Debian Bug report logs - #648017
RFP: local-file -- small clojure library

Package: wnpp; Maintainer for wnpp is wnpp@debian.org;

Reported by: Mathieu Malaterre <malat@debian.org>

Date: Tue, 8 Nov 2011 11:33:01 UTC

Severity: wishlist

Fix blocked by 641448: RFP: bio-formats -- Solution for reading proprietary microscopy image data and metadata

Blocking fix for 646811: RFP: clooj -- lightweight IDE for clojure

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Report forwarded to debian-bugs-dist@lists.debian.org, debian-devel@lists.debian.org, wnpp@debian.org:
Bug#648017; Package wnpp. (Tue, 08 Nov 2011 11:33:04 GMT) Full text and rfc822 format available.

Acknowledgement sent to Mathieu Malaterre <mathieu.malaterre@gmail.com>:
New Bug report received and forwarded. Copy sent to debian-devel@lists.debian.org, wnpp@debian.org. (Tue, 08 Nov 2011 11:33:05 GMT) Full text and rfc822 format available.

Message #5 received at submit@bugs.debian.org (full text, mbox):

From: Mathieu Malaterre <mathieu.malaterre@gmail.com>
To: Debian Bug Tracking System <submit@bugs.debian.org>
Subject: ITP: local-file -- small clojure library
Date: Tue, 08 Nov 2011 12:28:56 +0100
Package: wnpp
Severity: wishlist
Owner: Mathieu Malaterre <mathieu.malaterre@gmail.com>


* Package name    : local-file
  Version         : 0.1.0
  Upstream Author : Arthur Edelstein
* URL             : https://github.com/arthuredelstein/local-file/
* License         : 
  Programming Lang: Java
  Description     : small clojure library

 To use this very small clojure library, add [local-file "0.1.0"] to the
 dependencies list in your project.clj file. Then call (use 'local-file) or
 "use" local-file in your (ns...) macro call in a clojure source file.
 .
 To get the current clojure project's directory (the parent dir of the source
 dir) call project-dir with no arguments. The file* function takes a relative
 path and returns an absolute path relative to the project directory.
 .
 To read and write files in a clojure project's directory, use spit* and slurp*
 with the same signatures as the standard spit and slurp calls.




Added indication that bug 648017 blocks 646811 Request was from Mathieu Malaterre <mathieu.malaterre@gmail.com> to control@bugs.debian.org. (Tue, 08 Nov 2011 11:36:37 GMT) Full text and rfc822 format available.

Added blocking bug(s) of 648017: 647633 Request was from Mathieu Malaterre <mathieu.malaterre@gmail.com> to control@bugs.debian.org. (Tue, 08 Nov 2011 11:36:38 GMT) Full text and rfc822 format available.

Changed Bug submitter to 'Mathieu Malaterre <malat@debian.org>' from 'Mathieu Malaterre <mathieu.malaterre@gmail.com>' Request was from Mathieu Malaterre <malat@debian.org> to control@bugs.debian.org. (Wed, 28 Mar 2012 13:55:28 GMT) Full text and rfc822 format available.

Owner changed from Mathieu Malaterre <mathieu.malaterre@gmail.com> to Mathieu Malaterre <malat@debian.org>. Request was from Mathieu Malaterre <malat@debian.org> to control@bugs.debian.org. (Wed, 28 Mar 2012 13:55:59 GMT) Full text and rfc822 format available.

Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org:
Bug#648017; Package wnpp. (Thu, 06 Dec 2012 11:15:03 GMT) Full text and rfc822 format available.

Acknowledgement sent to Mathieu Malaterre <malat@debian.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org. (Thu, 06 Dec 2012 11:15:03 GMT) Full text and rfc822 format available.

Message #18 received at 648017@bugs.debian.org (full text, mbox):

From: Mathieu Malaterre <malat@debian.org>
To: Control bugs server <control@bugs.debian.org>
Cc: 648017@bugs.debian.org
Subject: micromanager vs bioformats
Date: Thu, 6 Dec 2012 12:13:26 +0100
block 648017 by 641448
thanks

Micro-Manager needs bio-formats to compile:


