for each
+ 	const Record * queryRec = hits.getKey();
+ 	for (size_t i= 0; i < _queryLen; i++) {
+-		_finalOutput = i +1;
++		_finalOutput = static_cast<uint32_t>(i+1);
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(_depthArray[i]);
++		_finalOutput.append(static_cast<uint32_t>(_depthArray[i]));
+ 
+ 		outputMgr->printRecord(queryRec, _finalOutput);
+ 	}
+@@ -181,11 +181,11 @@ void CoverageFile::doHist(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
+ 		size_t numBasesAtDepth = iter->second;
+ 		float coveredBases = (float)numBasesAtDepth / (float)_queryLen;
+ 
+-		_finalOutput = depth;
++		_finalOutput = static_cast<uint32_t>(depth);
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(numBasesAtDepth);
++		_finalOutput.append(static_cast<uint32_t>(numBasesAtDepth));
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(_queryLen);
++		_finalOutput.append(static_cast<uint32_t>(_queryLen));
+ 		_finalOutput.append("\t");
+ 		format(coveredBases);
+ 
+@@ -199,11 +199,11 @@ void CoverageFile::doDefault(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
+ 	size_t nonZeroBases = _queryLen - countBasesAtDepth(0);
+ 	float coveredBases = (float)nonZeroBases / (float)_queryLen;
+ 
+-	_finalOutput = hits.size();
++	_finalOutput = static_cast<uint32_t>(hits.size());
+ 	_finalOutput.append("\t");
+-	_finalOutput.append(nonZeroBases);
++	_finalOutput.append(static_cast<uint32_t>(nonZeroBases));
+ 	_finalOutput.append("\t");
+-	_finalOutput.append(_queryLen);
++	_finalOutput.append(static_cast<uint32_t>(_queryLen));
+ 	_finalOutput.append("\t");
+ 	format(coveredBases);
+ 
+diff --git a/src/utils/general/QuickString.cpp b/src/utils/general/QuickString.cpp
+index 0757009..a83263e 100644
+--- a/src/utils/general/QuickString.cpp
++++ b/src/utils/general/QuickString.cpp
+@@ -105,11 +105,11 @@ QuickString &QuickString::operator = (uint32_t val) {
+ 	return *this;
+ }
+ 
+-QuickString &QuickString::operator = (size_t val) {
+-	clear();
+-	append(val);
+-	return *this;
+-}
++// QuickString &QuickString::operator = (size_t val) {
++// 	clear();
++// 	append(val);
++// 	return *this;
++// }
+ 
+ QuickString &QuickString::operator = (float val) {
+ 	clear();
+@@ -158,10 +158,11 @@ QuickString &QuickString::operator += (uint32_t num) {
+ 	return *this;
+ }
+ 
+-QuickString &QuickString::operator += (size_t num) {
+-	append(num);
+-	return *this;
+-}
++// QuickString &QuickString::operator += (size_t num) {
++// 	append(num);
++// 	return *this;
++// }
++
+ QuickString &QuickString::operator += (float num) {
+ 	append(num);
+ 	return *this;
+@@ -273,12 +274,12 @@ void QuickString::append(int num) {
+ }
+ 
+ void QuickString::append(uint32_t num) {
+-	int2str((int)num, *this, true);
++ 	int2str((int)num, *this, true);
+ }
+ 
+-void QuickString::append(size_t num) {
+-	int2str((int)num, *this, true);
+-}
++// void QuickString::append(size_t num) {
++// 	int2str((int)num, *this, true);
++// }
+ 
+ void QuickString::append(float num) {
+ 	append(ToString(num));
+diff --git a/src/utils/general/QuickString.h b/src/utils/general/QuickString.h
+index b43fdfc..6e6fa94 100644
+--- a/src/utils/general/QuickString.h
++++ b/src/utils/general/QuickString.h
+@@ -38,7 +38,7 @@ class QuickString {
+ 	QuickString &operator = (char);
+ 	QuickString &operator = (int);
+ 	QuickString &operator = (uint32_t);
+-	QuickString &operator = (size_t);
++	//QuickString &operator = (size_t);
+ 	QuickString &operator = (float);
+ 	QuickString &operator = (double);
+ 	QuickString &operator += (const QuickString &);
+@@ -47,7 +47,7 @@ class QuickString {
+ 	QuickString &operator += (char);
+ 	QuickString &operator += (int);
+ 	QuickString &operator += (uint32_t);
+-	QuickString &operator += (size_t);
++	//QuickString &operator += (size_t);
+ 	QuickString &operator += (float);
+ 	QuickString &operator += (double);
+ 
+@@ -74,7 +74,7 @@ class QuickString {
+ 	//for better performance.
+ 	void append(int num);
+ 	void append(uint32_t num);
+-	void append(size_t num);
++	//void append(size_t num);
+ 	void append(float num);
+ 	void append(double num);
+ 
+
-- 
2.4.3

