[MOBY-dev] error installing Biomoby via ant

[Edward Kawas]

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]                            

_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev