* [PATCH 0/1] Update pardre source hash. @ 2016-12-08 13:12 Ben Woodcroft 2016-12-08 13:12 ` [PATCH] gnu: pardre: Update " Ben Woodcroft 2016-12-08 13:37 ` [PATCH 0/1] Update pardre " Marius Bakke 0 siblings, 2 replies; 7+ messages in thread From: Ben Woodcroft @ 2016-12-08 13:12 UTC (permalink / raw) To: guix-devel Hi, It seems that the pardre source has been updated in place. I'm not sure what the procedure is for verifying that nothing untoward has taken place, since I cannot download and old version from the hydra content addressed mirror - it does not seem to exist there either. So I just assume all is above board and push? Thanks, ben. ^ permalink raw reply [flat|nested] 7+ messages in thread
* [PATCH] gnu: pardre: Update source hash. 2016-12-08 13:12 [PATCH 0/1] Update pardre source hash Ben Woodcroft @ 2016-12-08 13:12 ` Ben Woodcroft 2016-12-08 13:37 ` [PATCH 0/1] Update pardre " Marius Bakke 1 sibling, 0 replies; 7+ messages in thread From: Ben Woodcroft @ 2016-12-08 13:12 UTC (permalink / raw) To: guix-devel * gnu/packages/bioinformatics.scm (pardre)[source]: Update hash. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 625935dfd..eac42e7ac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5707,7 +5707,7 @@ Needleman-Wunsch).") version ".tar.gz")) (sha256 (base32 - "0zkyjzv4s8q2h5npalhirbk17r5b1h0n2a42mh7njzlf047h9bhy")))) + "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no tests included -- 2.11.0 ^ permalink raw reply related [flat|nested] 7+ messages in thread
* Re: [PATCH 0/1] Update pardre source hash. 2016-12-08 13:12 [PATCH 0/1] Update pardre source hash Ben Woodcroft 2016-12-08 13:12 ` [PATCH] gnu: pardre: Update " Ben Woodcroft @ 2016-12-08 13:37 ` Marius Bakke 2016-12-08 14:17 ` Ricardo Wurmus 1 sibling, 1 reply; 7+ messages in thread From: Marius Bakke @ 2016-12-08 13:37 UTC (permalink / raw) To: Ben Woodcroft, guix-devel [-- Attachment #1: Type: text/plain, Size: 781 bytes --] Ben Woodcroft <donttrustben@gmail.com> writes: > Hi, > > It seems that the pardre source has been updated in place. I'm not sure what > the procedure is for verifying that nothing untoward has taken place, since I > cannot download and old version from the hydra content addressed mirror - > it does not seem to exist there either. "diffoscope" has native support for tarballs and can quickly point out any differences. Perhaps Ricardo has a copy at the MDC? Just checking the substitutes ought to be sufficient. That said, I've seen this happen in other distros, even at projects that "should know better" such as Chromium, so I assume it was just a "quick and dirty" bugfix. According to sourceforge it was updated July 6th, so it has likely been garbage collected on Hydra. [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 487 bytes --] ^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: [PATCH 0/1] Update pardre source hash. 2016-12-08 13:37 ` [PATCH 0/1] Update pardre " Marius Bakke @ 2016-12-08 14:17 ` Ricardo Wurmus 2016-12-08 14:19 ` Ricardo Wurmus 2016-12-08 14:45 ` Marius Bakke 0 siblings, 2 replies; 7+ messages in thread From: Ricardo Wurmus @ 2016-12-08 14:17 UTC (permalink / raw) To: Marius Bakke; +Cc: guix-devel Marius Bakke <mbakke@fastmail.com> writes: > Ben Woodcroft <donttrustben@gmail.com> writes: > >> Hi, >> >> It seems that the pardre source has been updated in place. I'm not sure what >> the procedure is for verifying that nothing untoward has taken place, since I >> cannot download and old version from the hydra content addressed mirror - >> it does not seem to exist there either. > > "diffoscope" has native support for tarballs and can quickly point out > any differences. Perhaps Ricardo has a copy at the MDC? I do! I still have a copy of /gnu/store/xp2yzil11yk9askvpp56a8jjqynqb12k-ParDRe-rel1.1.5.tar.gz The diff looks very familiar. Could it be that this has happened before? Or maybe I noticed the changed hash before and forgot to submit an update...? Anyway, here’s the full diff: diff -ur ParDRe-rel1.1.5* diff -ur ParDRe-rel1.1.5/.cproject ParDRe-rel1.1.5-new/.cproject --- ParDRe-rel1.1.5/.cproject 2015-12-21 13:02:38.000000000 +0100 +++ ParDRe-rel1.1.5-new/.cproject 2016-07-05 14:10:22.000000000 +0200 @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> <?fileVersion 4.0.0?><cproject storage_type_id="org.eclipse.cdt.core.XmlProjectDescriptionStorage"> <storageModule moduleId="org.eclipse.cdt.core.settings"> - <cconfiguration id="0.1063792236"> - <storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="0.1063792236" moduleId="org.eclipse.cdt.core.settings" name="Default"> + <cconfiguration id="0.1124212066"> + <storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="0.1124212066" moduleId="org.eclipse.cdt.core.settings" name="Default"> <externalSettings/> <extensions> <extension id="org.eclipse.cdt.core.VCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/> @@ -14,23 +14,23 @@ </extensions> </storageModule> <storageModule moduleId="cdtBuildSystem" version="4.0.0"> - <configuration buildProperties="" description="" id="0.1063792236" name="Default" parent="org.eclipse.cdt.build.core.prefbase.cfg"> - <folderInfo id="0.1063792236." name="/" resourcePath=""> - <toolChain id="org.eclipse.cdt.build.core.prefbase.toolchain.1515125278" name="No ToolChain" resourceTypeBasedDiscovery="false" superClass="org.eclipse.cdt.build.core.prefbase.toolchain"> - <targetPlatform id="org.eclipse.cdt.build.core.prefbase.toolchain.1515125278.1242880487" name=""/> - <builder id="org.eclipse.cdt.build.core.settings.default.builder.570926900" keepEnvironmentInBuildfile="false" managedBuildOn="false" name="Gnu Make Builder" superClass="org.eclipse.cdt.build.core.settings.default.builder"/> - <tool id="org.eclipse.cdt.build.core.settings.holder.libs.347518546" name="holder for library settings" superClass="org.eclipse.cdt.build.core.settings.holder.libs"/> - <tool id="org.eclipse.cdt.build.core.settings.holder.82023976" name="CUDA C" superClass="org.eclipse.cdt.build.core.settings.holder"> - <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1424918997" languageId="com.nvidia.cuda.ide.editor.cudac" languageName="CUDA C" sourceContentType="com.nvidia.cuda.ide.cudac" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> + <configuration buildProperties="" description="" id="0.1124212066" name="Default" parent="org.eclipse.cdt.build.core.prefbase.cfg"> + <folderInfo id="0.1124212066." name="/" resourcePath=""> + <toolChain id="org.eclipse.cdt.build.core.prefbase.toolchain.383755441" name="No ToolChain" resourceTypeBasedDiscovery="false" superClass="org.eclipse.cdt.build.core.prefbase.toolchain"> + <targetPlatform id="org.eclipse.cdt.build.core.prefbase.toolchain.383755441.64028961" name=""/> + <builder id="org.eclipse.cdt.build.core.settings.default.builder.665305288" keepEnvironmentInBuildfile="false" managedBuildOn="false" name="Gnu Make Builder" superClass="org.eclipse.cdt.build.core.settings.default.builder"/> + <tool id="org.eclipse.cdt.build.core.settings.holder.libs.867303933" name="holder for library settings" superClass="org.eclipse.cdt.build.core.settings.holder.libs"/> + <tool id="org.eclipse.cdt.build.core.settings.holder.1856622227" name="CUDA C" superClass="org.eclipse.cdt.build.core.settings.holder"> + <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.909738042" languageId="com.nvidia.cuda.ide.editor.cudac" languageName="CUDA