javac -source 1.5 -target 1.5 -sourcepath
../MMCoreJ_wrap:./src:../hcs/src:. -classpath
/usr/share/java/ij.jar:/usr/share/java/bsh.jar:/usr/share/java/swingx.jar:/usr/share/java/commons-math.jar:/usr/share/java/swing-layout-1.0.4.jar:/usr/share/java/*:/bin/MMCoreJ.jar:.
./src/*.java ./src/org/micromanager/acquisition/*.java
./src/org/micromanager/utils/*.java ./src/org/micromanager/api/*.java
./src/org/micromanager/conf2/*.java -d build
./src/org/micromanager/utils/ReportingUtils.java:155: warning:
unmappable character for encoding ASCII
         final JDialog dialog = new JDialog(owningFrame_, "??Manager
Warning: ", false);
                                                           ^
./src/org/micromanager/utils/ReportingUtils.java:155: warning:
unmappable character for encoding ASCII
         final JDialog dialog = new JDialog(owningFrame_, "??Manager
Warning: ", false);
                                                            ^
./src/org/micromanager/acquisition/MultipageTiffReader.java:39:
package loci.formats does not exist
import loci.formats.FormatException;
                   ^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:31:
package loci.common does not exist
import loci.common.DateTools;
                  ^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:32:
package loci.common.services does not exist
import loci.common.services.ServiceFactory;
                           ^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:33:
package loci.formats does not exist
import loci.formats.MetadataTools;
                   ^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:34:
package loci.formats.meta does not exist
import loci.formats.meta.IMetadata;
                        ^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:35:
package loci.formats.ome does not exist
import loci.formats.ome.OMEXMLMetadata;
                       ^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:36:
package loci.formats.services does not exist
import loci.formats.services.OMEXMLService;
                            ^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:37:
package loci.formats.services does not exist
import loci.formats.services.OMEXMLServiceImpl;
                            ^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:39:
package ome.xml.model.enums does not exist
import ome.xml.model.enums.Binning;
                          ^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:40:
package ome.xml.model.primitives does not exist
import ome.xml.model.primitives.*;
^
./src/org/micromanager/acquisition/OMEMetadata.java:27: package
loci.common does not exist
import loci.common.DateTools;
                  ^
./src/org/micromanager/acquisition/OMEMetadata.java:28: package
loci.common.services does not exist
import loci.common.services.ServiceFactory;
                           ^
./src/org/micromanager/acquisition/OMEMetadata.java:29: package
loci.formats does not exist
import loci.formats.MetadataTools;
                   ^
./src/org/micromanager/acquisition/OMEMetadata.java:30: package
loci.formats.meta does not exist
import loci.formats.meta.IMetadata;
                        ^
./src/org/micromanager/acquisition/OMEMetadata.java:31: package
loci.formats.services does not exist
import loci.formats.services.OMEXMLService;
                            ^
./src/org/micromanager/acquisition/OMEMetadata.java:32: package
ome.xml.model.primitives does not exist
import ome.xml.model.primitives.*;
^
./src/org/micromanager/acquisition/OMEMetadata.java:42: cannot find symbol
symbol  : class IMetadata
location: class org.micromanager.acquisition.OMEMetadata
   private IMetadata metadata_;
           ^
./src/org/micromanager/acquisition/OMEMetadata.java:59: cannot find symbol
symbol  : variable MetadataTools
location: class org.micromanager.acquisition.OMEMetadata
      metadata_ = MetadataTools.createOMEXMLMetadata();
                  ^
./src/org/micromanager/acquisition/OMEMetadata.java:64: cannot find symbol
symbol  : class OMEXMLService
location: class org.micromanager.acquisition.OMEMetadata
         OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
         ^
./src/org/micromanager/acquisition/OMEMetadata.java:64: cannot find symbol
symbol  : class OMEXMLService
location: class org.micromanager.acquisition.OMEMetadata
         OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
                                                                  ^
./src/org/micromanager/acquisition/OMEMetadata.java:64: cannot find symbol
symbol  : class ServiceFactory
location: class org.micromanager.acquisition.OMEMetadata
         OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
                                     ^
./src/org/micromanager/acquisition/OMEMetadata.java:81: cannot find symbol
symbol  : class PositiveInteger
location: class org.micromanager.acquisition.OMEMetadata
      metadata_.setPixelsSizeT(new PositiveInteger(numFrames), seriesIndex);
                                   ^
./src/org/micromanager/acquisition/OMEMetadata.java:89: cannot find symbol
symbol  : variable MetadataTools
location: class org.micromanager.acquisition.OMEMetadata
      MetadataTools.populateMetadata(metadata_, seriesIndex,
baseFileName, MultipageTiffWriter.BYTE_ORDER.equals(ByteOrder.LITTLE_ENDIAN),
      ^
./src/org/micromanager/acquisition/OMEMetadata.java:98: cannot find symbol
symbol  : class PositiveFloat
location: class org.micromanager.acquisition.OMEMetadata
            metadata_.setPixelsPhysicalSizeX(new
PositiveFloat(pixelSize), seriesIndex);
                                                 ^
./src/org/micromanager/acquisition/OMEMetadata.java:99: cannot find symbol
symbol  : class PositiveFloat
location: class org.micromanager.acquisition.OMEMetadata
            metadata_.setPixelsPhysicalSizeY(new
PositiveFloat(pixelSize), seriesIndex);
                                                 ^
./src/org/micromanager/acquisition/OMEMetadata.java:105: cannot find symbol
symbol  : class PositiveFloat
location: class org.micromanager.acquisition.OMEMetadata
            metadata_.setPixelsPhysicalSizeZ(new PositiveFloat(zStep),
seriesIndex);
