Closed amansgill closed 7 years ago
Would you re-run the entire process starting from "git clone"? Our server had some issue in the past day or two and some files might not be accessible. Let me know if that works this time. Thank you.
Benli Chai RDP Staff
On Sun, Mar 5, 2017 at 5:28 PM, gadarjat notifications@github.com wrote:
I'm trying to install RDPTools on a linux system (RHEL 7.3). When I run:
sudo git submodule init sudo git submodule update sudo make
I get an error:
ant -f Clustering/build.xml jar make: ant: Command not found make: *** [Clustering/dist/Clustering.jar] Error 127
Despite the "ant: Command not found" my system does recognize ant (and it's in the path); ant just seems to want a good build.xml file.
$ ant Buildfile: build.xml does not exist! Build failed
When I run ant using the RDP build.xml file I get a long output, below, which includes this error:
$ ant -f Clustering/build.xml jar [...] 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) $ ant -f Clustering/build.xml jar [...]
Full output:
$ ant -f Clustering/build.xml jar Buildfile: /usr/local/src/RDPTools/Clustering/build.xml
download-ivy: [mkdir] Created dir: /home/gadarjat/.ant/lib [get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar [get] To: /home/gadarjat/.ant/lib/ivy.jar
init-ivy:
resolve: [ivy:retrieve] :: Ivy 2.1.0-rc2 - 20090704004254 :: http://ant.apache.org/ivy/ :: [ivy:retrieve] :: loading settings :: url = jar:file:/home/gadarjat/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#clustering;working@carabid.espm.berkeley.edu [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] downloading http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7-javadoc.jar ... [ivy:retrieve] .............................................................................................................................................................................................................................................................. (1449kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] com.sun.xml.bind#jaxb-impl;2.2.7!jaxb-impl.jar(javadoc) (142ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7.jar ... [ivy:retrieve] .................................................................................................................................................. (898kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] com.sun.xml.bind#jaxb-impl;2.2.7!jaxb-impl.jar (58ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7-sources.jar ... [ivy:retrieve] ......................................................................................................................................................................... (1109kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] com.sun.xml.bind#jaxb-impl;2.2.7!jaxb-impl.jar(source) (77ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-cli/commons-cli/1.2/commons-cli-1.2.jar ... [ivy:retrieve] .. (40kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-cli#commons-cli;1.2!commons-cli.jar (19ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-cli/commons-cli/1.2/commons-cli-1.2-sources.jar ... [ivy:retrieve] .... (47kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-cli#commons-cli;1.2!commons-cli.jar(source) (19ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-cli/commons-cli/1.2/commons-cli-1.2-javadoc.jar ... [ivy:retrieve] ............................ (209kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-cli#commons-cli;1.2!commons-cli.jar(javadoc) (25ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2-sources.jar ... [ivy:retrieve] ...................... (143kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] junit#junit;4.8.2!junit.jar(source) (22ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2-javadoc.jar ... [ivy:retrieve] ........................................................... (387kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] junit#junit;4.8.2!junit.jar(javadoc) (29ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2.jar ... [ivy:retrieve] ............................... (231kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] junit#junit;4.8.2!junit.jar (24ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-codec/commons-codec/1.8/commons-codec-1.8-sources.jar ... [ivy:retrieve] .......................................... (271kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-codec#commons-codec;1.8!commons-codec.jar(source) (25ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-codec/commons-codec/1.8/commons-codec-1.8-javadoc.jar ... [ivy:retrieve] ...................................................... (389kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-codec#commons-codec;1.8!commons-codec.jar(javadoc) (27ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-codec/commons-codec/1.8/commons-codec-1.8.jar ... [ivy:retrieve] .................................... (257kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-codec#commons-codec;1.8!commons-codec.jar (24ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4-sources.jar ... [ivy:retrieve] ............................... (240kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-io#commons-io;2.4!commons-io.jar(source) (24ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4.jar ... [ivy:retrieve] ............................ (180kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-io#commons-io;2.4!commons-io.jar (31ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4-javadoc.jar ... [ivy:retrieve] ..................................................................................................... (707kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-io#commons-io;2.4!commons-io.jar(javadoc) (38ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-core/2.2.7/jaxb-core-2.2.7.jar ... [ivy:retrieve] ......................... (216kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] com.sun.xml.bind#jaxb-core;2.2.7!jaxb-core.jar (22ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/xml/fastinfoset/FastInfoset/1.2.12/FastInfoset-1.2.12.jar ... [ivy:retrieve] ....................................... (286kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] com.sun.xml.fastinfoset#FastInfoset;1.2.12!FastInfoset.jar (24ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/javax/xml/bind/jaxb-api/2.2.7/jaxb-api-2.2.7.jar ... [ivy:retrieve] ............. (97kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] javax.xml.bind#jaxb-api;2.2.7!jaxb-api.jar (20ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/istack/istack-commons-runtime/2.16/istack-commons-runtime-2.16.jar ... [ivy:retrieve] .. (22kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] com.sun.istack#istack-commons-runtime;2.16!istack-commons-runtime.jar (19ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/javax/xml/bind/jsr173_api/1.0/jsr173_api-1.0.jar ... [ivy:retrieve] ...... (48kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] javax.xml.bind#jsr173_api;1.0!jsr173_api.jar (19ms) [ivy:retrieve] :: resolution report :: resolve 1488ms :: artifacts dl 699ms
| | modules || artifacts | | conf | number| search|dwnlded|evicted|| number|dwnlded| --------------------------------------------------------------------- | default | 10 | 10 | 10 | 0 || 20 | 20 | ---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#clustering [ivy:retrieve] confs: [default]
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) at org.apache.ivy.ant.IvyRetrieve.doExecute(IvyRetrieve.java:59) at org.apache.ivy.ant.IvyTask.execute(IvyTask.java:277) at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) at org.apache.tools.ant.Task.perform(Task.java:348) at org.apache.tools.ant.Target.execute(Target.java:435) at org.apache.tools.ant.Target.performTasks(Target.java:456) at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1405) at org.apache.tools.ant.Project.executeTarget(Project.java:1376) at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41) at org.apache.tools.ant.Project.executeTargets(Project.java:1260) at org.apache.tools.ant.Main.runBuild(Main.java:857) at org.apache.tools.ant.Main.startAnt(Main.java:236) at org.apache.tools.ant.launch.Launcher.run(Launcher.java:287) at org.apache.tools.ant.launch.Launcher.main(Launcher.java:113) Caused by: java.io.FileNotFoundException: /usr/local/src/RDPTools/Clustering/lib/jaxb-impl-2.2.7.jar (No such file or directory) at java.io.FileOutputStream.open0(Native Method) at java.io.FileOutputStream.open(FileOutputStream.java:270) at java.io.FileOutputStream.
(FileOutputStream.java:213) at java.io.FileOutputStream. (FileOutputStream.java:162) at org.apache.ivy.util.FileUtil.copy(FileUtil.java:147) at org.apache.ivy.util.FileUtil.copy(FileUtil.java:122) at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:140) ... 20 more Total time: 3 seconds
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-- RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842
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
run the command bash before you setup rdptools
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)
Would you mind checking if exists: /usr/local/src/RDPTools/Clustering/lib/ jaxb-impl-2.2.7.jar?
From the output, jaxb-impl-2.2.7.jar was downloaded in your make.
Benli
On Mon, Mar 6, 2017 at 8:22 PM, gadarjat notifications@github.com wrote:
I'm not sure I understand the recommendation. Do I simply run the command bash before running the other steps?
[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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-- RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842
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?
can you try to install in your home directory
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.
It may also work if you log in as root ('su') instead on using 'sudo'.
Benli
On Wed, Mar 8, 2017 at 12:18 PM, gadarjat notifications@github.com wrote:
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.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/rdpstaff/RDPTools/issues/15#issuecomment-285105682, or mute the thread https://github.com/notifications/unsubscribe-auth/AKlEVvovyH0-0qYeVlnRUiAxaEp61utLks5rjuLJgaJpZM4MTk4S .
-- RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842
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.
Actually,I meet the same error,and no above solutions help me
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.
I'm trying to install RDPTools on a linux system (RHEL 7.3). When I run:
I get an error:
Despite the "ant: Command not found" my system does recognize ant (and it's in the path); ant just seems to want a good build.xml file.
When I run ant using the command in the initial error output, I get a long output, below, which includes this error:
Full output: