Problems in vardict inference

Any suggestions for resolving this error in a tumor-only realign/call workflow with vardict based calling? I've run a similar workflow previously on this machine successfully, but that was probably several code updates ago.  Appears to run smoothly through HLA typing. Nothing is writing into the work/vardict contig directories and work/bcbiotx fills with a changing set of temp folders. I initially ran this first with save_discspace=true; currently re-running with =false, but I'm seeing the same errors configured as below.
Thanks in advance for any help-
details:

algorithm:
aligner: bwa
bam_clean: false
bam_sort: false
clinical_reporting: true
mark_duplicates: false
min_allele_fraction: 2
platform: illumina
quality_format: standard
realign: false
recalibrate: false
remove_lcr: true
save_diskspace: false
variant_regions: /home/jfarrar/TARGET/validation/regions.bed
variantcaller: vardict
analysis: variant2
description: TARGET-20-PABLDZ-04A-02D
files:

/home/jfarrar/TARGET/validation/bam/PABLDZ-04.bam
genome_build: hg38
metadata:
batch: PABLDZ-04
phenotype: tumor

[2017-01-27T11:02Z] clusterhn.cluster.com: ipython: combine_sample_regions
[2017-01-27T11:32Z] n001.cluster.com: Identified 131 parallel analysis blocks
Block sizes:
min: 386977
5%: 4778911.0
25%: 16979036.5
median: 20571647.0
75%: 29569392.5
95%: 42877549.5
99%: 55446232.9
max: 56999081
Between block sizes:
min: 259
5%: 285.9
25%: 987.0
median: 3103.0
75%: 10710.5
95%: 186835.5
99%: 2875314.12
max: 9035899
[2017-01-27T11:32Z] clusterhn.cluster.com: Timing: hla typing
[2017-01-27T11:32Z] clusterhn.cluster.com: ipython: call_hla
[2017-01-27T11:32Z] clusterhn.cluster.com: Resource requests: gatk, picard, vardict; memory: 3.00, 3.00, 3.00; cores: 1, 1, 1
[2017-01-27T11:32Z] clusterhn.cluster.com: Configuring 94 jobs to run, using 1 cores each with 3.00g of memory reserved for each job
[2017-01-27T11:32Z] clusterhn.cluster.com: Timing: alignment post-processing
[2017-01-27T11:33Z] clusterhn.cluster.com: ipython: piped_bamprep
[2017-01-27T11:34Z] clusterhn.cluster.com: Timing: variant calling
[2017-01-27T11:35Z] clusterhn.cluster.com: ipython: variantcall_sample
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:35Z] n002.cluster.com: [W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:35Z] n002.cluster.com: tabix index PAKVGI-04-chr8_135521175_145138636-raw.vcf.gz
[2017-01-27T11:35Z] n002.cluster.com: Annotate with dbSNP
[2017-01-27T11:35Z] n001.cluster.com: [W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:35Z] n001.cluster.com: tabix index PAKVGI-04-chr4_84495637_105147028-raw.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n002.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n001.cluster.com: [W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n001.cluster.com: tabix index PAKVGI-04-chr8_0_38414924-raw.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:220: annotated 5 variants in 0.09 seconds (56.6 / second)
[2017-01-27T11:36Z] n001.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n003.cluster.com: [W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:220: annotated 1 variants in 0.02 seconds (64.5 / second)
[2017-01-27T11:36Z] n003.cluster.com: tabix index PAKVGI-04-chr10_0_17228541-raw.vcf.gz
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n003.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n003.cluster.com: [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:220: annotated 3 variants in 0.03 seconds (118.8 / second)
[2017-01-27T11:36Z] n003.cluster.com: tabix index PAKVGI-04-chr1_247418582_248956422-raw.vcf.gz
[2017-01-27T11:36Z] n003.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:220: annotated 5 variants in 0.05 seconds (101.5 / second)
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:220: annotated 7 variants in 0.04 seconds (198.5 / second)
[2017-01-27T11:36Z] n002.cluster.com: [W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n002.cluster.com: tabix index PAKVGI-04-chr3_143973293_179148715-raw.vcf.gz
[2017-01-27T11:36Z] n003.cluster.com: [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n003.cluster.com: [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n003.cluster.com: tabix index PAKVGI-04-chr1_0_20633955-raw.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n003.cluster.com: tabix index PAKVGI-04-chr1_204409453_247418309-raw.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n003.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n002.cluster.com: tabix index PAKVGI-04-chr8_135521175_145138636.vcf.gz
[2017-01-27T11:36Z] n003.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:220: annotated 3 variants in 0.03 seconds (95.7 / second)
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:220: annotated 7 variants in 0.03 seconds (219.9 / second)
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:220: annotated 6 variants in 0.03 seconds (222.2 / second)
[2017-01-27T11:36Z] n001.cluster.com: [W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n001.cluster.com: tabix index PAKVGI-04-chr13_44435979_66305052-raw.vcf.gz
[2017-01-27T11:36Z] n001.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n003.cluster.com: [W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n001.cluster.com: tabix index PAKVGI-04-chr8_0_38414924.vcf.gz
[2017-01-27T11:36Z] n003.cluster.com: tabix index PAKVGI-04-chr3_96866766_123284748-raw.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: [W::vcf_parse] contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n003.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:220: annotated 4 variants in 0.02 seconds (165.7 / second)
[2017-01-27T11:36Z] n002.cluster.com: tabix index PAKVGI-04-chr2_169529724_208237208-raw.vcf.gz
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n003.cluster.com: tabix index PAKVGI-04-chr10_0_17228541.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n003.cluster.com: tabix index PAKVGI-04-chr1_247418582_248956422.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n002.cluster.com: [W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n002.cluster.com: tabix index PAKVGI-04-chr3_27718527_47017280-raw.vcf.gz
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:220: annotated 2 variants in 0.03 seconds (75.8 / second)
[2017-01-27T11:36Z] n002.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:220: annotated 2 variants in 0.04 seconds (47.4 / second)
[2017-01-27T11:36Z] n001.cluster.com: tabix index PAKVGI-04-chr4_84495637_105147028.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:220: annotated 8 variants in 0.05 seconds (151.0 / second)
[2017-01-27T11:36Z] n003.cluster.com: [W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n003.cluster.com: tabix index PAKVGI-04-chr4_24529565_41746343-raw.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n002.cluster.com: tabix index PAKVGI-04-chr1_64009250_109253400-raw.vcf.gz
[2017-01-27T11:36Z] n001.cluster.com: [W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n003.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n001.cluster.com: tabix index PAKVGI-04-chr13_0_25098586-raw.vcf.gz
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n002.cluster.com: tabix index PAKVGI-04-chr3_143973293_179148715.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n003.cluster.com: [W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n002.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n003.cluster.com: [W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n003.cluster.com: tabix index PAKVGI-04-chr3_0_27717768-raw.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: [W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n003.cluster.com: tabix index PAKVGI-04-chr7_50318984_82758737-raw.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n001.cluster.com: [W::vcf_parse] contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n001.cluster.com: [W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n002.cluster.com: tabix index PAKVGI-04-chr7_18496202_50304971-raw.vcf.gz
[2017-01-27T11:36Z] n003.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n001.cluster.com: tabix index PAKVGI-04-chr12_25207507_45730180-raw.vcf.gz
[2017-01-27T11:36Z] n001.cluster.com: tabix index PAKVGI-04-chr6_0_16306883-raw.vcf.gz
[2017-01-27T11:36Z] n003.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n002.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n001.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:220: annotated 3 variants in 0.04 seconds (80.6 / second)
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n001.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:220: annotated 11 variants in 0.08 seconds (146.3 / second)
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n002.cluster.com: [W::vcf_parse] contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n002.cluster.com: tabix index PAKVGI-04-chr2_25749664_45006502-raw.vcf.gz
[2017-01-27T11:36Z] n003.cluster.com: [W::vcf_parse] contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:220: annotated 78 variants in 0.05 seconds (1581.5 / second)
[2017-01-27T11:36Z] n003.cluster.com: tabix index PAKVGI-04-chr5_0_31401592-raw.vcf.gz
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:220: annotated 9 variants in 0.09 seconds (101.9 / second)
[2017-01-27T11:36Z] n002.cluster.com: [W::vcf_parse] contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n002.cluster.com: [W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:220: annotated 15 variants in 0.12 seconds (129.2 / second)
[2017-01-27T11:36Z] n002.cluster.com: tabix index PAKVGI-04-chr2_45008532_61189109-raw.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: tabix index PAKVGI-04-chr10_110568885_127982374-raw.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:220: annotated 7 variants in 0.26 seconds (27.2 / second)
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:220: annotated 2 variants in 0.02 seconds (85.6 / second)
[2017-01-27T11:36Z] n002.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n003.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:220: annotated 9 variants in 0.01 seconds (799.0 / second)
[2017-01-27T11:36Z] n003.cluster.com: [W::vcf_parse] contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n001.cluster.com: [W::vcf_parse] contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n002.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n003.cluster.com: tabix index PAKVGI-04-chr11_0_32389218-raw.vcf.gz
[2017-01-27T11:36Z] n001.cluster.com: tabix index PAKVGI-04-chr2_144396381_160493825-raw.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: [W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n003.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n002.cluster.com: tabix index PAKVGI-04-chr6_138170597_156778799-raw.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n001.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n001.cluster.com: [W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n003.cluster.com:
[2017-01-27T11:36Z] n003.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n003.cluster.com: =============================================
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n001.cluster.com: tabix index PAKVGI-04-chr6_16326378_33392036-raw.vcf.gz
[2017-01-27T11:36Z] n002.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:220: annotated 21 variants in 0.16 seconds (133.4 / second)
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:220: annotated 3 variants in 0.06 seconds (48.1 / second)
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:220: annotated 9 variants in 0.06 seconds (159.6 / second)
[2017-01-27T11:36Z] n001.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n002.cluster.com:
[2017-01-27T11:36Z] n002.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n002.cluster.com: =============================================
[2017-01-27T11:36Z] n002.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n001.cluster.com: Annotate with dbSNP
[2017-01-27T11:36Z] n003.cluster.com: vcfanno.go:220: annotated 13 variants in 0.06 seconds (209.5 / second)
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno version 0.1.1-alpha [built with go1.8beta1]
[2017-01-27T11:36Z] n001.cluster.com:
[2017-01-27T11:36Z] n001.cluster.com: see: https://github.com/brentp/vcfanno
[2017-01-27T11:36Z] n001.cluster.com: =============================================
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:114: found 1 sources from 1 files
[2017-01-27T11:36Z] n003.cluster.com: [W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[2017-01-27T11:36Z] n001.cluster.com: vcfanno.go:220: annotated 2 variants in 0.06 seconds (34.4 / second)
[2017-01-27T11:36Z] n002.cluster.com: Failed to open -: unknown file type
[2017-01-27T11:36Z] n002.cluster.com: Uncaught exception occurred
Traceback (most recent call last):
File "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 102, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; unset R_HOME && unset JAVA_HOME && export PATH=/net/clusterhn.cluster.com/opt/bcbio/anaconda/bin:$PATH && export VAR_DICT_OPTS='-Xms750m -Xmx3000m -XX:+UseSerialGC -Djava.io.tmpdir=/net/clusterhn.cluster.com/home/jfarrar/TARGET/validation/VarDict/20170124_Unpaired/vardict-T-only/work/bcbiotx/tmp3SClLF' && vardict-java -G /opt/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa -f 0.02 -N TARGET-20-PAKVGI-04A-02D -b /home/jfarrar/TARGET/validation/VarDict/20170124_Unpaired/vardict-T-only/work/align/TARGET-20-PAKVGI-04A-02D/TARGET-20-PAKVGI-04A-02D-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /home/jfarrar/TARGET/validation/VarDict/20170124_Unpaired/vardict-T-only/work/vardict/chr14/PAKVGI-04-chr14_0_21070473-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -N TARGET-20-PAKVGI-04A-02D -E -f 0.02  | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $5) } {print}' |  awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /opt/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /net/clusterhn.cluster.com/home/jfarrar/TARGET/validation/VarDict/20170124_Unpaired/vardict-T-only/work/bcbiotx/tmp3SClLF/PAKVGI-04-chr14_0_21070473-raw.vcf.gz
Failed to open -: unknown file type
' returned non-zero exit status 1
[2017-01-27T11:36Z] n003.cluster.com: tabix index PAKVGI-04-chr7_116699047_135558032-raw.vcf.gz
[2017-01-27T11:36Z] n003.cluster.com: Genotyping with VarDict: Inference
[2017-01-27T11:36Z] n002.cluster.com: Unexpected error
Traceback (most recent call last):
File "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 50, in _setup_logging
yield config
File "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 344, in variantcall_sample
return ipython.zip_args(apply(genotype.variantcall_sample, *args))
File "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/genotype.py", line 316, in variantcall_sample
call_file = caller_fn(align_bams, items, sam_ref, assoc_files, region, call_file)
File "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/vardict.py", line 79, in run_vardict
assoc_files, region, out_file)
File "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/vardict.py", line 254, in _run_vardict_paired
assoc_files, region, out_file)
File "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/vardict.py", line 154, in _run_vardict_caller
do.run(cmd.format(**locals()), "Genotyping with VarDict: Inference", {})
File "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 102, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; unset R_HOME && unset JAVA_HOME && export PATH=/net/clusterhn.cluster.com/opt/bcbio/anaconda/bin:$PATH && export VAR_DICT_OPTS='-Xms750m -Xmx3000m -XX:+UseSerialGC -Djava.io.tmpdir=/net/clusterhn.cluster.com/home/jfarrar/TARGET/validation/VarDict/20170124_Unpaired/vardict-T-only/work/bcbiotx/tmp3SClLF' && vardict-java -G /opt/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa -f 0.02 -N TARGET-20-PAKVGI-04A-02D -b /home/jfarrar/TARGET/validation/VarDict/20170124_Unpaired/vardict-T-only/work/align/TARGET-20-PAKVGI-04A-02D/TARGET-20-PAKVGI-04A-02D-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /home/jfarrar/TARGET/validation/VarDict/20170124_Unpaired/vardict-T-only/work/vardict/chr14/PAKVGI-04-chr14_0_21070473-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -N TARGET-20-PAKVGI-04A-02D -E -f 0.02  | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $5) } {print}' |  awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /opt/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /net/clusterhn.cluster.com/home/jfarrar/TARGET/validation/VarDict/20170124_Unpaired/vardict-T-only/work/bcbiotx/tmp3SClLF/PAKVGI-04-chr14_0_21070473-raw.vcf.gz
Failed to open -: unknown file type
' returned non-zero exit status 1

Apologies about the issue. We just pushed a fix for this issue this morning (you can follow the discussion in #1788) and you can fix with:
bcbio_conda install -c bioconda vardict

which will get a new set of Perl post-processing scripts that handle this. You can restart your run after the fix and it'll pick up where it left off. Hope this helps get you analysis finished.


Allow updating and removing primitive values

The current text does not allow directly targeting a primitive value, for example a certain string in the tags array of an Operation Object, and thus does not allow a convenient/workable way to remove or replace a certain tag name without knowing all other tag names in the tags field.
Proposal
Allow target JSON Path expressions to select nodes of all JSON types.
For example allow
overlay: 1.0.0
info:
  title: Remove a string from the tags array of all operations
  version: 1.0.0
actions:
  - target: $.paths.*.*.tags[?@ == 'dummy']
    remove: true

and
overlay: 1.0.0
info:
  title: Preplace a string in the tags array of all operations
  version: 1.0.0
actions:
  - target: $.paths.*.*.tags[?@ == 'Foo']
    update: "Bar"

If this is allowed, #70 should be discarded in 2.0


Add example for locking screen orientation in a letterboxing environment

Android may choose to letterbox applications that lock orientation. This gets particularly bad on foldable devices, where a developer may want to lock orientation when the devices is folded and unlock when unfolded. However, if the app is letterboxed when unfolded, the MediaQuery.of(context).size will never report the full display size, only the letterboxed window size. This may result in an application getting "stuck" in portrait mode.
/cc @TytaniumDev

Thanks for fixing up the other example as well!


Clarify $relatedQuery documentation regarding relatedFindQueryMutates

The documentation suggests that the default behavior is to mutate the owner model, when the opposite is true in v2.
Examples (here):

Use this to build a query that only affects the items related to an instance through a relation. By default, any fetched or inserted items are also stored to the owner model’s property named after the relation. See relatedFindQueryMutates or relatedInsertQueryMutates to change this behaviour.

Fetch all items related to an item through a relation. The fetched items are also stored to the owner item's property named after the relation (by default):

const pets = await jennifer.$relatedQuery('pets');

console.log('jennifer has', pets.length, 'pets');
console.log(jennifer.pets === pets); // --> true

Yep the documentation is outdated. Thanks for bringing this up. I'll fix the docs.

Yep the documentation is outdated. Thanks for bringing this up. I'll fix the docs.


[WIP] Improved importer logic for password in users

refs #9150
This PR changes the logic when importing users:

don't set a default uid for every password so we're able to detect hashed passwords
detect hashed password (hashed with Bcrypt, when used Ghost for export) and don't run into the validations. Already hashed passwords get re-hashed and stored
run only non-hashed passwords through the password length validator. An invalid (=too short) password will cause the import to fail.
in importPersistUser mode, don't run into validations and don't hash the password. Just take it exactly as provided.

Todos:

[ ] More tests for these specific cases, especially importPersistUser mode (no test for this so far)

Closing this in favour of #9161


python311Packages.cnvkit: 0.9.10 -> 0.9.11

Automatic update generated by nixpkgs-update tools. This update was made based on information from passthru.updateScript.
meta.description for python311Packages.cnvkit is: A Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data
meta.homepage for python311Packages.cnvkit is: https://cnvkit.readthedocs.io
meta.changelog for python311Packages.cnvkit is: https://github.com/etal/cnvkit/releases/tag/v0.9.11
Updates performed

Ran passthru.UpdateScript

To inspect upstream changes
Impact
Checks done

built on NixOS
The tests defined in passthru.tests, if any, passed
found 0.9.11 with grep in /nix/store/17hqjdrl542yn15jy0yhpm1swsdgp66h-python3.11-cnvkit-0.9.11
found 0.9.11 in filename of file in /nix/store/17hqjdrl542yn15jy0yhpm1swsdgp66h-python3.11-cnvkit-0.9.11

Rebuild report (if merged into master) (click to expand)

3 total rebuild path(s)

3 package rebuild(s)

First fifty rebuilds by attrpath

python311Packages.cnvkit
python312Packages.cnvkit

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/17hqjdrl542yn15jy0yhpm1swsdgp66h-python3.11-cnvkit-0.9.11 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A python311Packages.cnvkit https://github.com/r-ryantm/nixpkgs/archive/509070d0a7d3523dcae44b43f021611616a8d00e.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/509070d0a7d3523dcae44b43f021611616a8d00e#python311Packages.cnvkit

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/17hqjdrl542yn15jy0yhpm1swsdgp66h-python3.11-cnvkit-0.9.11
ls -la /nix/store/17hqjdrl542yn15jy0yhpm1swsdgp66h-python3.11-cnvkit-0.9.11/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review --extra-nixpkgs-config '{ allowInsecurePredicate = x: true; }' run on x86_64-linux 1

4 packages built:

python311Packages.cnvkit
python311Packages.cnvkit.dist
python312Packages.cnvkit
python312Packages.cnvkit.dist

Maintainer pings
cc @jbedo for testing.

Result of nixpkgs-review pr 312171 run on x86_64-linux 1

4 packages built:

python311Packages.cnvkit
python311Packages.cnvkit.dist
python312Packages.cnvkit
python312Packages.cnvkit.dist


Clarify shallow rendering behavior with props

So our documentation has the following snippet:
http://airbnb.io/enzyme/docs/api/ShallowWrapper/prop.html
const wrapper = shallow(<MyComponent foo={10} />);
expect(wrapper.prop('foo')).to.equal(10);

The issue is that, unless this foo prop is being passed as props to a child element then this will actually fail. @lelandrichardson's explanation of shallow rendering here

@nfcampos @Aweary if you want to really understand the reason, it can be stated like this:

Consider the full react render tree as a tree in 3-dimensional space
Consider the root component of a shallow call (ie, Foo in the case of wrapper()) as z=0 in this space
In the case of shallow, we choose to look only at z=1, which includes essentially the full output of render() of the  component.
In the case of Foo being a DOM node, there is no z=1.

As a result, instead of making this an error case, we simply fall back to looking at z=0 instead of z=1.
I'm not sure if I consider this behavior wrong or less than ideal, but I do think that the fact that a large subset of our tests happen to test this case rather than the composite component case is the real problem.

I'm of the opinion that we should be looking at z=0 in all cases to properly support props that are defined on the root component in the shallow call. Users are doing stuff like:

class Foo extends Component {
  render () {
    return
{this.props.foo}

  }
}

...

const wrapper = shallow(<Foo foo="bar" />)
expect(wrapper.prop('foo')).to.equal('bar')

And it's failing because shallow is only looking at the returned div which only has a className and children prop.
We need to decide if this should be supported or not, and if so how we can do it. Any discussion/feedback would be great :)
@nfcampos @blainekasten @lelandrichardson @ljharb

I see why this is confusing, but why would you need to make assertions about the immutable props you literally just passed in? The assertions are on the wrapper, not on the element itself.

as @ljharb said, there's no use for getting a wrapper around the element you just rendered. The only reason I'd see for changing the behaviour of shallow would be to not confuse users who use both shallow and mount, as it can be easy to forget that when using mount you need to select the root rendered node to assert stuff about it (do what exactly I don't know, see #446) but with shallow that's what we return.

That's a good point, I can't think of a use case where you can't just assert on the value before its being passed via props. If we can't find a good reason to support this use case we should definitely update the docs and possibly do a write-up on how shallow builds the render tree.

Ah, I've just started using this tech, and I did find this a bit confusing

const wrapper = shallow(<MyComponent foo={10} />);
expect(wrapper.prop('foo')).to.equal(10);

This also doesn't seem to work if the prop has been set using setDefaultProps.
works when using mount though so maybe just a doc's update to clarify.

@atmd83 that shouldn't work. With shallow, you're testing with MyComponent renders - not the element you passed into shallow. You literally just passed it a "foo" prop of 10, why would you need to test that it has a "foo" prop of 10?

@ljharb if you are doing TDD then you want to specify your public API, which for a component is it's props. This would also include verifying that defaultProps are the values you expect them to be etc. you are not validating that it works, you are testing that it hasn't changed and also documenting it's functionality. TDD is more about documentation and design that it's about testing, the tests are a nice side effect. /cc @atmd83

@antz29 you should be testing the effect of your defaultProps, not the literal value of those props. TDD is about documenting the effect of your code - not its internal implementation, which is what defaultProps are.

@ljharb I disagree, for me, like I said, the documentation value of tests is critical. Documenting The public API of a component is important as it's both what it's users will use and the contract it has with other components. I open the test and and I see what props are defined, what the default values are (if any) and how I should use them. Without that, I need to open up the components code to find that. Tests give me confidence that the API I'm working with works the way it's specified in the test (or spec). In TDD I'm not really testing anything, I'm specifying it.

defaultProps remain an implementation detail that aren't part of the API.

@ljharb defaultProps an implementation detail? If I'm checking the docs for a method, I definitely care what the default values for arguments are. That documents what the engineer perceived the most likely / useful values would be. It tells me a lot about their assumptions. It's exactly the same for Components. The public API for a component is the defined props AND their default values if any, if default values were not part of the public API they wouldn't be documented.

Yo guys just had this issue at work and solved it by re-rendering the entire Swiper based on a Boolean - you can make this a little more DRY from here (which I'm about to do) but just posting so you guys know my work around...
_renderWithoutExpenses() {
		const sectionOneArray = this._renderSectionOne();
		const sectionThreeArray = this._renderSectionThree();

		const componentReturn = [...sectionOneArray, ...sectionThreeArray];
		const componentList = componentReturn.map((item) => item);

		return (
			<Swiper
				ref='swiper'
				showsPagination={false}
				style={styles.swiper}
				loop={false}
				onMomentumScrollEnd = {this._onMomentumScrollEnd}
				height={this._updateBoundaries()}
				>
					{ componentList }
			</Swiper>
		);
	}

_renderWithExpenses() {
		const sectionOneArray = this._renderSectionOne();
		const sectionTwoArray = this._renderSectionTwo();
		const sectionThreeArray = this._renderSectionThree();

		const componentReturn = [...sectionOneArray, ...sectionTwoArray, ...sectionThreeArray];
		const componentList = componentReturn.map((item) => item);

		return (
			<Swiper
				ref='swiper'
				showsPagination={false}
				style={styles.swiper}
				loop={false}
				onMomentumScrollEnd = {this._onMomentumScrollEnd}
				height={this._updateBoundaries()}
				>
					{ componentList }
			</Swiper>
		);

	}

	render() {
		return (
			<View>

				{ this.props.estimateExpenses ? this._renderWithExpenses() : this._renderWithoutExpenses() }
          	</View>
		);
	}

... then for each section, I had to deal with different component, so I returned an array of components for this._renderSectionOne() etc. - this prevented me from repeating component code where I could with the limitations.
As an example:
_renderSectionOne() {
	    return (
			[<ComponentOne key="0" />,
                          <ComponentTwo key="1" />]
		);
	}

_renderSectionTwo() {
	    return (
			[<AnotherComponentOne key="0" />,
                          <ComponentTwo key="1" />]
		);
	}

The important and slightly annoying thing is that I had to rewrite the <Swiper /> components in both the _renderWithExpenses() and _renderWithoutExpenses(), but this was as flexible as I got which managed to work.
All these methods fell within the one components class. It's also important that you combine all the dynamic section arrays into one array before using map() or your Swiper will be retarded af.
Hopefully this makes sense and helps out, fam.

I'm not saying they don't matter. I'm saying that a default function value and an "||" inside the function are equivalent, albeit one is more easily discoverable. That's why I said here that you should indeed be testing the effect of the defaults.
In the above example, if you pass a 10 or if you pass nothing, you should be testing only how that effects the render output - similarly to testing the return value of a pure function. Testing details of how things are defaulted separate from that is testing implementation details, and that makes for brittle, tightly coupled tests. I should be able to refactor freely between defaultProps, and this.props.a || whatever, without breaking any tests or requiring any test changes.

So I TDD.  If a parent component is passing props to a child, I'd wanna know that it successfully did so.  As you know, a parent could have logic in it.  That could be as simple as if someone say took that prop you passed into the parent, and lets say they set it to another variable for whatever reason then used that other variable as the value to be passed into a child's props.  OR  maybe they're taking a subset of the data from the parent's props, or manipulating the data before sending it off to a child's props.
In any case, there will be logic sometimes in your parent.  There's a need to test that the parent successfully passed the expected data to child props...because if any of that behavior stated above in the parent fails, the child props may not receive the data you expected hence you've just discovered a bug or someone or you just broke your code if that test of passing props to child fails, you have something what went wrong in your parent.
So I agree with don't test the props you just sent into the wrapper...makes no sense.  Test the outcome of the parent's render.  So if you have the parent rendering a child, you'd wanna shallowly test that the child got the right props from the parent.  I haven't found a way though to do that with child as you can't use instance() on a child component, only the root component with shallow().

and...my head hurts after reading this entire thread :P.  Did you end up documenting how shallow renders the tree yet?

@dschinkel If you have a <Parent> that renders a <Child>, you shallow-render the Parent, then do wrapper.find(Child).props() and assert on that.

yea in issue (848)[https://github.com/airbnb/enzyme/issues/848] that I just posted, I stated that I've tried that already before posting all this, and  it's not working for me...

My use case is that I'd like to pass in mock functions by default and not hold onto their reference. Usually I do something like this:
const shallowComponent = (props = {}) => (
  shallow(<Button onCancel={jest.fn()} onSave={jest.fn()}/>)
)

Then in my test I want to be able to say something like...
expect(wrapper.props().onCancel).toHaveBeenCalledTimes(1)

Right now I have to hold onto a reference of the mock function, or do a full mount.
... I realize it's not a huge use case, but I find it quite handy.

That use case would be analogous to calling a function with arguments and expecting to be able to retrieve a reference to those arguments later from the function.
Definitely just hold on to a separate reference. It's clearer anyways.

I hear what you're saying, I guess I'm viewing it more from an OOP perspective, where it's ordinary to access properties you passed in on initialization.

@ljharb in response to your question "why would you need to make assertions about the immutable props you literally just passed in?" here's an example that's pretty common in the codebase I'm working in:
const Item = ({ type }) => {
    const itemType = type === 'file' ? 'File' : 'Folder';
    const subsection = <Subsection description={ itemType } />;
    return <Something subsection={ subsection } />;
}

how do I test that the description prop on the subsection is correct (without doing a full mount)? My first approach would be to shallow render the subsection:
const wrapper = shallow(<Something type="file" />);
const subsection = shallow(wrapper.prop('subsection'));

and then I run into the problem described in this thread. The subsection wrapper in this example actually shallow-renders the children of Subsection rather than Subsection itself (e.g. subsection.is('Subsection') returns false, and subsection.prop('description') doesn't return what I want it to).
The two solutions to this problem:

Wrap the component with a span:

const Item = ({ type }) => {
    const itemType = type === 'file' ? 'File' : 'Folder';
    const subsection = <Subsection description={ itemType } />;
    return <Something subsection={ subsection } />;
}

not great for obvious reasons

(What I've actually been doing) directly access the React instance in the test:

const wrapper = shallow(<Something type="file" />);
const subsection = wrapper.prop('subsection');
assert.equal(subsection.props.description, 'File');

which is fine, but then you're no longer using enzyme and lose out on all its other features
is there a better solution to this problem that I'm missing?

@davomgz ah, that's a different case. In that case, you're doing something more like the following:
const wrapper = shallow(<Item type="file" />);
const subsection = wrapper.prop('subsection');
const subsectionWrapper = shallow(() => subsection);
// make your assertions here.

#1444 may be relevant to your question.


Update lodash in package.json to match yarn.lock.

Update the version of lodash in package.json to match the version in the yarn.lock. Without this, yarn audit in consuming projects report react-chartjs-2 as having a high severity vulnerability with lodash:

The actual vulnerability appears to have been patched here, but without the package json reflecting the change, auditing tools still flag this as vulnerable.