C" sourceContentType="com.nvidia.cuda.ide.cudac" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> </tool> - <tool id="org.eclipse.cdt.build.core.settings.holder.6574913" name="Assembly" superClass="org.eclipse.cdt.build.core.settings.holder"> - <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1386917292" languageId="org.eclipse.cdt.core.assembly" languageName="Assembly" sourceContentType="org.eclipse.cdt.core.asmSource" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> + <tool id="org.eclipse.cdt.build.core.settings.holder.725125478" name="Assembly" superClass="org.eclipse.cdt.build.core.settings.holder"> + <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.724128993" languageId="org.eclipse.cdt.core.assembly" languageName="Assembly" sourceContentType="org.eclipse.cdt.core.asmSource" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> </tool> - <tool id="org.eclipse.cdt.build.core.settings.holder.262515108" name="GNU C++" superClass="org.eclipse.cdt.build.core.settings.holder"> - <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1691140733" languageId="org.eclipse.cdt.core.g++" languageName="GNU C++" sourceContentType="org.eclipse.cdt.core.cxxSource,org.eclipse.cdt.core.cxxHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> + <tool id="org.eclipse.cdt.build.core.settings.holder.1986690789" name="GNU C++" superClass="org.eclipse.cdt.build.core.settings.holder"> + <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.732922424" languageId="org.eclipse.cdt.core.g++" languageName="GNU C++" sourceContentType="org.eclipse.cdt.core.cxxSource,org.eclipse.cdt.core.cxxHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> </tool> - <tool id="org.eclipse.cdt.build.core.settings.holder.1213540964" name="GNU C" superClass="org.eclipse.cdt.build.core.settings.holder"> - <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.452835573" languageId="org.eclipse.cdt.core.gcc" languageName="GNU C" sourceContentType="org.eclipse.cdt.core.cSource,org.eclipse.cdt.core.cHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> + <tool id="org.eclipse.cdt.build.core.settings.holder.549406725" name="GNU C" superClass="org.eclipse.cdt.build.core.settings.holder"> + <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1364314318" languageId="org.eclipse.cdt.core.gcc" languageName="GNU C" sourceContentType="org.eclipse.cdt.core.cSource,org.eclipse.cdt.core.cHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> </tool> </toolChain> </folderInfo> @@ -41,41 +41,44 @@ </cconfiguration> </storageModule> <storageModule moduleId="cdtBuildSystem" version="4.0.0"> - <project id="ParDRe-V5.null.640329154" name="ParDRe-V5"/> + <project id="ParDRe-rel1.1.5.null.1822510023" name="ParDRe-rel1.1.5"/> </storageModule> <storageModule moduleId="scannerConfiguration"> <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> - <scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.cpp.956304547"> - <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/> - </scannerConfigBuildInfo> <scannerConfigBuildInfo instanceId="0.1927259477"> <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> </scannerConfigBuildInfo> - <scannerConfigBuildInfo instanceId="0.823736429"> + <scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.c.198358939"> + <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/> + </scannerConfigBuildInfo> + <scannerConfigBuildInfo instanceId="0.1063792236"> <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> </scannerConfigBuildInfo> - <scannerConfigBuildInfo instanceId="0.1602656032"> + <scannerConfigBuildInfo