Unsatisfied dependency, cannot install HiTS
KVJanos
Trying to install HiTS I get the error message:
Cannot complete the request. See the details.
Unsatisfied dependency: [ie.tcd.imm.hits.common 0.0.4.200912041736]
requiredCapability: java.package/javax.annotation.concurrent/0.0.0
Unsatisfied dependency: [ie.tcd.imm.hits.common 0.0.4.200912041736]
requiredCapability: java.package/javax.annotation.meta/0.0.0
[...]
and some more unsatisfied dependencies for hits.common, missing the
java.package/javax.annotation...
I strictly followed Gabor's dependency installation instructions
( https://code.google.com/p/hits/wiki/Dependencies ).
Config details:
KNIME v2.1.1.0023926
linux 64 bit
java.version=1.6.0_14
Any idea or similar experience?
Cheers,
Janos
aborg
Sorry for the late reply. The message you describe looks like a
missing dependency from the 3rd party feature, please be sure that you
have selected that. The other possible cause might be of selecting
something experimental, or old.
Could you try following the video [1] below (sorry, it is under
Windows 7, but at least it is 64 bit)? Thanks, gabor
[1] http://www.youtube.com/watch?v=ryHBxvyzUPg
KVJanos
Thanks the idea. I installed the 3rd party feature before, that was
not the problem. I had no problem to install HiTS under Windows. I
checked the same features to install under Linux as well, so HiTS is
not the problem. It seems to be something with my Java installation
under Linux (possibly involved KNIME as well). I can run HiTS under
Windows so that solves the problem.
I have 2 more questions:
(1) Is it possible to run the Heatmap visualization outside of KNIME?
For example in R?
(2) I tried to run the sample1.zip workflow
( http://hits.googlecode.com/svn/ie.tcd.imm.knime.test/trunk/testdata/workflows/sampleCellHTS2/sample1.zip
)
using the plate8 sample dataset ( .../trunk/testdata/plate8/ ).
I adjusted the paths of the input files for the various nodes for
Description.txt, Plateconf.txt, etc. but I still got various error
messages, and finally I could not run the test workflow.
This thread is not for the sample1.zip workflow issues, so I start a
new relevant one with all the details if you agree.
Thanks again and cheers,
Janos
KVJanos
Thanks the idea. I installed the 3rd party feature before, that was
not the problem. I had no problem to install HiTS under Windows. I
checked the same features to install under Linux as well, so HiTS is
not the problem. It seems to be something with my Java installation
under Linux (possibly involved KNIME as well). I can run HiTS under
Windows so that solves the problem.
I have 2 more questions:
(1) Is it possible to run the Heatmap visualization outside of KNIME?
For example in R?
(2) I tried to run the sample1.zip workflow
using the plate8 sample dataset ( .../trunk/testdata/plate8/ ).
I adjusted the paths of the input files for the various nodes for
Description.txt, Plateconf.txt, etc. but I still got various error
messages, and finally I could not run the test workflow.
This thread is not for the sample1.zip workflow issues, so I start a
new relevant one with all the details if you agree.
Thanks again and cheers,
Janos
aborg
Could be your problem related to permissions? I have seen some
problems of Linux users on KNIME forums...
Regarding your questions:
1) sorry, that heatmap is on available in KNIME; it is written in
Java, so it might be not too hard to make it available in other Java
based solutions.
2) I will try the sample1.zip workflow, if it is no longer working I
will update it; thanks for reporting the problem. If you can describe
your problems that might be useful for others.
Thanks, gabor
On Feb 1, 6:10 am, KVJanos <kvja...@gmail.com> wrote:
> Hi Gabor,
>
> Thanks the idea. I installed the 3rd party feature before, that was
> not the problem. I had no problem to install HiTS under Windows. I
> checked the same features to install under Linux as well, so HiTS is
> not the problem. It seems to be something with my Java installation
> under Linux (possibly involved KNIME as well). I can run HiTS under
> Windows so that solves the problem.
>
> I have 2 more questions:
> (1) Is it possible to run the Heatmap visualization outside of KNIME?
> For example in R?
>
> (2) I tried to run the sample1.zip workflow
>
> http://hits.googlecode.com/svn/ie.tcd.imm.knime.test/trunk/testdata/w...
KVJanos
Thanks Gabor, I appreciate your time and help.
The following error stopped me with the sample1.zip workflow:
Import sample1 workflow into KNIME: OK.
Downloaded the plate8 folder with all the files: OK.
Configuring Simple Configurator for cellHTS2 node (Plate configuration
file, Description file): OK, become yellow.
Configuring File Reader node (add the Screenlog.txt path, column
delimiter:TAB): OK, become yellow.
Configuring INCell xls Importer node: NOT OK, still red after the
following configurations:
- Folder of xls files : seems OK
- Annotation file path (GeneID.txt): seems OK.
- Well count : 96, Plate count: 1, Replicate count: 3 Default
values.
Error messages in the console after these:
WARN FileAnalyzer Didn't get any value for column(s) with index #0.
Please verify column type(s).
WARN FileAnalyzer Didn't get any value for column(s) with index #0,
#1, #2, #3. Please verify column type(s).
WARN INCell xls Importer Unable to convert file name ([path]
\plate8\GeneID.txt) to URI: Illegal character in path at index 12:
[path]/plate8/GeneID.txt
Wondering what went wrong...
Cheers,
Janos
Gábor Bakos
I think I know what is your problem. Recently -to make the reading more flexible- I have modified the input field behaviour. If you want an easier go, please try the updated workflow[1].
It seems that -for some reason- the selected GeneID.txt path was \plate8\GeneID.txt in your case. That should be file:///plate8/GeneID.txt, or something similar.
Thanks for your patience, gabor
[1] http://hits.googlecode.com/svn/ie.tcd.imm.knime.test/trunk/testdata/workflows/sampleCellHTS2/sample1.zip
If we knew what it was we were doing, it would not be called research, would it? ~~~ Albert E...