Thanks for the contribution! This should be resolved in 2.10.0


Virtual Desktop with Animations and Enhancements

Description of the new feature / enhancement
I would love to see a Tool to manage my virtual Desktops but in a better way than it is build in Windows itself (WIN + TAB). The most anoying thing with the built in "Virtual Desktop" is, that there is no Animation when the Desktop is switched via Keystrokes (WIN + CTRL + Arrow Left/Right). Also there is no Hint oder something on which Desktop you are. If there would be a solution to make a Feature / Tool. It would be a significant Update to my Productivity.
Scenario when this would be used?
I often switch from Visual Studio Code to the Browser or Teams, but I often have so many Windows open that the ALT + TAB Switch often causes me to switch to the wrong Window. It would be just a big improvement for me to switch via Desktop. Also when sharing my screen with customers, I could make one Desktop to share - so the customer won't see any Windows which aren't supposed to be shared...
Supporting information
There is already an older Tool called Microsoft Desktop
Maybe there is a way to improve this?

this is a lot of different requests in one


Consider moving some helper functions from haskell-ide-engine into haskell-lsp-types

It would make sense to make them available for other users.  The prior link is dead.
I have moved

rangeLinesFromVfs
PosPrefixInfo(..)
getCompletionPrefix

over in https://github.com/alanz/haskell-lsp/pull/164

Some work was done, @bubba, are there more functions to move (taking in account that now we are deprecating hie)? In that case a list or any general consideration would be useful

I think this is no longer relevant.


How to Redraw/notifyDatachange when after property value change

Hi,
I have an ObservableArrayList of a simple Pojo Message
private final ObservableArrayList<Message> messageList = new ObservableArrayList<>();

new LastAdapter(messageList, BR.message)
                .map(Message.class, R.layout.item_message)
                .into(mRecycleView);

When the user clicks on an ImageView I wanna mark it as read and redraw this line/item. I have added an event handler for this.
<import type="..Handler" />

<variable
    name="message"
    type="....model.Message" />

<ImageView
    android:id="@+id/read"
    android:onClick="@{(view) -> Handler.markAsread(view, message)}"
<EMAIL_ADDRESS>? View.GONE : View.VISIBLE}"
    ...
 />

public static class Handler {
    public static void markAsread(View view, Message message) {
        message.setRead(true);
    }
}

But I have no idea how to redraw this item on the RecyclerView. Just change the Message attribute seems does not work.

I know I can do view.setVisibility(View.GONE); on markAsread but it's only a example code ;)

To redraw an item when you click on it, you can use adapter.notifyItemChanged(position)


Signature of [Modified] Bessel Functions [of the Second Kind]

I am trying to implement a Matern Covariance function, which depends on K_v.  I believe that v may take on non-integer values, e.g v=1/2 is quite significant from a theoretical standpoint.
However, when I supply both arguments as real (nu is a real<lower=0.5> parameter):
Sigma[i,j] <- sigmasq * 1.0/(tgamma(nu)*pow(2.0,nu-1.0) *
pow(sqrt(2.0*nu)*D[i,j]/phi,nu) * modified_bessel_second_kind(nu,
sqrt(2.0*nu)*D[i,j]/phi);

I get a compilation error:
DIAGNOSTIC(S) FROM PARSER:
no matches for function name="modified_bessel_second_kind"
   arg 0 type=real
   arg 1 type=real
available function signatures for modified_bessel_second_kind:
0.  modified_bessel_second_kind(int, real) : real

which seems to make me think that K_v only takes integer v.
Is it possible to make it take two real arguments?

This issue was moved to stan-dev/math#23


Tweak dockerfile to rebuild gulp

Gents, could you do a full rebuild on your machines to test this.
Gulp builds now happen in the image, no longer on make run. You won't even see a local node_modules folder - it's all inside the image.
The tradeoff is that you'll need to remember to do a make rebuild when you change anything gulp builds.
The old behaviour can be emulated with make rebuild run.

To test, delete your build/node_modules folder.

@danjoneslf we should get this merged, if you agree? Very happy with the new aggressively-cached dockerfile!

@danjoneslf Yes, I think the package.lock file is now useless, I will remove it from the repo


Change link redirect

The redirect link stays the same and only changes after refresh. While the greetings change ,the link should randomly change as - well

Bug was taken care of long time ago, forgot to close issue


NATIVE-597: Configurable icons

This pull request belongs to an issue on our bugtracker.
You can find it there by looking for an issue with the key which is mentioned in the title of this pull request.
It starts with the keyword NATIVE.

Apart from the design question this is ready for merging :)

@maxammann do you mean this comment https://github.com/Integreat/integreat-react-native-app/pull/300#discussion_r475556685 by this?

Apart from the design question this is ready for merging :)


enable exact balance listener option via metadata

Please provide a description of this PR:
Fixes https://github.com/istio/istio/issues/42374
To help us figure out who should review this PR, please put an X in all the areas that this PR affects.

[ ] Ambient
[ ] Configuration Infrastructure
[ ] Docs
[ ] Installation
[X ] Networking
[ ] Performance and Scalability
[ ] Policies and Telemetry
[ ] Security
[ ] Test and Release
[ ] User Experience
[ ] Developer Infrastructure

Hi @bwallacef5. Thanks for your PR.
I'm waiting for a istio member to verify that this patch is reasonable to test. If it is, they should reply with /ok-to-test on its own line. Until that is done, I will not automatically test new commits in this PR, but the usual testing commands by org members will still work. Regular contributors should join the org to skip this step.
Once the patch is verified, the new status will be reflected by the ok-to-test label.
I understand the commands that are listed here.

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository.

/ok-to-test

@bwallacef5: The following test failed, say /retest to rerun all failed tests or /retest-required to rerun all mandatory failed tests:

Test name
Commit
Details
Required
Rerun command

lint_istio
b0bd7f7d3debd60efa149001d9a8d07568908822
link
true
/test lint

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.

/cherry-pick release-1.17

@jacob-delgado: once the present PR merges, I will cherry-pick it on top of release-1.17 in a new PR and assign it to you.

In response to this:

/cherry-pick release-1.17

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository.

currently only inbound is functional, but I am looking for input on the overall approach.


feat: parse dates, times, and timestamps

This PR adds support for some Arrow temporal formats - dates, times, and timestamps. I'm primarily using ADBC with Snowflake, which doesn't support the full set of Arrow temporal formats (no timestamps with timezones, durations, or intervals).
These three formats can be tested using the following query:
db_opts = [driver: :snowflake, ..]
{:ok, db} = Adbc.Database.start_link(db_opts)
{:ok, conn} = Adbc.Connection.start_link(database: db)

query = """
select
  '2023-03-01T10:23:45.123456'::timestamp \"datetime\",
  '2023-03-01'::date \"date\",
  '10:23:45.123456'::time \"time\"
"""

Adbc.Connection.query!(conn, query)
# %Adbc.Result{
#   num_rows: 1,
#   data: %{
#     "date" => [~D[2023-03-01]],
#     "datetime" => [~N[2023-03-01 10:23:45.123456]],
#     "time" => [~T[10:23:45.123456]]
#   }
# }