Re: [PATCH] gnu: bedtools: Update to 2.24.0.

[Andreas Enge]

Hello Ben,

thanks for your quick reply!

On Sat, Jul 25, 2015 at 11:02:27PM +1000, Ben Woodcroft wrote:
> -    (version "2.22.0")
> +    (version "2.24.0")

Now that 2.24.0 is in git master, could you please prepare your patch with
respect to this version? In particular, the above two lines should not
appear any more, and the commit message will have to be modified.

> +              ;; Fixed in upstream, see
> +              ;; https://github.com/arq5x/bedtools2/issues/271
> +              (patches (list (search-patch "bedtools-32bit-compilation.patch")))))

You will also need to reference the patch file in gnu-system.am to include
it into the distribution.

Thanks!

Andreas

Re: [PATCH] gnu: bedtools: Update to 2.24.0.

[Ben Woodcroft]

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On 25/07/15 23:10, Andreas Enge wrote:
>
> Now that 2.24.0 is in git master, could you please prepare your patch with
> respect to this version? In particular, the above two lines should not
> appear any more, and the commit message will have to be modified.

Attached. Lemme know if I messed up.

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From 2a09480f4ac5c02c706d39be1cdaf6e6e51f9670 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 25 Jul 2015 23:32:55 +1000
Subject: [PATCH] gnu: bedtools: settle on uint32_t signature for QuickString.

* gnu/packages/patches/bedtools-32bit-compilation.patch: New file.
* gnu/packages/bioinformatics.scm (bedtools)[source]: Add patch.
---
 gnu-system.am                                      |   1 +
 gnu/packages/bioinformatics.scm                    |   5 +-
 .../patches/bedtools-32bit-compilation.patch       | 168 +++++++++++++++++++++
 3 files changed, 173 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/bedtools-32bit-compilation.patch

