Forum: >>> Magnum BBS <<<

Bug#1103009: genomicsdb: FTBFS in testing/arm64: tests failed (4/9)

From Lucas Nussbaum@21:1/5 to All on Sun Apr 13 18:50:03 2025

[continued from previous message]

21: 13:46:22.251 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.252 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.252 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.252 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.252 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: 0.007 s: Try query with a filter
21: 0.024 s: api query_variant_calls with protobuf
21: 13:46:22.258 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.258 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.258 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.259 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.259 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.259 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.259 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: ----------------
21: Interval:[0,1000000000]
21:
21: sample=HG00141
21: row=0 position=12140
21: genomic_interval=1:12141,12295
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG01958
21: row=1 position=12144
21: genomic_interval=1:12145,12277
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG00141
21: row=0 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1
21: sample=HG01958
21: row=1 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
21: sample=HG01530
21: row=2 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
21: 13:46:22.267 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.267 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.267 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.268 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.268 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.268 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.268 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: ----------------
21: Interval:[0,1000000000]
21:
21: sample=HG00141
21: row=0 position=12140
21: genomic_interval=1:12141,12295
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG01958
21: row=1 position=12144
21: genomic_interval=1:12145,12277
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG00141
21: row=0 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1
21: sample=HG01958
21: row=1 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
21: sample=HG01530
21: row=2 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
21: 13:46:22.275 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.275 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.276 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.276 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.276 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.276 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.276 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: 0.007 s: Try query with a filter and workspace with GT ploidy
21: 0.024 s: api query_variant_calls with protobuf
21: 13:46:22.282 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.282 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.282 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.283 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.283 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.283 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.283 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: ----------------
21: Interval:[0,1000000000]
21:
21: sample=HG00141
21: row=0 position=12140
21: genomic_interval=1:12141,12295
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG01958
21: row=1 position=12144
21: genomic_interval=1:12145,12277
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG00141
21: row=0 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1
21: sample=HG01958
21: row=1 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
21: sample=HG01530
21: row=2 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
7: Randomness seeded to: 384332532
21: 13:46:22.290 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.290 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.291 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.291 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.291 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.292 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.292 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: ----------------
21: Interval:[0,1000000000]
21:
21: sample=HG00141
21: row=0 position=12140
21: genomic_interval=1:12141,12295
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG01958
21: row=1 position=12144
21: genomic_interval=1:12145,12277
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG00141
21: row=0 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1
21: sample=HG01958
21: row=1 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
21: sample=HG01530
21: row=2 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
21: 13:46:22.299 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.299 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.300 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.301 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.301 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.301 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.301 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: 0.008 s: Try query with a filter and a small segment size to force TileDB buffers overflow
21: 0.025 s: api query_variant_calls with protobuf
21: 13:46:22.307 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.307 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.307 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.308 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.308 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.308 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.308 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: ----------------
21: Interval:[0,1000000000]
21:
21: sample=HG00141
21: row=0 position=12140
21: genomic_interval=1:12141,12295
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG01958
21: row=1 position=12144
21: genomic_interval=1:12145,12277
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG00141
21: row=0 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1
21: sample=HG01958
21: row=1 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
21: sample=HG01530
21: row=2 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
21: 13:46:22.316 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.316 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.317 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.317 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.317 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.317 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.317 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: ----------------
21: Interval:[0,1000000000]
21:
21: sample=HG00141
21: row=0 position=12140
21: genomic_interval=1:12141,12295
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG01958
21: row=1 position=12144
21: genomic_interval=1:12145,12277
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG00141
21: row=0 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1
21: sample=HG01958
21: row=1 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
21: sample=HG01530
21: row=2 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
21: 13:46:22.325 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.325 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.325 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.326 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.326 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.326 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.326 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: 0.007 s: Try query with POS and ROW with no match
21: 0.025 s: api query_variant_calls with protobuf
21: 13:46:22.332 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.332 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.333 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.333 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.333 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.333 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.333 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: ----------------
21: Interval:[0,1000000000]
21:
21: sample=HG00141
21: row=0 position=12140
21: genomic_interval=1:12141,12295
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG01958
21: row=1 position=12144
21: genomic_interval=1:12145,12277
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG00141
21: row=0 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1
21: sample=HG01958
21: row=1 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
21: sample=HG01530
21: row=2 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
21: 13:46:22.340 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.340 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.341 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.341 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.341 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.341 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.341 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: ----------------
21: Interval:[0,1000000000]
21:
21: sample=HG00141
21: row=0 position=12140
21: genomic_interval=1:12141,12295
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG01958
21: row=1 position=12144
21: genomic_interval=1:12145,12277
21: genomic_fields
21: REF:C ALT:[<NON_REF>] GT:0/0
21: sample=HG00141
21: row=0 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1
21: sample=HG01958
21: row=1 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[T, <NON_REF>] GT:1/1 DP:120
21: sample=HG01530
21: row=2 position=17384
21: genomic_interval=1:17385,17385
21: genomic_fields
21: REF:G ALT:[A, <NON_REF>] GT:0/1 DP:76
21: 13:46:22.349 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.349 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.349 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.349 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.349 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.350 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets):

missing field sample_name

21: 13:46:22.350 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular

JSON file instead

21: 0.007 s: Try query with POS and ROW
21: 0.023 s: api query_variant_calls with protobuf
21: 13:46:22.355 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].

begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn

21: 13:46:22.355 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
21: 13:46:22.356 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
21: 13:46:22.356 DEBUG NativeGenomicsDB - pid=7318 tid=7318 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field

name

21: 13:46:22.356 WARN NativeGenomicsDB - pid=7318 tid=7318 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead

[continued in next message]

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

Who's Online
Recent Visitors
- Krenn
  Mon Jun 8 05:45:38 2026
  from Sydney, Nsw via Telnet
- Bob Worm
  Sun Jun 7 20:58:28 2026
  from Wales, Uk via Telnet
- Michal Wronka
  Sun Jun 7 19:26:28 2026
  from Wroclaw, Poland via SSH
- Centurion
  Sun Jun 7 16:59:51 2026
  from Berea, Ohio via Telnet
- Furryboy
  Sun Jun 7 13:40:29 2026
  from Romania, Galati via SSH
- Krenn
  Sun Jun 7 10:02:33 2026
  from Sydney, Nsw via Telnet
- Spearb0y
  Sun Jun 7 07:41:05 2026
  from Massachusetts via SSH
- Krenn
  Sun Jun 7 03:07:26 2026
  from Sydney, Nsw via Telnet

System Info

Sysop:	Keyop
Location:	Huddersfield, West Yorkshire, UK
Users:	715
Nodes:	16 (2 / 14)
Uptime:	14:12:03
Calls:	12,101
Calls today:	1
Files:	15,004
Messages:	6,518,022

Bug#1103009: genomicsdb: FTBFS in testing/arm64: tests failed (4/9)

Who's Online

Recent Visitors

System Info