While working on parsing times, I ran into this Go panic
panic: arrow/array: column "time" type mismatch: got=float64, want=time64[ns]

goroutine 31 [running]:
github.com/apache/arrow/go/v13/arrow/array.NewRecord(0xc000577b00, {0xc0004efa80, 0x4, 0xc0004efa00?}, 0x1)
  /Users/runner/go/pkg/mod/github.com/apache/arrow/go/v13@v13.0.0-20230620164925-94af6c3c9646/arrow/array/record.go:151 +0x173
github.com/apache/arrow-adbc/go/adbc/driver/snowflake.getRecTransformer.func1({0x113ffcf58, 0xc0008563c0}, {0x11401ab10, 0xc000524900})
  /Users/runner/work/arrow-adbc/arrow-adbc/adbc/go/adbc/driver/snowflake/record_reader.go:65 +0x1ad
github.com/apache/arrow-adbc/go/adbc/driver/snowflake.newRecordReader.func2()
  /Users/runner/work/arrow-adbc/arrow-adbc/adbc/go/adbc/driver/snowflake/record_reader.go:283 +0x1c3
golang.org/x/sync/errgroup.(*Group).Go.func1()
  /Users/runner/go/pkg/mod/golang.org/x/sync@v0.3.0/errgroup/errgroup.go:75 +0x64
created by golang.org/x/sync/errgroup.(*Group).Go
  /Users/runner/go/pkg/mod/golang.org/x/sync@v0.3.0/errgroup/errgroup.go:72 +0xa5

Hi @superhawk610! I believe the bug you are seeing is this one: https://github.com/apache/arrow-adbc/pull/1021
You can try using v0.7.0-rc and see if it address it. https://github.com/apache/arrow-adbc/releases/tag/apache-arrow-adbc-0.7.0
I will add a guide on updating ADBC, but it should be:

Copy root files and c/ directory from ADBC into 3rdparty
Update the driver version: https://github.com/elixir-explorer/adbc/blob/main/lib/adbc_driver.ex#L9
...
Profit

Thanks for the PR and let me know if there is anything else we can help with. :)

That fixed it! Should I check in the driver version upgrade with this PR?

@superhawk610 I will do it in another PR. That's because if it is an external contribution, I need to review all code. :) I will ping you in the PR for double checking.

Btw, can you add tests using sqlite or PG? Or should I push them after merging?

I can add tests early next week!

:green_heart: :blue_heart: :purple_heart: :yellow_heart: :heart:


[NFC] Split up the "special convention" for runtime async functions

The special convention currently means three things:

There is no async FP symbol for the function.  Calls should go directly to the function symbol, and an async context of fixed static size should be allocated.  This is mandatory for calling runtime-provided async functions.

The callee context should be allocated but not initialized.  The main context pointer passed should be the caller's context, and the continuation function pointer and callee context should be passed as separate arguments.  The function will resume the continuation function pointer with the caller's context.  This is a micro-optimization appropriate for functions that are expected to frequently return immediately; other functions shouldn't bother.

Generic arguments should be suppressed.  This is a microoptimization for certain specific runtime functions where we happen to know that the runtime already stores the appropriate information internally.  Other functions probably don't want this.

Obviously, these different treatments should be split into different predicates so that functions can opt in to different subsets of them.
I've also set the code up so that runtime functions can more easily request a specific static async context size.  Previously, it was a confusingly embedded assumption that the static context size was always exactly two pointers more than the header.

@swift-ci Please test

@swift-ci Please test macOS

Thank you very much @rjmccall !


First test done

So used the same image with the same setting ( besides clicking all options in Rasterizer ) and the preview shows a difference in color tone detection on the left. Added LW for compare.

Top is Rasterizer
Bottom is LW
Btw cool change on starting from the bottom. Diagonal at 200 mms almost disasembles my machine lol

Now this one looks much more detailed. The image with "more" white space is Restarizer.
Again same setup, size but all options checked in Restarizer

never mind all this, it was my mistake by increasing the contrast, that comes as a consequence of the settings not going to default after refresh


KSM CLI - Expand hostname abbreviations in JSON profile export

In working with the KSM SDKs, I encountered errors stating that the hostname could not be resolved by the system's DNS. Upon further inspection of the errors produced by the SDK, it appears that the request URL is built by pulling whatever value is included for the hostname field in the config file. This appeared consistent across the SDK for multiple languages.
If the config file was created/initialized using the SDK, the hostname is fully expanded to a domain name in the config file. However, if the config file was created with a JSON export from KSM CLI, the hostname will be kept in the two-letter abbreviated form if it uses that format in the keeper.ini file used by KSM CLI.
Since KSM CLI does not output JSON files that conform to what the SDKs are expecting, I made a small addition that decodes the two-letter abbreviation to the full hostname when exporting since the primary purpose of exporting the config file in JSON is for consumption by the SDK.

In the unit test ...
integration/keeper_secrets_manager_cli/tests/init_test.py
There are 3 lines (78, 100, 172) that are looking for US as the hostname. Those need to be changed to keepersecurity.com for the PR to pass its test.
Beside that, the changes look good. Thanks.


[rancher 1.6] optimize ingress controller requests to Rancher

As a part of fixing https://github.com/rancher/rancher/issues/15288 and https://github.com/rancher/rancher/issues/8254 we have changed the rancher ingress controller logic to the full sync between k8s ingresses and rancher lbs. It solved the original problem, but introduced a performance issue seen on the user's setup having 600+ ingresses and lb version v0.9.11. Rancher responses to ingress controller would have more data now - 100 lbs by default, and it can cause issues on the setups having slower connection between ingress host and rancher server or/and slower API responses on the Rancher side when fetching a big set of data. We have also observed memory going up to 2GB for hte ingress controller
We have to investigate on the fix. A couple of thoughts:

Check if fetching info from the metadata instead of sending the request to rancher is possible
Re-evaluate the original fix and see if we can come up with the better solution that wouldn't require a full sync.

As 1.6 is EOL as of June 30, 2020, we are closing 1.6 issues.


include order data in event payload

please include order data in the event payload.
we need it in order to buy or accept an offer for an asset.
without those data, stream API is almost useless.

please include order data in the event payload. we need it in order to buy or accept an offer for an asset.
without those data, stream API is almost useless.

do you have a solution


Allow name property for custom input URI

Thanks for this plugin, it has been working great. I have been using it to launch Youtube playlists on my TV in the morning, however it is becoming quite cumbersome to remember which is which.
This change adjusts the customInputURIs field to instead supply an object with an id and name. I am unsure if there is an option with homebridge to do a more elegant cutover, it seems this might remove existing custom uri properties.
If this does not align with the vision of this project, no drama.

Hi @Chris-SG ,
my vision of the project is to make everything as HomeKit native as possible. In this specific case, I have implemented the set-handler for the characteristic ConfiguredName. That means that you can just change the Name of any input in the Home app.
https://github.com/maxileith/homebridge-appletv-enhanced/blob/0082a8680c428189b782917600fcd3295742c686/src/appleTVEnhancedAccessory.ts#L742-L754

Hi @maxileith
Thanks for your comment. I was not aware that is a feature in the Home app! It does seem like a much better option. In saying that, I am somewhat struggling to find how to rename these in the app. (pretty new to Home as a whole 😅)

With that being said, I really appreciate that you have taken the time to open a PR 👍


Stop testing iOS 7.0.3 on Travis CI

Adds 8.3 and 8.4 tasks to the Travis Matrix.
Thought that this might be a controversial change and that a pull request would be best.
According to MixPanel, iOS 7.0 accounts for less than ~2% of all iOS users in the last six months.

I don't think it's that controversial.  however we should keep support for the last 7.x release as long as we can, IMO
We're also overdue to specify osx_image
👍

Totally agree about supporting iOS 7, @akitchen. Seems like one of these changes broke the build horribly, so we'll have to look into that.
I've been quite surprised at how quickly TravisCI has been at updating their osx_image list lately. There's already an Xcode6_4 image available!

I really wanted to use the osx_image Travis key, but apparently that locks you into a single SDK. When I specified Xcode 6.4 as the osx_image then we only had the ability to build against the 8.4 SDK -- earlier ones were not present.
For more info, check out this issue I opened against Travis-CI.

This page documents which SDKs are available on the various Travis OS X images: http://docs.travis-ci.com/user/languages/objective-c/
Long story short, the default Xcode 6.1 image is the only one that has more than a single iOS SDK version. This complicates matters as well now that the iOS 9 SDKs are getting added to the mix.

@tjarratt FYI I've hijacked this PR a bit to include getting Travis to run with Xcode 7/iOS 9 using a newly discovered technique allowing us to use different Travis images for different build variations. Still got a few kinks to work out though!

Rebasing this on top of master. I'd like to get this merged in this week so we can also merge in https://github.com/pivotal/PivotalCoreKit/pull/168.


[Bug] TC-CNET-4.16 semi-automated procedure needs to be updated

Describe the bug
When running TC-CNET-4.16 there are precondition instruction popups to commission the TH to the DUT however the test case then proceeds to attempt automated commissioning. If tester follows the prompts, test will fail to run to completion.
To workaround existing UI instructions follow prompt to reset the DUT to factory defaults and confirm by selecting "Pass." For subsequent instructions do not follow the prompt and select "Pass." Test will complete with automation.
Steps to reproduce the behavior

Execute TC-CNET-4.16 following prompts to commission the DUT.

Expected behavior

Test case pop-up prompts for manual instructions will only appear with commands the Tester must execute.

Log files
CNET-4.16_procedure.log
PICS file
No response
Screenshots
No response
Environment
TH: v2.10-beta3+spring2024
Additional Information
No response

TC-CNET-4.6.log

@dkaytuv is this still happening?

Closing due to inactivity. Please reopen if needed.


Fix(eos_cli_config_gen): management api http-commands vrf order

Issue Summary
management api http-commands vrf order does not match eos on box outtput
Which component(s) of AVD impacted
eos_cli_config_gen
How do you run AVD ?

Relevant log output
No response
Contributing Guide

[X] I agree to follow this project's Code of Conduct

It seems we need a new sort filter to sort capitalized letters ahead of lower case letters.

Should this be reopened?


Update Schema Documentation for Array Relationship

Lost a little bit of time today trying to understand the compiler and runtime errors thrown when using an array return type from a function.
In the example, friends is a function which resolves an array of users.
With the current documentation, this will throw a compiler error complaining about the instance keypath being provided.
When replaced with User.friends, it compiles but at runtime you get a crash due to the unsupported array type. By boxing the type using the underlying TypeReference generic, this runtime error goes and it works as expected.
This syntax is demonstrated in the upstream Star Wars example but the Pioneer documentation did not include this which may cause confusion to new users.

Apologies for the many issues/PRs, as I'm sure you can tell, we're working on a production Vapor GraphQL service and so we're facing a couple minor issues and wishes. We will of course do what we can to provide fixes for elements we spot, or raise issues for things we can't get to right now but may loop back round to.
An issue does not mean we're expecting you to pick it up, though a discussion is always appreciated and if you do find the time then we will never decline 😄

No worries, I am glad you are finding issues that I wasn't aware of and also submitting changes to fix those issues.


broadcast_server example and server description update.

-Update examples/server.rs description.
-Add new examples/broadcast_server.rs

You'll want to do this PR against https://github.com/snapview/tokio-tungstenite when https://github.com/snapview/tokio-tungstenite/pull/68 is merged

Ok thanks.


ENG-16033: Updates info about KFTO base images

ENG-16033: Updates info about KFTO base images

@Fiona-Waters Was waiting for confirmation that we should do that now - see latest commit! And thank you for the prompt review!


Add the two loss functions instead of multiplying them

I take it these two loss functions are from Eq. (6) in the paper, where they are added together instead of multiplied.

omg yes, lol


Outpost icons

Describe the Bug
If you set the outpost icon, only one icon is displayed at a time, even if you have 2-3 outposts from one city.
With dynmap-towny this works without any problems.
Please fix that (:
Plugin Version
MapTowny-2.2.0
Towny Version
<IP_ADDRESS>
Server Software Version
This server is running Paper version git-Paper-196 (MC: 1.20.1) (Implementing API version 1.20.1-R0.1-SNAPSHOT) (Git: 773dd72)
You are running the latest version
Previous version: git-Paper-182 (MC: 1.20.1)
Best regards

I think I know the issue. This will be fixed in 3.0.0. Thanks for filing a bug ticket!

Thank you. (:
Is there a release for 3.0.0?

Unfortunately, there's no hard timeline on 3.0.0 yet due to my inconsistent schedule. It's almost feature complete, however there's a few features I'm reworking. Since it has taken me longer than expected, I plan to release an alpha version with the current features/fixes in a couple weeks.

Should be fixed in v3.0.0, please try the alpha version and let me know if it doesn't work. Thanks!


[Entity Service Loader] The Entity Loader does not seem to work correctly

I'm submitting a...

[ ] Regression (a behavior that used to work and stopped working in a new release)
[ x] Bug report
[ ] Performance issue
[ ] Feature request
[ ] Documentation issue or request
[ ] Support request
[ ] Other... Please describe:

Current behavior
Trying to show loading indicators in an Angular component for GET. POST, PUT and DELETE actions is not successful when using the Entity Service Loader.
Expected behavior
As shown in the Documentation, the loaders object from the NgEntityServiceLoader now contains loading indicators for each of the PostsService methods; Each one holding an observable boolean value, indicating the method’s loading status. Therefore, when an HTTP call is being made, the loader should be able to show the status.
Minimal reproduction of the problem with instructions
https://stackblitz.com/edit/akita-loader-async-pipe-problem?file=src%2Fapp%2Fhello.component.ts
Environment

Angular version: 11.2.7

Browser:
- [ x] Chrome (desktop) version XX
- [ ] Chrome (Android) version XX
- [ ] Chrome (iOS) version XX
- [ x] Firefox version XX
- [ ] Safari (desktop) version XX
- [ ] Safari (iOS) version XX
- [ ] IE version XX
- [x ] Edge version XX

See https://github.com/datorama/akita/pull/670
Update to the latest version and use:
connector() {
  return new ReplaySubject(1)
}

Thank you :)

@NetanelBasal I was able to get this working by Updating and adding the connector to the Config object. The following code works perfectly well:
# users.component.ts

loaders = this.loader.loadersFor('users');

# users.component.html

Users are Loading!

However, when I am trying to Update a specific entity, the Loading Indicator does not work. Like:
# users.component.ts

Users with ID [{{ user.id }}] is updating.

Could I be missing something? Thank you.

Please update the stackblitz.

@NetanelBasal I can confirm it works as expected on stackblitz:
https://akita-loader-async-pipe-problem-nq7e44.stackblitz.io
The issue is on my code base.
Thanks.


Handle bad OEmbed responses and return message

When requesting an OEmbed object, handle the situation that the provider might return a non-successful response. In that case, render a message for the user explaining that there was an error with the embedded element.
For this, standardize the OEbedResolver::Base#source_url method and add a #name method which will be included in the text for the user.
The text for the user will be rendered within the <figure> element within a nested span with the class unavailable-embed. This also allows the consumer to have custom CSS for this case.

+1


How to implement multi select input with remove button.

How do I implement this? Your documentation just gives the options and what they are responsible for, and the web-site with examples does not have code snippets that are responsible for the examples, so I am struggling to implement this.
Appreciate any help.

If you view source on the demo page you can see how each instance is created

I was about to say that I will look at source. Thanks. Closing this now. Is there any plan to make code snippets next to the examples, or at least mention that at the top. Just a suggestion.