instanceId="0.1124212066"> <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> </scannerConfigBuildInfo> + <scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.cpp.956304547"> + <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/> + </scannerConfigBuildInfo> <scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.cu.2021164641"> <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/> </scannerConfigBuildInfo> - <scannerConfigBuildInfo instanceId="0.1773641691"> + <scannerConfigBuildInfo instanceId="0.823736429"> <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> </scannerConfigBuildInfo> - <scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.c.198358939"> - <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/> + <scannerConfigBuildInfo instanceId="0.1773641691"> + <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> </scannerConfigBuildInfo> <scannerConfigBuildInfo instanceId="0.629582981"> <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> </scannerConfigBuildInfo> - <scannerConfigBuildInfo instanceId="0.1063792236"> + <scannerConfigBuildInfo instanceId="0.553699542"> <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> </scannerConfigBuildInfo> <scannerConfigBuildInfo instanceId="0.620900899"> <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> </scannerConfigBuildInfo> - <scannerConfigBuildInfo instanceId="0.553699542"> + <scannerConfigBuildInfo instanceId="0.1602656032"> <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> </scannerConfigBuildInfo> </storageModule> diff -ur ParDRe-rel1.1.5/PairedEnd.cpp ParDRe-rel1.1.5-new/PairedEnd.cpp --- ParDRe-rel1.1.5/PairedEnd.cpp 2016-05-18 11:46:38.000000000 +0200 +++ ParDRe-rel1.1.5-new/PairedEnd.cpp 2016-07-06 12:15:02.000000000 +0200 @@ -210,6 +210,7 @@ } } } + fflush(NULL); } MPI::COMM_WORLD.Barrier(); } diff -ur ParDRe-rel1.1.5/SingleEnd.cpp ParDRe-rel1.1.5-new/SingleEnd.cpp --- ParDRe-rel1.1.5/SingleEnd.cpp 2016-05-18 11:47:07.000000000 +0200 +++ ParDRe-rel1.1.5-new/SingleEnd.cpp 2016-07-06 12:13:13.000000000 +0200 @@ -27,12 +27,12 @@ if(!myRank){ Utils::log("Process %d/%d: To print in %s\n", myRank, MPI::COMM_WORLD.Get_size(), outPath.c_str()); } - if(myRank){ + /*if(myRank){ outPath.append("_id"); outPath.append(to_string(myRank)); } _parserOut = new SeqFileParser(options, outPath.c_str(), true, false); - _parserOut->setFormat(_parser->getFormat()); + _parserOut->setFormat(_parser->getFormat());*/ } } @@ -186,6 +186,7 @@ } } } + fflush(NULL); } MPI::COMM_WORLD.Barrier(); } diff -ur ParDRe-rel1.1.5/Utils.cpp ParDRe-rel1.1.5-new/Utils.cpp --- ParDRe-rel1.1.5/Utils.cpp 2015-11-17 16:16:54.000000000 +0100 +++ ParDRe-rel1.1.5-new/Utils.cpp 2016-05-27 14:03:38.000000000 +0200 @@ -62,5 +62,12 @@ } uint64_t Utils::popcount(uint64_t v){ - return __builtin_popcount(v); + uint64_t b = (v & 0x5555555555555555LU) + (v >> 1 & 0x5555555555555555LU); + b = (b & 0x3333333333333333LU) + (b >> 2 & 0x3333333333333333LU); + b = b + (b >> 4) & 0x0F0F0F0F0F0F0F0FLU; + b = b + (b >> 8); + b = b + (b >> 16); + b = b + (b >> 32) & 0x0000007F; + + return b; } ^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: [PATCH 0/1] Update pardre source hash. 2016-12-08 14:17 ` Ricardo Wurmus @ 2016-12-08 14:19 ` Ricardo Wurmus 2016-12-08 14:45 ` Marius Bakke 1 sibling, 0 replies; 7+ messages in thread From: Ricardo Wurmus @ 2016-12-08 14:19 UTC (permalink / raw) To: Marius Bakke; +Cc: guix-devel Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes: > Marius Bakke <mbakke@fastmail.com> writes: > >> Ben Woodcroft <donttrustben@gmail.com> writes: >> >>> Hi, >>> >>> It seems that the pardre source has been updated in place. I'm not sure what >>> the procedure is for verifying that nothing untoward has taken place, since I >>> cannot download and old version from the hydra content addressed mirror - >>> it does not seem to exist there either. >> >> "diffoscope" has native support for tarballs and