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Comments (12)

gunturus avatar gunturus commented on September 22, 2024 1

can you try to install in your home directory

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andersonnb6 avatar andersonnb6 commented on September 22, 2024 1

I have managed to resolve these issues. First of all, I use Linux 16.04 LTS 64 bits.

For the 'gadarjat' problem I installed the 'ant' command using:

: ~ $ sudo apt-get install ant

However, when I continued, I came across the problem of 'najouamghazli': This in turn, I resolved as follows:

  1. I noticed that this seemed to have some relationship with Java's 'Javac'.

  2. I used this version of java: "jdk-11.0.1"

  3. So I switched to the version: "jdk1.8.0_191". Link to download: [Link]

  4. For the installation I used the following tutorial (Sorry PT-BR): [Link]

Note: It is important to follow the tutorial because it teaches you how to set the new java installed, as well as Javac and Javaws.

Hope this helps.

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rdpstaffmsu avatar rdpstaffmsu commented on September 22, 2024

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amansgill avatar amansgill commented on September 22, 2024

I just tried that, but I'm still getting the same error:

$ sudo make
mkdir lib
ant -f Clustering/build.xml jar
make: ant: Command not found
make: *** [Clustering/dist/Clustering.jar] Error 127

I also tried running the ant command separately but got the same error as above (error not shown again)
ant -f Clustering/build.xml jar

Full set of commands and output for make process:

[gadarjat@home src]$ sudo rm -r RDPTools
[sudo] password for gadarjat: 
[gadarjat@home src]$ 
[gadarjat@home src]$ sudo git clone https://github.com/rdpstaff/RDPTools.git
Cloning into 'RDPTools'...
remote: Counting objects: 197, done.
remote: Total 197 (delta 0), reused 0 (delta 0), pack-reused 197
Receiving objects: 100% (197/197), 29.19 KiB | 0 bytes/s, done.
Resolving deltas: 100% (100/100), done.
[gadarjat@home src]$ cd RDPTools/
[gadarjat@home RDPTools]$ 
[gadarjat@home RDPTools]$ sudo git submodule init
Submodule 'AbundanceStats' (https://github.com/rdpstaff/AbundanceStats/) registered for path 'AbundanceStats'
Submodule 'AlignmentTools' (https://github.com/rdpstaff/AlignmentTools.git) registered for path 'AlignmentTools'
Submodule 'Clustering' (https://github.com/rdpstaff/Clustering) registered for path 'Clustering'
Submodule 'Framebot' (https://github.com/rdpstaff/Framebot) registered for path 'Framebot'
Submodule 'KmerFilter' (https://github.com/rdpstaff/KmerFilter.git) registered for path 'KmerFilter'
Submodule 'ProbeMatch' (https://github.com/rdpstaff/ProbeMatch) registered for path 'ProbeMatch'
Submodule 'ReadSeq' (https://github.com/rdpstaff/ReadSeq.git) registered for path 'ReadSeq'
Submodule 'SeqFilters' (https://github.com/rdpstaff/SeqFilters) registered for path 'SeqFilters'
Submodule 'SequenceMatch' (https://github.com/rdpstaff/SequenceMatch.git) registered for path 'SequenceMatch'
Submodule 'TaxonomyTree' (git://github.com/rdpstaff/TaxonomyTree) registered for path 'TaxonomyTree'
Submodule 'Xander-HMMgs' (https://github.com/rdpstaff/Xander-HMMgs.git) registered for path 'Xander-HMMgs'
Submodule 'Xander_assembler' (https://github.com/rdpstaff/Xander_assembler.git) registered for path 'Xander_assembler'
Submodule 'classifier' (https://github.com/rdpstaff/classifier.git) registered for path 'classifier'
[gadarjat@home RDPTools]$ sudo git submodule update
Cloning into 'AbundanceStats'...
remote: Counting objects: 84, done.
remote: Total 84 (delta 0), reused 0 (delta 0), pack-reused 84
Unpacking objects: 100% (84/84), done.
Submodule path 'AbundanceStats': checked out 'c690a6f361b7a8652ceeda7cb663f007f8917b27'
Cloning into 'AlignmentTools'...
remote: Counting objects: 323, done.
remote: Total 323 (delta 0), reused 0 (delta 0), pack-reused 323
Receiving objects: 100% (323/323), 1.20 MiB | 0 bytes/s, done.
Resolving deltas: 100% (99/99), done.
Submodule path 'AlignmentTools': checked out '9230ba6ebf83e3f2809d94c0e6865feb4da0af59'
Cloning into 'Clustering'...
remote: Counting objects: 378, done.
remote: Total 378 (delta 0), reused 0 (delta 0), pack-reused 378
Receiving objects: 100% (378/378), 14.97 MiB | 8.25 MiB/s, done.
Resolving deltas: 100% (133/133), done.
Submodule path 'Clustering': checked out 'a0490b09db52c2750e317314944aa1d89234215c'
Cloning into 'Framebot'...
remote: Counting objects: 275, done.
remote: Total 275 (delta 0), reused 0 (delta 0), pack-reused 275
Receiving objects: 100% (275/275), 3.84 MiB | 5.57 MiB/s, done.
Resolving deltas: 100% (90/90), done.
Submodule path 'Framebot': checked out '32cac097904e7c650ca73612b448d016cd543e6b'
Cloning into 'KmerFilter'...
remote: Counting objects: 191, done.
remote: Total 191 (delta 0), reused 0 (delta 0), pack-reused 191
Receiving objects: 100% (191/191), 93.97 KiB | 0 bytes/s, done.
Resolving deltas: 100% (64/64), done.
Submodule path 'KmerFilter': checked out '002c053a2b12a3746cd950f1f5343e48cb9f3cff'
Cloning into 'ProbeMatch'...
remote: Counting objects: 74, done.
remote: Compressing objects: 100% (38/38), done.
remote: Total 74 (delta 23), reused 74 (delta 23), pack-reused 0
Unpacking objects: 100% (74/74), done.
Submodule path 'ProbeMatch': checked out '1948013273b72e0ce9762cb6c98cd08320d2e36b'
Cloning into 'ReadSeq'...
remote: Counting objects: 560, done.
remote: Total 560 (delta 0), reused 0 (delta 0), pack-reused 560
Receiving objects: 100% (560/560), 32.03 MiB | 12.41 MiB/s, done.
Resolving deltas: 100% (237/237), done.
Submodule path 'ReadSeq': checked out 'b967aa72a60b2701421447fd9295cf204d1908ef'
Cloning into 'SeqFilters'...
remote: Counting objects: 197, done.
remote: Total 197 (delta 0), reused 0 (delta 0), pack-reused 197
Receiving objects: 100% (197/197), 73.57 KiB | 0 bytes/s, done.
Resolving deltas: 100% (62/62), done.
Submodule path 'SeqFilters': checked out '76814eb6da68e449faeaca05a51ed25c11e9c08c'
Cloning into 'SequenceMatch'...
remote: Counting objects: 133, done.
remote: Total 133 (delta 0), reused 0 (delta 0), pack-reused 133
Receiving objects: 100% (133/133), 108.01 KiB | 0 bytes/s, done.
Resolving deltas: 100% (31/31), done.
Submodule path 'SequenceMatch': checked out 'd9e902f7a38b2889d9c295b1c6d32af890b0f6e6'
Cloning into 'TaxonomyTree'...
remote: Counting objects: 72, done.
remote: Total 72 (delta 0), reused 0 (delta 0), pack-reused 72
Receiving objects: 100% (72/72), 43.66 KiB | 0 bytes/s, done.
Resolving deltas: 100% (21/21), done.
Submodule path 'TaxonomyTree': checked out '8a971c3a4d953a7da607797e925c291bd89fc8ac'
Cloning into 'Xander-HMMgs'...
remote: Counting objects: 362, done.
remote: Total 362 (delta 0), reused 0 (delta 0), pack-reused 362
Receiving objects: 100% (362/362), 204.01 KiB | 0 bytes/s, done.
Resolving deltas: 100% (159/159), done.
Submodule path 'Xander-HMMgs': checked out '5237c8fbf66459f3f1a5a132df527a362d24b06e'
Cloning into 'Xander_assembler'...
remote: Counting objects: 311, done.
remote: Total 311 (delta 0), reused 0 (delta 0), pack-reused 311
Receiving objects: 100% (311/311), 4.08 MiB | 7.18 MiB/s, done.
Resolving deltas: 100% (144/144), done.
Submodule path 'Xander_assembler': checked out '36d84c1135c8f620820f637705124cf3a4cd8952'
Cloning into 'classifier'...
remote: Counting objects: 662, done.
remote: Total 662 (delta 0), reused 0 (delta 0), pack-reused 662
Receiving objects: 100% (662/662), 955.77 KiB | 0 bytes/s, done.
Resolving deltas: 100% (292/292), done.
Submodule path 'classifier': checked out '701e229dde7cbe53d4261301e23459d91615999d'
[gadarjat@home RDPTools]$ sudo make
mkdir lib
ant -f Clustering/build.xml jar
make: ant: Command not found
make: *** [Clustering/dist/Clustering.jar] Error 127

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gunturus avatar gunturus commented on September 22, 2024

run the command bash before you setup rdptools

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amansgill avatar amansgill commented on September 22, 2024

I'm not sure I understand the recommendation. Do I simply run the command bash before running the other steps like this? Didn't seem to help...

[gadarjat@home RDPTools]$ bash
[gadarjat@home RDPTools]$ sudo make
ant -f Clustering/build.xml jar
make: ant: Command not found
make: *** [Clustering/dist/Clustering.jar] Error 127

Not sure if this is a clue, but if I run 'make' without 'sudo', I got the same error as with running the 'ant -f ...' command above, with the main error as follows

[gadarjat@home RDPTools]$ bash
[gadarjat@home RDPTools]$ make
ant -f Clustering/build.xml jar
Buildfile: /usr/local/src/RDPTools/Clustering/build.xml
[...]
BUILD FAILED
/usr/local/src/RDPTools/Clustering/build.xml:104: impossible to ivy retrieve: java.lang.RuntimeException: problem during retrieve of edu.cme.rdp#clustering: java.io.FileNotFoundException: /usr/local/src/RDPTools/Clustering/lib/jaxb-impl-2.2.7.jar (No such file or directory)
	at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:206)
	at org.apache.ivy.Ivy.retrieve(Ivy.java:540)

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rdpstaffmsu avatar rdpstaffmsu commented on September 22, 2024

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amansgill avatar amansgill commented on September 22, 2024

That file doesn't exist,

$ ls /usr/local/src/RDPTools/Clustering/lib/jaxb-impl-2.2.7.jar
ls: cannot access /usr/local/src/RDPTools/Clustering/lib/jaxb-impl-2.2.7.jar: No such file or directory

In fact, there seems to be no Clustering/lib directory:

$ ls /usr/local/src/RDPTools/Clustering/
build.xml  ivy.xml  manifest.mf  nbproject  src
hadoop     LICENSE  mcupgma.py   README.md

And I can't find jaxb-impl-2.2.7.jar elsewhere, using 'which' or 'whereis'. Strange, since I see the output line you mentioned saying it was downloaded. By the way, I obtained the RDPTools repository using 'git clone'. Is it possible to manually download this file?

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amansgill avatar amansgill commented on September 22, 2024

This worked, thank you! I assume this means the problem was with write permissions to /usr/local/src despite use of 'sudo'. Seems like an obvious thing to try in retrospect but it would have taken me a while to think to try this. Thanks again.

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rdpstaffmsu avatar rdpstaffmsu commented on September 22, 2024

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najouamghazli avatar najouamghazli commented on September 22, 2024

Hello,

I am encountering the same error but none of the solutions cited above worked for me !!

$ make

mkdir lib
ant -f Clustering/build.xml jar
Buildfile: /RDPTools/Clustering/build.xml

download-ivy:
      [get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
      [get] To: /root/.ant/lib/ivy.jar
      [get] Not modified - so not downloaded

init-ivy:

resolve:
[ivy:retrieve] :: Ivy 2.1.0-rc2 - 20090704004254 :: http://ant.apache.org/ivy/ ::
[ivy:retrieve] :: loading settings :: url = jar:file:/root/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#clustering;working@frogs-metagenomics
[ivy:retrieve] 	confs: [default]
[ivy:retrieve] 	found com.sun.xml.bind#jaxb-impl;2.2.7 in public
[ivy:retrieve] 	found com.sun.xml.bind#jaxb-core;2.2.7 in public
[ivy:retrieve] 	found javax.xml.bind#jaxb-api;2.2.7 in public
[ivy:retrieve] 	found com.sun.istack#istack-commons-runtime;2.16 in public
[ivy:retrieve] 	found com.sun.xml.fastinfoset#FastInfoset;1.2.12 in public
[ivy:retrieve] 	found javax.xml.bind#jsr173_api;1.0 in public
[ivy:retrieve] 	found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] 	found junit#junit;4.8.2 in public
[ivy:retrieve] 	found commons-codec#commons-codec;1.8 in public
[ivy:retrieve] 	found commons-io#commons-io;2.4 in public
[ivy:retrieve] :: resolution report :: resolve 1183ms :: artifacts dl 59ms
	---------------------------------------------------------------------
	|                  |            modules            ||   artifacts   |
	|       conf       | number| search|dwnlded|evicted|| number|dwnlded|
	---------------------------------------------------------------------
	|      default     |   10  |   0   |   0   |   0   ||   20  |   0   |
	---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#clustering
[ivy:retrieve] 	confs: [default]
[ivy:retrieve] 	20 artifacts copied, 0 already retrieved (7237kB/390ms)

-pre-init:

-init-private:

-init-user:

-init-project:

-init-macrodef-property:

-do-init:

-post-init:

-init-check:

-init-ap-cmdline-properties:

-init-macrodef-javac-with-processors:

-init-macrodef-javac-without-processors:

-init-macrodef-javac:

-init-macrodef-test-impl:

-init-macrodef-junit-init:

-init-macrodef-junit-single:

-init-test-properties:

-init-macrodef-junit-batch:

-init-macrodef-junit:

-init-macrodef-junit-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl

-init-macrodef-testng:

-init-macrodef-testng-impl:

-init-macrodef-test:

-init-macrodef-junit-debug:

-init-macrodef-junit-debug-batch:

-init-macrodef-junit-debug-impl:

-init-macrodef-test-debug-junit:

-init-macrodef-testng-debug:

-init-macrodef-testng-debug-impl:

-init-macrodef-test-debug-testng:

-init-macrodef-test-debug:

-init-debug-args:

-init-macrodef-nbjpda:

-init-macrodef-debug:

-init-macrodef-java:

-init-presetdef-jar:

-init-ap-cmdline-supported:

-init-ap-cmdline:

init:

-deps-jar-init:

deps-jar:
    [mkdir] Created dir: /RDPTools/Clustering/build

-warn-already-built-jar:
[propertyfile] Updating property file: /RDPTools/Clustering/build/built-jar.properties

-check-call-dep:

-maybe-call-dep:

download-ivy:
      [get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
      [get] To: /root/.ant/lib/ivy.jar
      [get] Not modified - so not downloaded

init-ivy:

resolve:
[ivy:retrieve] :: loading settings :: url = jar:file:/root/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#AlignmentTools;working@frogs-metagenomics
[ivy:retrieve] 	confs: [default]
[ivy:retrieve] 	found commons-lang#commons-lang;2.6 in public
[ivy:retrieve] 	found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] :: resolution report :: resolve 206ms :: artifacts dl 56ms
	---------------------------------------------------------------------
	|                  |            modules            ||   artifacts   |
	|       conf       | number| search|dwnlded|evicted|| number|dwnlded|
	---------------------------------------------------------------------
	|      default     |   2   |   0   |   0   |   0   ||   6   |   0   |
	---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#AlignmentTools
[ivy:retrieve] 	confs: [default]
[ivy:retrieve] 	6 artifacts copied, 0 already retrieved (2524kB/61ms)

-pre-init:

-init-private:

-init-user:

-init-project:

-init-macrodef-property:

-do-init:

-post-init:

-init-check:

-init-ap-cmdline-properties:

-init-macrodef-javac-with-processors:

-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac

-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend

-init-macrodef-test-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl

-init-macrodef-junit-init:

-init-macrodef-junit-single:

-init-test-properties:

-init-macrodef-junit-batch:

-init-macrodef-junit:

-init-macrodef-junit-impl:

-init-macrodef-testng:

-init-macrodef-testng-impl:

-init-macrodef-test:

-init-macrodef-junit-debug:

-init-macrodef-junit-debug-batch:

-init-macrodef-junit-debug-impl:

-init-macrodef-test-debug-junit:

-init-macrodef-testng-debug:

-init-macrodef-testng-debug-impl:

-init-macrodef-test-debug-testng:

-init-macrodef-test-debug:

-init-debug-args:

-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart

-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug

-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java

-init-presetdef-jar:

-init-ap-cmdline-supported:

-init-ap-cmdline:

init:

-deps-jar-init:

deps-jar:
    [mkdir] Created dir: /RDPTools/AlignmentTools/build

-warn-already-built-jar:
[propertyfile] Updating property file: /RDPTools/Clustering/build/built-jar.properties

-check-call-dep:

-maybe-call-dep:

download-ivy:
      [get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
      [get] To: /root/.ant/lib/ivy.jar
      [get] Not modified - so not downloaded

init-ivy:

resolve:
[ivy:retrieve] :: loading settings :: url = jar:file:/root/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#ReadSeq;working@frogs-metagenomics
[ivy:retrieve] 	confs: [default]
[ivy:retrieve] 	found commons-lang#commons-lang;2.6 in public
[ivy:retrieve] 	found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] 	found commons-io#commons-io;2.4 in public
[ivy:retrieve] :: resolution report :: resolve 263ms :: artifacts dl 24ms
	---------------------------------------------------------------------
	|                  |            modules            ||   artifacts   |
	|       conf       | number| search|dwnlded|evicted|| number|dwnlded|
	---------------------------------------------------------------------
	|      default     |   3   |   0   |   0   |   0   ||   9   |   0   |
	---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#ReadSeq
[ivy:retrieve] 	confs: [default]
[ivy:retrieve] 	9 artifacts copied, 0 already retrieved (3653kB/44ms)

-pre-init:

-init-private:

-init-user:

-init-project:

-init-macrodef-property:

-do-init:

-post-init:

-init-check:

-init-ap-cmdline-properties:

-init-macrodef-javac-with-processors:

-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac

-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend

-init-macrodef-test-impl:

-init-macrodef-junit-init:

-init-macrodef-junit-single:

-init-test-properties:

-init-macrodef-junit-batch:

-init-macrodef-junit:

-init-macrodef-junit-impl:

-init-macrodef-testng:

-init-macrodef-testng-impl:

-init-macrodef-test:

-init-macrodef-junit-debug:

-init-macrodef-junit-debug-batch:

-init-macrodef-junit-debug-impl:

-init-macrodef-test-debug-junit:

-init-macrodef-testng-debug:

-init-macrodef-testng-debug-impl:

-init-macrodef-test-debug-testng:

-init-macrodef-test-debug:

-init-debug-args:

-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart

-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug

-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java

-init-presetdef-jar:

-init-ap-cmdline-supported:

-init-ap-cmdline:

init:

-deps-jar-init:

deps-jar:
    [mkdir] Created dir: /RDPTools/ReadSeq/build

-warn-already-built-jar:
[propertyfile] Updating property file: /RDPTools/Clustering/build/built-jar.properties

-check-automatic-build:

-clean-after-automatic-build:

-verify-automatic-build:

-pre-pre-compile:
    [mkdir] Created dir: /RDPTools/ReadSeq/build/classes

-pre-compile:

-copy-persistence-xml:

-compile-depend:

-do-compile:
    [mkdir] Created dir: /RDPTools/ReadSeq/build/empty
    [javac] Compiling 73 source files to /RDPTools/ReadSeq/build/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5
    [javac] error: Source option 1.5 is no longer supported. Use 1.6 or later.
    [javac] error: Target option 1.5 is no longer supported. Use 1.6 or later.

BUILD FAILED
/RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line:
/RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line:
/RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line:
/RDPTools/ReadSeq/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.

Total time: 8 seconds
Makefile:15: recipe for target 'Clustering/dist/Clustering.jar' failed
make: *** [Clustering/dist/Clustering.jar] Error 1

Does someone have any idea about how to resolve this error ? Thank you.

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caijian89 avatar caijian89 commented on September 22, 2024

Actually，I meet the same error，and no above solutions help me

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