                                                 ^
./src/org/micromanager/acquisition/OMEMetadata.java:118: cannot find symbol
symbol  : variable MetadataTools
location: class org.micromanager.acquisition.OMEMetadata
      String instrumentID = MetadataTools.createLSID("Microscope");
                            ^
./src/org/micromanager/acquisition/OMEMetadata.java:131: cannot find symbol
symbol  : class Color
location: class org.micromanager.acquisition.OMEMetadata
         metadata_.setChannelColor(new Color(channel.getInt("Color")),
seriesIndex, channelIndex);
                                       ^
./src/org/micromanager/acquisition/OMEMetadata.java:137: cannot find symbol
symbol  : class OMEXMLService
location: class org.micromanager.acquisition.OMEMetadata
            OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
            ^
./src/org/micromanager/acquisition/OMEMetadata.java:137: cannot find symbol
symbol  : class OMEXMLService
location: class org.micromanager.acquisition.OMEMetadata
            OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
                                                                     ^
./src/org/micromanager/acquisition/OMEMetadata.java:137: cannot find symbol
symbol  : class ServiceFactory
location: class org.micromanager.acquisition.OMEMetadata
            OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
                                        ^
./src/org/micromanager/acquisition/OMEMetadata.java:159: cannot find symbol
symbol  : class Timestamp
location: class org.micromanager.acquisition.OMEMetadata
               metadata_.setImageAcquisitionDate(new Timestamp(
                                                     ^
./src/org/micromanager/acquisition/OMEMetadata.java:160: cannot find symbol
symbol  : variable DateTools
location: class org.micromanager.acquisition.OMEMetadata
                       DateTools.formatDate(tags.getString("Time"),
"yyyy-MM-dd HH:mm:ss")), seriesIndex);
                       ^
./src/org/micromanager/acquisition/OMEMetadata.java:181: cannot find symbol
symbol  : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
            metadata_.setTiffDataFirstZ(new NonNegativeInteger(slice),
seriesIndex, indices.tiffDataIndex_);
                                            ^
./src/org/micromanager/acquisition/OMEMetadata.java:182: cannot find symbol
symbol  : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
            metadata_.setTiffDataFirstC(new
NonNegativeInteger(channel), seriesIndex, indices.tiffDataIndex_);
                                            ^
./src/org/micromanager/acquisition/OMEMetadata.java:183: cannot find symbol
symbol  : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
            metadata_.setTiffDataFirstT(new NonNegativeInteger(frame),
seriesIndex, indices.tiffDataIndex_);
                                            ^
./src/org/micromanager/acquisition/OMEMetadata.java:184: cannot find symbol
symbol  : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
            metadata_.setTiffDataIFD(new NonNegativeInteger(ifdCount),
seriesIndex, indices.tiffDataIndex_);
                                         ^
./src/org/micromanager/acquisition/OMEMetadata.java:190: cannot find symbol
symbol  : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
         metadata_.setTiffDataPlaneCount(new
NonNegativeInteger(indices.tiffDataPlaneCount_),
                                             ^
./src/org/micromanager/acquisition/OMEMetadata.java:194: cannot find symbol
symbol  : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
         metadata_.setPlaneTheZ(new NonNegativeInteger(slice),
seriesIndex, indices.planeIndex_);
                                    ^
./src/org/micromanager/acquisition/OMEMetadata.java:195: cannot find symbol
symbol  : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
         metadata_.setPlaneTheC(new NonNegativeInteger(channel),
seriesIndex, indices.planeIndex_);
                                    ^
./src/org/micromanager/acquisition/OMEMetadata.java:196: cannot find symbol
symbol  : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
         metadata_.setPlaneTheT(new NonNegativeInteger(frame),
seriesIndex, indices.planeIndex_);
                                    ^
./src/org/micromanager/acquisition/OMEMetadata.java:240: cannot find symbol
symbol  : class OMEXMLService
location: class org.micromanager.acquisition.OMEMetadata
            OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
            ^
./src/org/micromanager/acquisition/OMEMetadata.java:240: cannot find symbol
symbol  : class OMEXMLService
location: class org.micromanager.acquisition.OMEMetadata
            OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
                                                                     ^
./src/org/micromanager/acquisition/OMEMetadata.java:240: cannot find symbol
symbol  : class ServiceFactory
location: class org.micromanager.acquisition.OMEMetadata
            OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
                                        ^
./src/org/micromanager/acquisition/OMEMetadata.java:272: cannot find symbol
symbol  : variable MetadataTools
location: class org.micromanager.acquisition.OMEMetadata
         String detectorID = MetadataTools.createLSID(camera);
                             ^
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
45 errors
2 warnings



Added blocking bug(s) of 648017: 641448 Request was from Mathieu Malaterre <malat@debian.org> to control@bugs.debian.org. (Thu, 06 Dec 2012 11:15:05 GMT) Full text and rfc822 format available.

Changed Bug title to 'RFP: local-file -- small clojure library' from 'ITP: local-file -- small clojure library' Request was from "Mathieu Malaterre" <malat@debian.org> to control@bugs.debian.org. (Thu, 11 Apr 2013 11:00:14 GMT) Full text and rfc822 format available.

Removed annotation that Bug was owned by Mathieu Malaterre <malat@debian.org>. Request was from Mathieu Malaterre <malat@debian.org> to control@bugs.debian.org. (Thu, 11 Apr 2013 11:51:05 GMT) Full text and rfc822 format available.

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