[MOBY-dev] error installing Biomoby via ant

[Michael Gerlich]

Hi Eddie,

I'am using Suns JDK 1.5 Version 16. I also encountered this behavivour 
with JDK 6 with compliance level 1.5 (as I had trouble with JDK 6 
generated services and axis 1.4 and Tomcat5.5).

This problem also occurs when I run install from a fresh CVS checkout 
(including a fresh Biomoby cache directory). All SOTEST* datatypes are 
only registered at Central registry, so they are fetched when Biomoby 
fills its cache (retrieving datatypes).

Regards,

Michael

> Hi Michael,
>
> What version of JAVA are you using? What registry are you generating these
> datatypes from?
>
> Thanks,
>
> Eddie 
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Michael Gerlich
> Sent: March-10-09 4:28 PM
> To: MOBY-dev at lists.open-bio.org
> Subject: [MOBY-dev] error installing Biomoby via ant
>
> Hi all,
>
> I checked out Biomoby from CVS and tried to install it via the corresponding
> ant tasks, but after fetching all necessary libraries, the compilation fails
> with a lot of error messages regarding datatypes SOTEST*.
>
> I also encountered this behavior when I tried to run Moses Generator for one
> of my services with an existing Biomoby instance on another machine. There
> the build also fails. 
> I tested this on 3 different machines, including both Ubuntu and XP os. The
> error log is attached, taken from Dashboad.
>
> Does anyone encounter similar problems? Should I try cleaning Maven
> repository, Biomoby cache and/or new Eclipse workspace?
>
> Thanks in advance and regards,
> Michael
>
>
> Excerpt follows (100 error messages like this):
>
> home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/datat
> ypes/SOTest2_engineered_foreign_gene.java:152: getMoby_Parent() in
> org.biomoby.shared.datatypes.SOTest2_engineered_foreign_gene cannot override
> getMoby_Parent() in org.biomoby.shared.datatypes.SOTest2_engineered_gene;
> attempting to use incompatible return type
>     [javac] found   : org.biomoby.shared.datatypes.SOTest2_foreign_gene
>     [javac] required: org.biomoby.shared.datatypes.SOTest2_engineered_region
>     [javac]     public SOTest2_foreign_gene getMoby_Parent() {
>     [javac]                                 ^
>     [javac]
> /home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_engineered_foreign_transposable_element.java:121:
> getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_engineered_foreign_transposable_element
> cannot override getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_mobile_genetic_element; attempting to
> use incompatible return type
>     [javac] found   : org.biomoby.shared.datatypes.SOTest2_foreign[]
>     [javac] required: org.biomoby.shared.datatypes.SOTest2_mobile[]
>     [javac]     public SOTest2_foreign[] getMoby_has_quality() {
>     [javac]                              ^
>     [javac]
> /home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_foreign_transposable_element.java:112: getMoby_has_quality()
> in org.biomoby.shared.datatypes.SOTest2_foreign_transposable_element cannot
> override getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_mobile_genetic_element; attempting to
> use incompatible return type
>     [javac] found   : org.biomoby.shared.datatypes.SOTest2_foreign[]
>     [javac] required: org.biomoby.shared.datatypes.SOTest2_mobile[]
>     [javac]     public SOTest2_foreign[] getMoby_has_quality() {
>     [javac]                              ^
>     [javac]
> /home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_engineered_fusion_gene.java:122: getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_engineered_fusion_gene cannot override
> getMoby_has_quality() in org.biomoby.shared.datatypes.SOTest2_fusion_gene;
> attempting to use incompatible return type
>     [javac] found   : org.biomoby.shared.datatypes.SOTest2_engineered[]
>     [javac] required: org.biomoby.shared.datatypes.SOTest2_fusion[]
>     [javac]     public SOTest2_engineered[] getMoby_has_quality() {
>     [javac]                                 ^
>     [javac]
> /home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_engineered_rescue_region.java:120: getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_engineered_rescue_region cannot
> override getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_rescue_region; attempting to use
> incompatible return type
>     [javac] found   : org.biomoby.shared.datatypes.SOTest2_engineered[]
>     [javac] required: org.biomoby.shared.datatypes.SOTest2_rescue[]
>     [javac]     public SOTest2_engineered[] getMoby_has_quality() {
>     [javac]                                 ^
>     [javac]
> /home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_engineered_transposable_element.java:121:
> getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_engineered_transposable_element cannot
> override getMoby_has_quality() in
> org.biomoby.shared.datatypes.SOTest2_mobile_genetic_element; attempting to
> use incompatible return type
>     [javac] found   : org.biomoby.shared.datatypes.SOTest2_engineered[]
>     [javac] required: org.biomoby.shared.datatypes.SOTest2_mobile[]
>     [javac]     public SOTest2_engineered[] getMoby_has_quality() {
>     [javac]                                 ^
>     [javac]
> /home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_five_prime_coding_exon_noncoding_region.java:114:
> getMoby_part_of() in
> org.biomoby.shared.datatypes.SOTest2_five_prime_coding_exon_noncoding_region
> cannot override getMoby_part_of() in
> org.biomoby.shared.datatypes.SOTest2_transcript_region; attempting to use
> incompatible return type
>     [javac] found   :
> org.biomoby.shared.datatypes.SOTest2_five_prime_coding_exon[]
>     [javac] required: org.biomoby.shared.datatypes.SOTest2_transcript[]
>     [javac]     public SOTest2_five_prime_coding_exon[] getMoby_part_of() {
>     [javac]                                             ^
>     [javac]
> /home/mgerlich/workspace/Biomoby/generated/datatypes/org/biomoby/shared/data
> types/SOTest2_five_prime_exon_coding_region.java:114: getMoby_part_of() in
> org.biomoby.shared.datatypes.SOTest2_five_prime_exon_coding_region cannot
> override getMoby_part_of() in
> org.biomoby.shared.datatypes.SOTest2_transcript_region; attempting to use
> incompatible return type
>     [javac] found   :
> org.biomoby.shared.datatypes.SOTest2_five_prime_coding_exon[]
>     [javac] required: org.biomoby.shared.datatypes.SOTest2_transcript[]
>     [javac]     public SOTest2_five_prime_coding_exon[] getMoby_part_of() {
>     [javac]                            
>
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>   


-- 

Michael Gerlich
Group Bioinformatics & Mass Spectrometry
Leibniz Institute of Plant Biochemistry
06120 Halle, Germany