[Debian-med-packaging] Droping symbols file from staden-io-lib?

Tue Jul 7 09:00:49 UTC 2015

Hi Charles,

On Tue, Jul 07, 2015 at 05:09:36PM +0900, Charles Plessy wrote:
>  - in the master branch, pull the upstream master branch and its tags.
> 
>     git pull https://github.com/arq5x/bedtools2 --tags

Hmmmm, I added a debian/README.source to enable me (or others)
remembering how to work with this repository.  This file basically
contains the items you wrote here but also a

   FIXME: If this leads to lot of merge conflicts, do what?

I'm just in the first step confronted with lots of conflicts which
do not seem to be fun to solve.

> Whenever there are chances that I may have changes to propose upstream via
> pull requests on GitHub, I prefer this workflow. 

I do not wnat to sound stubborn and I'm perfectly willing to learn but
the problems I am facing as a packager (see attached conflict log) seem
to be larger than the difference between a pull request and a

   git am <quiltpatch>

at upstream side.  Am I missing something?

>From a Debian users perspective I think bedtools last version would have
been uploaded yesterday (provided no build problems might occure) if
bedtools would have a default workflow.  This is IMHO in the interest of
our users.  Don't you think upstream could import quilt patches
similarly easy as they could pull?

Kind regards

       Andreas.

-- 
http://fam-tille.de
-------------- next part --------------
>From https://github.com/arq5x/bedtools2
 * branch            HEAD       -> FETCH_HEAD
Auto packing the repository in background for optimum performance.
See "git help gc" for manual housekeeping.
First, rewinding head to replay your work on top of it...
Applying: Imported Upstream version 2.20.1
Using index info to reconstruct a base tree...
M	Makefile
M	README.md
M	RELEASE_HISTORY
M	docs/conf.py
M	docs/content/installation.rst
M	docs/content/tools/jaccard.rst
M	docs/content/tools/map.rst
M	docs/content/tools/merge.rst
M	docs/content/tools/unionbedg.rst
M	docs/index.rst
M	src/intersectFile/intersectFile.cpp
M	src/jaccard/Makefile
M	src/jaccard/jaccard.cpp
M	src/jaccard/jaccard.h
A	src/jaccard/jaccardMain.cpp
M	src/mapFile/mapFile.h
A	src/mapFile/mapMain.cpp
A	src/mergeBed/Makefile
A	src/mergeBed/mergeBed.cpp
A	src/mergeBed/mergeBed.h
A	src/mergeBed/mergeMain.cpp
M	src/nekSandbox1/nekSandboxMain.cpp
M	src/nucBed/nucBed.cpp
A	src/sampleFile/SampleFile.cpp
M	src/shuffleBed/shuffleBed.cpp
M	src/shuffleBed/shuffleBedMain.cpp
M	src/slopBed/slopBed.cpp
M	src/utils/BamTools/src/api/BamAlignment.h
M	src/utils/BamTools/src/api/SamHeader.h
M	src/utils/BamTools/src/api/internal/io/TcpSocketEngine_p.h
M	src/utils/BamTools/src/api/internal/sam/SamHeaderValidator_p.h
M	src/utils/BinTree/BinTree.cpp
M	src/utils/BlockedIntervals/BlockedIntervals.cpp
M	src/utils/Contexts/ContextBase.cpp
M	src/utils/Contexts/ContextBase.h
M	src/utils/Contexts/ContextMap.cpp
M	src/utils/Contexts/ContextMap.h
M	src/utils/Contexts/Makefile
M	src/utils/FileRecordTools/FileReaders/BamFileReader.cpp
M	src/utils/FileRecordTools/FileReaders/BamFileReader.h
M	src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
M	src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
M	src/utils/FileRecordTools/FileReaders/InputStreamMgr.h
M	src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp
M	src/utils/FileRecordTools/FileRecordMgr.cpp
M	src/utils/FileRecordTools/FileRecordMgr.h
M	src/utils/FileRecordTools/Makefile
M	src/utils/FileRecordTools/Records/BamRecord.cpp
M	src/utils/FileRecordTools/Records/BamRecord.h
M	src/utils/FileRecordTools/Records/BlockMgr.cpp
M	src/utils/FileRecordTools/Records/BlockMgr.h
M	src/utils/FileRecordTools/Records/Makefile
M	src/utils/FileRecordTools/Records/Record.h
M	src/utils/FileRecordTools/Records/RecordMgr.cpp
M	src/utils/FileRecordTools/Records/RecordMgr.h
A	src/utils/FileRecordTools/Records/recordsTar.tar.gz
M	src/utils/GenomeFile/NewGenomeFile.cpp
M	src/utils/KeyListOps/KeyListOps.cpp
M	src/utils/KeyListOps/KeyListOps.h
M	src/utils/KeyListOps/KeyListOpsMethods.cpp
M	src/utils/KeyListOps/KeyListOpsMethods.h
M	src/utils/NewChromsweep/NewChromsweep.cpp
M	src/utils/RecordOutputMgr/RecordOutputMgr.cpp
M	src/utils/RecordOutputMgr/RecordOutputMgr.h
M	src/utils/bedFile/bedFile.cpp
M	src/utils/bedFile/bedFile.h
M	src/utils/fileType/FileRecordTypeChecker.cpp
M	src/utils/fileType/FileRecordTypeChecker.h
M	src/utils/fileType/fileType.cpp
A	src/utils/general/DualQueue.h
M	src/utils/general/Makefile
M	src/utils/general/ParseTools.cpp
M	src/utils/general/ParseTools.h
M	src/utils/general/QuickString.h
M	src/utils/version/version_release.txt
M	test/general/test-general.sh
M	test/intersect/new_test-intersect.sh
M	test/jaccard/test-jaccard.sh
M	test/map/test-map.sh
M	test/merge/test-merge.sh
M	test/sample/test-sample.sh
M	test/slop/test-slop.sh
M	test/test.sh
<stdin>:160: trailing whitespace.
3. In addition, it supports multiple chromosome sorting criterion by supplying a genome file that defines the expected chromosome order. Here is an example of how to run map with datasets having chromosomes sorted in "version" order, as opposed to the lexicographical chrom order that is the norm. 
<stdin>:166: trailing whitespace.
bedtools 
<stdin>:202: trailing whitespace.
The 2.18.0 release leverages these improvements in the "intersect" tool.  Forthcoming releases will see the new API applied to other tools, but we started with intersect as it is the most widely used tool in the suite. 
<stdin>:204: trailing whitespace.
Performance with sorted datasets. The "chromsweep" algorithm we use for detecting intersections is now **60 times faster** than when it was first release in version 2.16.2, and is 15 times than the 2.17 release. This makes the algorithm slightly faster that the algorithm used in the bedops ``bedmap`` tool. As an example, the following [figure](https://dl.dropboxusercontent.com/u/515640/bedtools-intersect-sorteddata.png) demonstrates the speed when intersecting GENCODE exons against 1, 10, and 100 million BAM alignments from an exome capture experiment. Whereas in version 2.16.2 this wuld have taken 80 minutes, **it now takes 80 seconds**. 
<stdin>:214: trailing whitespace.
order (e.g. chr1, chr10, etc. or 1, 10, etc.). Starting with this release, we now simply require by default 
warning: squelched 136 whitespace errors
warning: 141 lines add whitespace errors.
Falling back to patching base and 3-way merge...
Auto-merging test/test.sh
CONFLICT (content): Merge conflict in test/test.sh
Auto-merging test/slop/test-slop.sh
CONFLICT (content): Merge conflict in test/slop/test-slop.sh
Auto-merging test/merge/test-merge.sh
CONFLICT (content): Merge conflict in test/merge/test-merge.sh
Auto-merging test/merge/bamCol9Mean.txt
CONFLICT (add/add): Merge conflict in test/merge/bamCol9Mean.txt
Auto-merging test/merge/bamCol8Mean.txt
CONFLICT (add/add): Merge conflict in test/merge/bamCol8Mean.txt
Auto-merging test/merge/bamCol5Mean.txt
CONFLICT (add/add): Merge conflict in test/merge/bamCol5Mean.txt
Auto-merging test/merge/bamCol4Mean.txt
CONFLICT (add/add): Merge conflict in test/merge/bamCol4Mean.txt
Auto-merging test/map/test-map.sh
CONFLICT (content): Merge conflict in test/map/test-map.sh
Auto-merging test/jaccard/test-jaccard.sh
CONFLICT (content): Merge conflict in test/jaccard/test-jaccard.sh
Auto-merging test/intersect/new_test-intersect.sh
CONFLICT (content): Merge conflict in test/intersect/new_test-intersect.sh
Auto-merging test/general/test-general.sh
CONFLICT (content): Merge conflict in test/general/test-general.sh
Auto-merging src/utils/version/version_release.txt
CONFLICT (content): Merge conflict in src/utils/version/version_release.txt
Auto-merging src/utils/general/Tokenizer.h
CONFLICT (add/add): Merge conflict in src/utils/general/Tokenizer.h
Auto-merging src/utils/general/Tokenizer.cpp
CONFLICT (add/add): Merge conflict in src/utils/general/Tokenizer.cpp
Auto-merging src/utils/general/ParseTools.cpp
CONFLICT (content): Merge conflict in src/utils/general/ParseTools.cpp
Auto-merging src/utils/general/Makefile
CONFLICT (content): Merge conflict in src/utils/general/Makefile
Auto-merging src/utils/fileType/FileRecordTypeChecker.h
CONFLICT (content): Merge conflict in src/utils/fileType/FileRecordTypeChecker.h
Auto-merging src/utils/fileType/FileRecordTypeChecker.cpp
CONFLICT (content): Merge conflict in src/utils/fileType/FileRecordTypeChecker.cpp
Auto-merging src/utils/RecordOutputMgr/RecordOutputMgr.h
CONFLICT (content): Merge conflict in src/utils/RecordOutputMgr/RecordOutputMgr.h
Auto-merging src/utils/RecordOutputMgr/RecordOutputMgr.cpp
CONFLICT (content): Merge conflict in src/utils/RecordOutputMgr/RecordOutputMgr.cpp
Auto-merging src/utils/NewChromsweep/NewChromsweep.cpp
CONFLICT (content): Merge conflict in src/utils/NewChromsweep/NewChromsweep.cpp
Auto-merging src/utils/KeyListOps/KeyListOpsMethods.h
CONFLICT (content): Merge conflict in src/utils/KeyListOps/KeyListOpsMethods.h
Auto-merging src/utils/KeyListOps/KeyListOpsMethods.cpp
CONFLICT (content): Merge conflict in src/utils/KeyListOps/KeyListOpsMethods.cpp
Auto-merging src/utils/KeyListOps/KeyListOps.h
CONFLICT (content): Merge conflict in src/utils/KeyListOps/KeyListOps.h
Auto-merging src/utils/KeyListOps/KeyListOps.cpp
CONFLICT (content): Merge conflict in src/utils/KeyListOps/KeyListOps.cpp
Auto-merging src/utils/FileRecordTools/Records/StrandQueue.h
CONFLICT (add/add): Merge conflict in src/utils/FileRecordTools/Records/StrandQueue.h
Auto-merging src/utils/FileRecordTools/Records/Record.h
CONFLICT (content): Merge conflict in src/utils/FileRecordTools/Records/Record.h
Auto-merging src/utils/FileRecordTools/Records/Makefile
CONFLICT (content): Merge conflict in src/utils/FileRecordTools/Records/Makefile
Auto-merging src/utils/FileRecordTools/Records/BlockMgr.h
Auto-merging src/utils/FileRecordTools/Records/BamRecord.h
CONFLICT (content): Merge conflict in src/utils/FileRecordTools/Records/BamRecord.h
Auto-merging src/utils/FileRecordTools/Records/BamRecord.cpp
CONFLICT (content): Merge conflict in src/utils/FileRecordTools/Records/BamRecord.cpp
Auto-merging src/utils/FileRecordTools/Makefile
CONFLICT (content): Merge conflict in src/utils/FileRecordTools/Makefile
Auto-merging src/utils/FileRecordTools/FileRecordMgr.h
CONFLICT (content): Merge conflict in src/utils/FileRecordTools/FileRecordMgr.h
Auto-merging src/utils/FileRecordTools/FileRecordMgr.cpp
CONFLICT (content): Merge conflict in src/utils/FileRecordTools/FileRecordMgr.cpp
Auto-merging src/utils/FileRecordTools/FileRecordMergeMgr.h
CONFLICT (add/add): Merge conflict in src/utils/FileRecordTools/FileRecordMergeMgr.h
Auto-merging src/utils/FileRecordTools/FileRecordMergeMgr.cpp
CONFLICT (add/add): Merge conflict in src/utils/FileRecordTools/FileRecordMergeMgr.cpp
Auto-merging src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
CONFLICT (content): Merge conflict in src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
Auto-merging src/utils/Contexts/Makefile
CONFLICT (content): Merge conflict in src/utils/Contexts/Makefile
Auto-merging src/utils/Contexts/ContextMerge.cpp
CONFLICT (add/add): Merge conflict in src/utils/Contexts/ContextMerge.cpp
Auto-merging src/utils/Contexts/ContextMap.h
CONFLICT (content): Merge conflict in src/utils/Contexts/ContextMap.h
Auto-merging src/utils/Contexts/ContextMap.cpp
CONFLICT (content): Merge conflict in src/utils/Contexts/ContextMap.cpp
Auto-merging src/utils/Contexts/ContextJaccard.h
CONFLICT (add/add): Merge conflict in src/utils/Contexts/ContextJaccard.h
Auto-merging src/utils/Contexts/ContextJaccard.cpp
CONFLICT (add/add): Merge conflict in src/utils/Contexts/ContextJaccard.cpp
Auto-merging src/utils/Contexts/ContextBase.h
CONFLICT (content): Merge conflict in src/utils/Contexts/ContextBase.h
Auto-merging src/utils/Contexts/ContextBase.cpp
CONFLICT (content): Merge conflict in src/utils/Contexts/ContextBase.cpp
Auto-merging src/utils/BinTree/BinTree.cpp
CONFLICT (content): Merge conflict in src/utils/BinTree/BinTree.cpp
Auto-merging src/slopBed/slopBed.cpp
CONFLICT (content): Merge conflict in src/slopBed/slopBed.cpp
Auto-merging src/mergeFile/mergeFile.h
CONFLICT (add/add): Merge conflict in src/mergeFile/mergeFile.h
Auto-merging src/mergeFile/mergeFile.cpp
CONFLICT (add/add): Merge conflict in src/mergeFile/mergeFile.cpp
Auto-merging src/mergeFile/Makefile
CONFLICT (add/add): Merge conflict in src/mergeFile/Makefile
CONFLICT (modify/delete): src/mapFile/mapMain.cpp deleted in HEAD and modified in Imported Upstream version 2.20.1. Version Imported Upstream version 2.20.1 of src/mapFile/mapMain.cpp left in tree.
Auto-merging src/mapFile/mapFile.h
CONFLICT (content): Merge conflict in src/mapFile/mapFile.h
CONFLICT (modify/delete): src/jaccard/jaccardMain.cpp deleted in HEAD and modified in Imported Upstream version 2.20.1. Version Imported Upstream version 2.20.1 of src/jaccard/jaccardMain.cpp left in tree.
CONFLICT (modify/delete): src/jaccard/jaccard.h deleted in Imported Upstream version 2.20.1 and modified in HEAD. Version HEAD of src/jaccard/jaccard.h left in tree.
CONFLICT (modify/delete): src/jaccard/jaccard.cpp deleted in Imported Upstream version 2.20.1 and modified in HEAD. Version HEAD of src/jaccard/jaccard.cpp left in tree.
Auto-merging src/jaccard/Makefile
CONFLICT (content): Merge conflict in src/jaccard/Makefile
Auto-merging src/intersectFile/intersectFile.cpp
CONFLICT (content): Merge conflict in src/intersectFile/intersectFile.cpp
CONFLICT (rename/delete): src/expand/Makefile deleted in Imported Upstream version 2.20.1 and renamed in HEAD. Version HEAD of src/expand/Makefile left in tree.
Auto-merging docs/content/tools/merge.rst
CONFLICT (content): Merge conflict in docs/content/tools/merge.rst
Auto-merging docs/content/history.rst
CONFLICT (add/add): Merge conflict in docs/content/history.rst
Auto-merging docs/conf.py
CONFLICT (content): Merge conflict in docs/conf.py
Auto-merging RELEASE_HISTORY
CONFLICT (content): Merge conflict in RELEASE_HISTORY
Auto-merging README.md
CONFLICT (content): Merge conflict in README.md
Auto-merging Makefile
CONFLICT (content): Merge conflict in Makefile
Failed to merge in the changes.
Patch failed at 0001 Imported Upstream version 2.20.1
The copy of the patch that failed is found in:
   /home/andreas/debian-maintain/alioth/debian-med_git/bedtools/.git/rebase-apply/patch

When you have resolved this problem, run "git rebase --continue".
If you prefer to skip this patch, run "git rebase --skip" instead.
To check out the original branch and stop rebasing, run "git rebase --abort".