Can't use global theme overrides for Button disabled

Duplicates

[X] I have searched the existing issues

Latest version

[X] I have tested the latest version

Current behavior 😯
When using global style overrides to target the "disabled" css slot on a Button like so:
const theme = createTheme({
  components: {
    MuiButton: {
      styleOverrides: {
        disabled: {
          fontSize: "55rem"
        }
      }
    }
  }
});

The global style override does not apply.
Expected behavior 🤔
Any styles contained in MuiButton.styleOverrides.disabled should be applied to a .MuiButton-root.Mui-disabled.
Steps to reproduce 🕹
Steps:

Open https://codesandbox.io/s/globalthemeoverride-material-demo-forked-dpvi1?file=/demo.tsx
Observe output: the font size should be gigantic (55 rem), but is clearly the default font size, meaning the override failed

Context 🔦
No response
Your environment 🌎

`npx @mui/envinfo`
 System:
    OS: Linux 5.10 Ubuntu 20.04.3 LTS (Focal Fossa)
    CPU: (12) x64 AMD Ryzen 5 5600X 6-Core Processor
    Memory: 8.35 GB / 12.43 GB
    Container: Yes
    Shell: 5.0.17 - /bin/bash
  Binaries:
    Node: 16.13.0 - ~/.nvm/versions/node/v16.13.0/bin/node
    Yarn: 1.22.15 - ~/.yarn/bin/yarn
    npm: 8.1.0 - ~/.nvm/versions/node/v16.13.0/bin/npm
  Managers:
    Apt: 2.0.6 - /usr/bin/apt
  Utilities:
    Git: 2.25.1 - /usr/bin/git
  IDEs:
    Nano: 4.8 - /usr/bin/nano
    VSCode: 1.62.2 - /home/ian/.vscode-server/bin/3a6960b964327f0e3882ce18fcebd07ed191b316/bin/code
    Vim: 8.1 - /usr/bin/vim
  Languages:
    Bash: 5.0.17 - /usr/bin/bash
    Perl: 5.30.0 - /usr/bin/perl
    Python3: 3.8.10 - /usr/bin/python3

(I use Chrome)

I think you need to use the '&.Mui-disabled' syntax:
{
"root": {
"&.Mui-disabled": {
"fontSize": "5rem"
}
}
}
The MuiButton component increases the CSS specificity of the disabled internal state.
You can not override it like this:
{
"disabled": {
"fontSize": "55rem"

}
}
The MuiButton component increases the CSS specificity of the disabled internal state.
You can not override it like this:
{
"disabled": {
"fontSize": "55rem"

}
}
Complete solution https://codesandbox.io/s/globalthemeoverride-material-demo-forked-xgoyp?file=/demo.tsx

@jasurkurbanovinit Thanks for pointing that out. However, as I go through the doc, it says that:
The list of each component's classes is documented under the CSS section of its API page.

This means disabled should work. I am still reluctant to say if we should fix the doc or we should make disabled styleOverrides work?
cc @oliviertassinari @mnajdova

Yes, what @siriwatknp said. I'm currently working around this issue by using styleOverrides:
  MuiButton: {
      styleOverrides: {
        root: {
          // other properties...
          "&:disabled": {
            color: baseTheme.palette.midtoneBrighterer.main,
            backgroundColor: baseTheme.palette.dark.main,
          },
        },
      },
    },

... but this should not be necessary.

We should remove these keys from the styleOverrides in v6, till then hopefully the warning can guide developers

Is it possible to "unset" default  color and background color of .Mui-disabled instead of overwriting it? I want it to keep color from root (i.e primary color if primary was specified, secondary if secondary was specified, etc.)

@hoangbn , i used to be able to do this in material ui
import palette from '../palette.js';

export default {
  containedPrimary: {
    '&$disabled': {
      opacity: palette.action.disabled.opacity,
      backgroundColor: palette.primary.main,
    },
  },
  containedSecondary: {
    '&$disabled': {
      opacity: palette.action.disabled.opacity,
      backgroundColor: palette.secondary.main,
    },
  },
};

and then referenced in the theme object like
...
overrides: {
    MuiButton: buttonOverrides,
    MuiSwitch: toggleWithBarOverrides,
    MuiCheckbox: toggleOverrides,
    MuiRadio: toggleOverrides,
  },
...

and porting to v5 sort of broke this. so here is what i do now for this kind of override:
import palette from 'style/palette';
import { buttonClasses } from '@mui/material';

const override = {
    containedPrimary: {
        ['&.' + buttonClasses.disabled]: {
            opacity: palette.action.disabledOpacity,
            backgroundColor: palette.primary.main,
        },
    },
    containedSecondary: {
        ['&.' + buttonClasses.disabled]: {
            opacity: palette.action.disabledOpacity,
            backgroundColor: palette.secondary.main,
        },
    },
};

export default override;

and referenced in the main theme like
import {
    createTheme
} from '@mui/material/styles';

import palette from "style/palette";
import buttonOverrides from 'style/overrides/buttonOverrides';
import toggleWithBarOverrides from 'style/overrides/toggleWithBarOverrides';
import toggleOverrides from 'style/overrides/toggleOverrides';

const theme = createTheme({
    palette,
    shape: {
        borderRadius: 2,
    },
    components: {
        MuiButton: {
            styleOverrides: buttonOverrides,
        },
        MuiSwitch: {
            styleOverrides: toggleWithBarOverrides,
        },
        MuiCheckbox: {
            styleOverrides: toggleOverrides,
        },
        MuiRadio: {
            styleOverrides: toggleOverrides,
        },
    },
});

export default theme;

Is it possible to "unset" default color and background color of .Mui-disabled instead of overwriting it? I want it to keep color from root (i.e primary color if primary was specified, secondary if secondary was specified, etc.)

if you provide invalid property. value for color like color: 'none' it will use currentColor which is your primary, secondary, etc.

Is it possible to "unset" default color and background color of .Mui-disabled instead of overwriting it? I want it to keep color from root (i.e primary color if primary was specified, secondary if secondary was specified, etc.)

Unfortunately you can't. You need to describe all the colours with disabled class. Luckily, you only need to provide color for the root. In my case for slider i used this:
MuiSlider: {       styleOverrides: {         root: {           '&.Mui-disabled': {             '&.MuiSlider-colorPrimary': {               color: '#006FF6'             },             '&.MuiSlider-colorSecondary': {               color: '#F68700'             },             '.MuiSlider-thumb': {               backgroundColor: '#0a0a0a'             }           }         }       }     }

My code worked, I needed a different disable color for each variant:
"@mui/material": "^5.6.4",
"@mui/styles": "^5.6.1",
    MuiButton: {       styleOverrides: {         root: {           '&.MuiButton-contained': {             '&.Mui-disabled': {               backgroundColor:: 'color',               color:: 'color',             },           },           '&.MuiButton-outlined': {             '&.Mui-disabled': {               borderColor: 'borderColor',               color: 'color',               backgroundColor: 'unset',             },           },         },       },     },

How do I override the variant border color for JoyUI's JoyButton globally? JoyButton-outlined is not working
`   JoyButton: {
styleOverrides: {
root: {
'&.JoyButton-variantOutlined': {
borderColor: 'green', // Customize border color for outlined variant
color: 'var(--joy-palette-neutral-outlinedColor)' // Customize text color for outlined variant
      }
    }
  }
}`


[WIP] Refactor visiting strategy

This PR does away with the custom traverser, and instead adds correct node visitors to get accurate scopes (and references/definitions) for flow types. It's written for easy upstreaming into eslint-scope (see #438) if that becomes a thing. How? New node type visitors are added (look for //new), and only node type visitors were overwritten (look for //override) instead of visit* functions. There's some copy/paste from escope in the overwritten methods to clearly show where the new flow type code must go (look for <custom></custom>).
TODO:

[ ]  Fix declare (Correct scoping, especially with declare module).
[ ] More scope tests.

fyi eslint pr is https://github.com/eslint/eslint/pull/8280


Inference TruthValue refactoring 1

dispatcher for TruthValue
binary case

So when are we going to start documenting our code then?