can quickly point out >> any differences. Perhaps Ricardo has a copy at the MDC? > > I do! I still have a copy of > /gnu/store/xp2yzil11yk9askvpp56a8jjqynqb12k-ParDRe-rel1.1.5.tar.gz > > The diff looks very familiar. Could it be that this has happened > before? Or maybe I noticed the changed hash before and forgot to submit > an update...? In fact, Leo informed me about this in July, but it seems that both of us forgot to follow up on this. Thanks, Ben, for catching it! ~~ Ricardo ^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: [PATCH 0/1] Update pardre source hash. 2016-12-08 14:17 ` Ricardo Wurmus 2016-12-08 14:19 ` Ricardo Wurmus @ 2016-12-08 14:45 ` Marius Bakke 2016-12-10 1:08 ` Ben Woodcroft 1 sibling, 1 reply; 7+ messages in thread From: Marius Bakke @ 2016-12-08 14:45 UTC (permalink / raw) To: Ricardo Wurmus; +Cc: guix-devel [-- Attachment #1: Type: text/plain, Size: 13733 bytes --] Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes: > Marius Bakke <mbakke@fastmail.com> writes: > >> Ben Woodcroft <donttrustben@gmail.com> writes: >> >>> Hi, >>> >>> It seems that the pardre source has been updated in place. I'm not sure what >>> the procedure is for verifying that nothing untoward has taken place, since I >>> cannot download and old version from the hydra content addressed mirror - >>> it does not seem to exist there either. >> >> "diffoscope" has native support for tarballs and can quickly point out >> any differences. Perhaps Ricardo has a copy at the MDC? > > I do! I still have a copy of > /gnu/store/xp2yzil11yk9askvpp56a8jjqynqb12k-ParDRe-rel1.1.5.tar.gz > > The diff looks very familiar. Could it be that this has happened > before? Or maybe I noticed the changed hash before and forgot to submit > an update...? > > Anyway, here’s the full diff: > > > diff -ur ParDRe-rel1.1.5* > diff -ur ParDRe-rel1.1.5/.cproject ParDRe-rel1.1.5-new/.cproject > --- ParDRe-rel1.1.5/.cproject 2015-12-21 13:02:38.000000000 +0100 > +++ ParDRe-rel1.1.5-new/.cproject 2016-07-05 14:10:22.000000000 +0200 > @@ -1,8 +1,8 @@ > <?xml version="1.0" encoding="UTF-8" standalone="no"?> > <?fileVersion 4.0.0?><cproject storage_type_id="org.eclipse.cdt.core.XmlProjectDescriptionStorage"> > <storageModule moduleId="org.eclipse.cdt.core.settings"> > - <cconfiguration id="0.1063792236"> > - <storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="0.1063792236" moduleId="org.eclipse.cdt.core.settings" name="Default"> > + <cconfiguration id="0.1124212066"> > + <storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="0.1124212066" moduleId="org.eclipse.cdt.core.settings" name="Default"> > <externalSettings/> > <extensions> > <extension id="org.eclipse.cdt.core.VCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/> > @@ -14,23 +14,23 @@ > </extensions> > </storageModule> > <storageModule moduleId="cdtBuildSystem" version="4.0.0"> > - <configuration buildProperties="" description="" id="0.1063792236" name="Default" parent="org.eclipse.cdt.build.core.prefbase.cfg"> > - <folderInfo id="0.1063792236." name="/" resourcePath=""> > - <toolChain id="org.eclipse.cdt.build.core.prefbase.toolchain.1515125278" name="No ToolChain" resourceTypeBasedDiscovery="false" superClass="org.eclipse.cdt.build.core.prefbase.toolchain"> > - <targetPlatform id="org.eclipse.cdt.build.core.prefbase.toolchain.1515125278.1242880487" name=""/> > - <builder id="org.eclipse.cdt.build.core.settings.default.builder.570926900" keepEnvironmentInBuildfile="false" managedBuildOn="false" name="Gnu Make Builder" superClass="org.eclipse.cdt.build.core.settings.default.builder"/> > - <tool id="org.eclipse.cdt.build.core.settings.holder.libs.347518546" name="holder for library