diff --git a/gnu-system.am b/gnu-system.am
index f4e121a..d6635fe 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -392,6 +392,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/avahi-localstatedir.patch		\
   gnu/packages/patches/avrdude-fix-libusb.patch			\
   gnu/packages/patches/bash-completion-directories.patch	\
+  gnu/packages/patches/bedtools-32bit-compilation.patch         \
   gnu/packages/patches/bowtie-fix-makefile.patch		\
   gnu/packages/patches/bigloo-gc-shebangs.patch			\
   gnu/packages/patches/binutils-ld-new-dtags.patch		\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 92b9394..e01e428 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -204,7 +204,10 @@ computational cluster.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))))
+                "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))
+              ;; Fixed in upstream, see
+              ;; https://github.com/arq5x/bedtools2/issues/271
+              (patches (list (search-patch "bedtools-32bit-compilation.patch")))))
     (build-system gnu-build-system)
     (native-inputs `(("python" ,python-2)))
     (inputs `(("samtools" ,samtools)
diff --git a/gnu/packages/patches/bedtools-32bit-compilation.patch b/gnu/packages/patches/bedtools-32bit-compilation.patch
new file mode 100644
index 0000000..0a4e710
--- /dev/null
+++ b/gnu/packages/patches/bedtools-32bit-compilation.patch
@@ -0,0 +1,168 @@
+From b47dbefcb57f8e6c4fe397f64346338620740b71 Mon Sep 17 00:00:00 2001
+From: arq5x <arq5x@virginia.edu>
+Date: Wed, 15 Jul 2015 15:15:23 -0600
+Subject: [PATCH] settle on uint32_t signature for QuickString. Resolves #267
+ and #271?
+
+---
+ src/coverageFile/coverageFile.cpp | 24 ++++++++++++------------
+ src/utils/general/QuickString.cpp | 27 ++++++++++++++-------------
+ src/utils/general/QuickString.h   |  6 +++---
+ 3 files changed, 29 insertions(+), 28 deletions(-)
+
+diff --git a/src/coverageFile/coverageFile.cpp b/src/coverageFile/coverageFile.cpp
+index 859cfdc..0fb544b 100644
+--- a/src/coverageFile/coverageFile.cpp
++++ b/src/coverageFile/coverageFile.cpp
+@@ -83,11 +83,11 @@ void CoverageFile::giveFinalReport(RecordOutputMgr *outputMgr) {
+ 		float depthPct = (float)basesAtDepth / (float)_totalQueryLen;
+ 
+ 		_finalOutput = "all\t";
+-		_finalOutput.append(depth);
++		_finalOutput.append(static_cast<uint32_t>(depth));
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(basesAtDepth);
++		_finalOutput.append(static_cast<uint32_t>(basesAtDepth));
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(_totalQueryLen);
++		_finalOutput.append(static_cast<uint32_t>(_totalQueryLen));
+ 		_finalOutput.append("\t");
+ 		format(depthPct);
+ 
+@@ -138,7 +138,7 @@ size_t CoverageFile::countBasesAtDepth(size_t depth) {
+ 
+ void CoverageFile::doCounts(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
+ {
+-	_finalOutput = hits.size();
++	_finalOutput = static_cast<uint32_t>(hits.size());
+ 	outputMgr->printRecord(hits.getKey(), _finalOutput);
+ }
+ 
+@@ -147,9 +147,9 @@ void CoverageFile::doPerBase(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
+ 	//loop through all bases in query, printing full record and metrics for each
+ 	const Record * queryRec = hits.getKey();
+ 	for (size_t i= 0; i < _queryLen; i++) {
+-		_finalOutput = i +1;
++		_finalOutput = static_cast<uint32_t>(i+1);
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(_depthArray[i]);
++		_finalOutput.append(static_cast<uint32_t>(_depthArray[i]));
+ 
+ 		outputMgr->printRecord(queryRec, _finalOutput);
+ 	}
+@@ -181,11 +181,11 @@ void CoverageFile::doHist(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
+ 		size_t numBasesAtDepth = iter->second;
+ 		float coveredBases = (float)numBasesAtDepth / (float)_queryLen;
+ 
+-		_finalOutput = depth;
++		_finalOutput = static_cast<uint32_t>(depth);
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(numBasesAtDepth);
++		_finalOutput.append(static_cast<uint32_t>(numBasesAtDepth));
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(_queryLen);
++		_finalOutput.append(static_cast<uint32_t>(_queryLen));
+ 		_finalOutput.append("\t");
+ 		format(coveredBases);
+ 
+@@ -199,11 +199,11 @@ void CoverageFile::doDefault(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
+ 	size_t nonZeroBases = _queryLen - countBasesAtDepth(0);
+ 	float coveredBases = (float)nonZeroBases / (float)_queryLen;
+ 
+-	_finalOutput = hits.size();
++	_finalOutput = static_cast<uint32_t>(hits.size());
+ 	_finalOutput.append("\t");
+-	_finalOutput.append(nonZeroBases);
++	_finalOutput.append(static_cast<uint32_t>(nonZeroBases));
+ 	_finalOutput.append("\t");
+-	_finalOutput.append(_queryLen);
++	_finalOutput.append(static_cast<uint32_t>(_queryLen));
+ 	_finalOutput.append("\t");
+ 	format(coveredBases);
+ 
+diff --git a/src/utils/general/QuickString.cpp b/src/utils/general/QuickString.cpp
+index 0757009..a83263e 100644
+--- a/src/utils/general/QuickString.cpp
++++ b/src/utils/general/QuickString.cpp
+@@ -105,11 +105,11 @@ QuickString &QuickString::operator = (uint32_t val) {
+ 	return *this;
+ }
+ 
+-QuickString &QuickString::operator = (size_t val) {
+-	clear();
+-	append(val);
+-	return *this;
+-}
++// QuickString &QuickString::operator = (size_t val) {
++// 	clear();
++// 	append(val);
++// 	return *this;
++// }
+ 
+ QuickString &QuickString::operator = (float val) {
+ 	clear();
+@@ -158,10 +158,11 @@ QuickString &QuickString::operator += (uint32_t num) {
+ 	return *this;
+ }
+ 
+-QuickString &QuickString::operator += (size_t num) {
+-	append(num);
+-	return *this;
+-}
++// QuickString &QuickString::operator += (size_t num) {
++// 	append(num);
++// 	return *this;
++// }
++
+ QuickString &QuickString::operator += (float num) {
+ 	append(num);
+ 	return *this;
+@@ -273,12 +274,12 @@ void QuickString::append(int num) {
+ }
+ 
+ void QuickString::append(uint32_t num) {
+-	int2str((int)num, *this, true);
++ 	int2str((int)num, *this, true);
+ }
+ 
+-void QuickString::append(size_t num) {
+-	int2str((int)num, *this, true);
+-}
++// void QuickString::append(size_t num) {
++// 	int2str((int)num, *this, true);
++// }
+ 
+ void QuickString::append(float num) {
+ 	append(ToString(num));
+diff --git a/src/utils/general/QuickString.h b/src/utils/general/QuickString.h
+index b43fdfc..6e6fa94 100644
+--- a/src/utils/general/QuickString.h
++++ b/src/utils/general/QuickString.h
+@@ -38,7 +38,7 @@ class QuickString {
+ 	QuickString &operator = (char);
+ 	QuickString &operator = (int);
+ 	QuickString &operator = (uint32_t);
+-	QuickString &operator = (size_t);
++	//QuickString &operator = (size_t);
+ 	QuickString &operator = (float);
+ 	QuickString &operator = (double);
+ 	QuickString &operator += (const QuickString &);
+@@ -47,7 +47,7 @@ class QuickString {
+ 	QuickString &operator += (char);
+ 	QuickString &operator += (int);
+ 	QuickString &operator += (uint32_t);
+-	QuickString &operator += (size_t);
++	//QuickString &operator += (size_t);
+ 	QuickString &operator += (float);
+ 	QuickString &operator += (double);
+ 
+@@ -74,7 +74,7 @@ class QuickString {
+ 	//for better performance.
+ 	void append(int num);
+ 	void append(uint32_t num);
+-	void append(size_t num);
++	//void append(size_t num);
+ 	void append(float num);
+ 	void append(double num);
+ 
+
-- 
2.4.3

Re: [PATCH] gnu: bedtools: Update to 2.24.0.

[Andreas Enge]

Hi Ben,

thanks a lot!

I made a few small modifications and pushed:

On Sat, Jul 25, 2015 at 11:37:57PM +1000, Ben Woodcroft wrote:
> * gnu/packages/patches/bedtools-32bit-compilation.patch: New file.
> * gnu/packages/bioinformatics.scm (bedtools)[source]: Add patch.

gnu-system.am was also modified.

> +              ;; Fixed in upstream, see
> +              ;; https://github.com/arq5x/bedtools2/issues/271

I moved this into the patch, we usually mention its rationale there.

The package still compiles on x86_64, let us hope that this patch solves
the problem on the other architectures!

Andreas