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PapenfussLab / StructuralVariantAnnotation

R package designed to simplify structural variant analysis
GNU General Public License v3.0
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%na% Missing During Test #15

Closed DarioS closed 5 years ago

DarioS commented 5 years ago 
$test/gridss_annotate_insertions_repeatmaster.R --input $test/LS13anno.vcf --output $test/LS13annoRetro.vcf --repeatmasker $test/hg38.fa.out.gz --scriptdir $test/

results in

Loading required package: BSgenome
Error: Test failed: '.linked_assemblies_fix_indels corrects indels'
* could not find function "%na%"
d-cameron commented 5 years ago

We are in the process of submitting the StructuralVariantAnnotation package to BioConductor and as part of that process, we have removed some of the functionality that does not belong in the package (such as %na%). Please use the following version while we make this transition:

devtools::install_github("PapenfussLab/StructuralVariantAnnotation@pre_bioconductor ")

On Mon, Apr 15, 2019 at 12:00 PM Dario Strbenac notifications@github.com wrote:

$test/gridss_annotate_insertions_repeatmaster.R --input $test/LS13anno.vcf --output $test/LS13annoRetro.vcf --repeatmasker $test/hg38.fa.out.gz --scriptdir $test/

results in

Loading required package: BSgenome Error: Test failed: '.linked_assemblies_fix_indels corrects indels'

  • could not find function "%na%"

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