settings" superClass="org.eclipse.cdt.build.core.settings.holder.libs"/> > - <tool id="org.eclipse.cdt.build.core.settings.holder.82023976" name="CUDA C" superClass="org.eclipse.cdt.build.core.settings.holder"> > - <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1424918997" languageId="com.nvidia.cuda.ide.editor.cudac" languageName="CUDA C" sourceContentType="com.nvidia.cuda.ide.cudac" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> > + <configuration buildProperties="" description="" id="0.1124212066" name="Default" parent="org.eclipse.cdt.build.core.prefbase.cfg"> > + <folderInfo id="0.1124212066." name="/" resourcePath=""> > + <toolChain id="org.eclipse.cdt.build.core.prefbase.toolchain.383755441" name="No ToolChain" resourceTypeBasedDiscovery="false" superClass="org.eclipse.cdt.build.core.prefbase.toolchain"> > + <targetPlatform id="org.eclipse.cdt.build.core.prefbase.toolchain.383755441.64028961" name=""/> > + <builder id="org.eclipse.cdt.build.core.settings.default.builder.665305288" keepEnvironmentInBuildfile="false" managedBuildOn="false" name="Gnu Make Builder" superClass="org.eclipse.cdt.build.core.settings.default.builder"/> > + <tool id="org.eclipse.cdt.build.core.settings.holder.libs.867303933" name="holder for library settings" superClass="org.eclipse.cdt.build.core.settings.holder.libs"/> > + <tool id="org.eclipse.cdt.build.core.settings.holder.1856622227" name="CUDA C" superClass="org.eclipse.cdt.build.core.settings.holder"> > + <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.909738042" languageId="com.nvidia.cuda.ide.editor.cudac" languageName="CUDA C" sourceContentType="com.nvidia.cuda.ide.cudac" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> > </tool> > - <tool id="org.eclipse.cdt.build.core.settings.holder.6574913" name="Assembly" superClass="org.eclipse.cdt.build.core.settings.holder"> > - <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1386917292" languageId="org.eclipse.cdt.core.assembly" languageName="Assembly" sourceContentType="org.eclipse.cdt.core.asmSource" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> > + <tool id="org.eclipse.cdt.build.core.settings.holder.725125478" name="Assembly" superClass="org.eclipse.cdt.build.core.settings.holder"> > + <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.724128993" languageId="org.eclipse.cdt.core.assembly" languageName="Assembly" sourceContentType="org.eclipse.cdt.core.asmSource" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> > </tool> > - <tool id="org.eclipse.cdt.build.core.settings.holder.262515108" name="GNU C++" superClass="org.eclipse.cdt.build.core.settings.holder"> > - <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1691140733" languageId="org.eclipse.cdt.core.g++" languageName="GNU C++" sourceContentType="org.eclipse.cdt.core.cxxSource,org.eclipse.cdt.core.cxxHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> > + <tool id="org.eclipse.cdt.build.core.settings.holder.1986690789" name="GNU C++" superClass="org.eclipse.cdt.build.core.settings.holder"> > + <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.732922424" languageId="org.eclipse.cdt.core.g++" languageName="GNU C++" sourceContentType="org.eclipse.cdt.core.cxxSource,org.eclipse.cdt.core.cxxHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> > </tool> > - <tool id="org.eclipse.cdt.build.core.settings.holder.1213540964" name="GNU C" superClass="org.eclipse.cdt.build.core.settings.holder"> > - <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.452835573" languageId="org.eclipse.cdt.core.gcc" languageName="GNU C" sourceContentType="org.eclipse.cdt.core.cSource,org.eclipse.cdt.core.cHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> > + <tool id="org.eclipse.cdt.build.core.settings.holder.549406725" name="GNU C" superClass="org.eclipse.cdt.build.core.settings.holder"> > + <inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1364314318" languageId="org.eclipse.cdt.core.gcc" languageName="GNU C" sourceContentType="org.eclipse.cdt.core.cSource,org.eclipse.cdt.core.cHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/> > </tool> > </toolChain> > </folderInfo> > @@ -41,41 +41,44 @@ > </cconfiguration> > </storageModule> > <storageModule moduleId="cdtBuildSystem" version="4.0.0"> > - <project id="ParDRe-V5.null.640329154" name="ParDRe-V5"/> > + <project id="ParDRe-rel1.1.5.null.1822510023" name="ParDRe-rel1.1.5"/> > </storageModule> > <storageModule moduleId="scannerConfiguration"> > <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> > - <scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.cpp.956304547"> > - <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/> > - </scannerConfigBuildInfo> > <scannerConfigBuildInfo instanceId="0.1927259477"> > <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> > </scannerConfigBuildInfo> > - <scannerConfigBuildInfo instanceId="0.823736429"> > + <scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.c.198358939"> > + <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/> > + </scannerConfigBuildInfo> > + <scannerConfigBuildInfo instanceId="0.1063792236"> > <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> > </scannerConfigBuildInfo> > - <scannerConfigBuildInfo instanceId="0.1602656032"> > + <scannerConfigBuildInfo instanceId="0.1124212066"> > <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> > </scannerConfigBuildInfo> > + <scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.cpp.956304547"> > + <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/> > + </scannerConfigBuildInfo> > <scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.cu.2021164641"> > <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/> > </scannerConfigBuildInfo> > - <scannerConfigBuildInfo instanceId="0.1773641691"> > + <scannerConfigBuildInfo instanceId="0.823736429"> > <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> > </scannerConfigBuildInfo> > - <scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.c.198358939"> > - <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/> > + <scannerConfigBuildInfo instanceId="0.1773641691"> > + <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> > </scannerConfigBuildInfo> > <scannerConfigBuildInfo instanceId="0.629582981"> > <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> > </scannerConfigBuildInfo> > - <scannerConfigBuildInfo instanceId="0.1063792236"> > + <scannerConfigBuildInfo instanceId="0.553699542"> > <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> > </scannerConfigBuildInfo> > <scannerConfigBuildInfo instanceId="0.620900899"> > <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> > </scannerConfigBuildInfo> > - <scannerConfigBuildInfo instanceId="0.553699542"> > + <scannerConfigBuildInfo instanceId="0.1602656032"> > <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/> > </scannerConfigBuildInfo> > </storageModule> > diff -ur ParDRe-rel1.1.5/PairedEnd.cpp ParDRe-rel1.1.5-new/PairedEnd.cpp > --- ParDRe-rel1.1.5/PairedEnd.cpp 2016-05-18 11:46:38.000000000 +0200 > +++ ParDRe-rel1.1.5-new/PairedEnd.cpp 2016-07-06 12:15:02.000000000 +0200 > @@ -210,6 +210,7 @@ > } > } > } > + fflush(NULL); > } > MPI::COMM_WORLD.Barrier(); > } > diff -ur ParDRe-rel1.1.5/SingleEnd.cpp ParDRe-rel1.1.5-new/SingleEnd.cpp > --- ParDRe-rel1.1.5/SingleEnd.cpp 2016-05-18 11:47:07.000000000 +0200 > +++ ParDRe-rel1.1.5-new/SingleEnd.cpp 2016-07-06 12:13:13.000000000 +0200 > @@ -27,12 +27,12 @@ > if(!myRank){ > Utils::log("Process %d/%d: To print in %s\n", myRank, MPI::COMM_WORLD.Get_size(), outPath.c_str()); > } > - if(myRank){ > + /*if(myRank){ > outPath.append("_id"); > outPath.append(to_string(myRank)); > } > _parserOut = new SeqFileParser(options, outPath.c_str(), true, false); > - _parserOut->setFormat(_parser->getFormat()); > + _parserOut->setFormat(_parser->getFormat());*/ > } > } > > @@ -186,6 +186,7 @@ > } > } > } > + fflush(NULL); > } > MPI::COMM_WORLD.Barrier(); > } > diff -ur ParDRe-rel1.1.5/Utils.cpp ParDRe-rel1.1.5-new/Utils.cpp > --- ParDRe-rel1.1.5/Utils.cpp 2015-11-17 16:16:54.000000000 +0100 > +++ ParDRe-rel1.1.5-new/Utils.cpp 2016-05-27 14:03:38.000000000 +0200 > @@ -62,5 +62,12 @@ > } > > uint64_t Utils::popcount(uint64_t v){ > - return __builtin_popcount(v); > + uint64_t b = (v & 0x5555555555555555LU) + (v >> 1 & 0x5555555555555555LU); > + b = (b & 0x3333333333333333LU) + (b >> 2 & 0x3333333333333333LU); > + b = b + (b >> 4) & 0x0F0F0F0F0F0F0F0FLU; > + b = b + (b >> 8); > + b = b + (b >> 16); > + b = b + (b >> 32) & 0x0000007F; > + > + return b; > } Looks like a portability fix, although I can't really tell what that bitshifting is about. Assuming it's the same as the GCC builtin :-) [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 487 bytes --] ^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: [PATCH 0/1] Update pardre source hash. 2016-12-08 14:45 ` Marius Bakke @ 2016-12-10 1:08 ` Ben Woodcroft 0 siblings, 0 replies; 7+ messages in thread From: Ben Woodcroft @ 2016-12-10 1:08 UTC (permalink / raw) To: Marius Bakke, Ricardo Wurmus; +Cc: guix-devel On 09/12/16 00:45, Marius Bakke wrote: > Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes: > >> Marius Bakke <mbakke@fastmail.com> writes: >> >>> Ben Woodcroft <donttrustben@gmail.com> writes: >>> >>>> Hi, >>>> >>>> It seems that the pardre source has been updated in place. I'm not sure what >>>> the procedure is for verifying that nothing untoward has taken place, since I >>>> cannot download and old version from the hydra content addressed mirror - >>>> it does not seem to exist there either. >>> "diffoscope" has native support for tarballs and can quickly point out >>> any differences. Perhaps Ricardo has a copy at the MDC? >> I do! I still have a copy of >> /gnu/store/xp2yzil11yk9askvpp56a8jjqynqb12k-ParDRe-rel1.1.5.tar.gz >> >> The diff looks very familiar. Could it be that this has happened >> before? Or maybe I noticed the changed hash before and forgot to submit >> an update...?} >> >> [..] > Looks like a portability fix, although I can't really tell what that > bitshifting is about. Assuming it's the same as the GCC builtin :-) Seems harmless enough, thanks you two. I pushed an update to the hash to master, updating the version to "1.1.5-1" to reflect the fact that a change has been made, '7922ab8fe87154f3ccaa7daf9304632f974fbe5d'. Is it possible to exclude sources from the GC on hydra or more importantly the new build system, for this reason? ben ^ permalink raw reply [flat|nested] 7+ messages in thread
end of thread, other threads:[~2016-12-10 1:08 UTC | newest] Thread overview: 7+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2016-12-08 13:12 [PATCH 0/1] Update pardre source hash Ben Woodcroft 2016-12-08 13:12 ` [PATCH] gnu: pardre: Update " Ben Woodcroft 2016-12-08 13:37 ` [PATCH 0/1] Update pardre " Marius Bakke 2016-12-08 14:17 ` Ricardo Wurmus 2016-12-08 14:19 ` Ricardo Wurmus 2016-12-08 14:45 ` Marius Bakke 2016-12-10 1:08 ` Ben Woodcroft
Code repositories for project(s) associated with this external index https://git.savannah.gnu.org/cgit/guix.git This is an external index of several public inboxes, see mirroring instructions on how to clone and mirror all data and code used by this external index.