Michael Steinbaugh

tput error inside Docker

5

Hi, I'm seeing this error pop up inside Docker images using shunit2 for unit tests: ``` tput: No value for $TERM and no -T specified /usr/local/bin/shunit2: line 840: [: :...

Hi @supermihi , [TagLib](https://github.com/taglib/taglib) 2.0 was released yesterday, and pytaglib currently fails to build when linking to this version instead of the previous 1.13.1 release. I'm happy to help test...

Ensembl GRCh38

10

As discussed at length in #159 , the current default GRCh38 genome (iGenome) confusingly uses the NCBI reference, whereas other genomes use Ensembl by default (e.g. GRCh37, GRCm38). This configuration...

brca_tcga_pan_can_atlas_2018 data_sv.txt is not formatted correctly

4

Hi cBioPortal team, I noticed a parsing issue with `data_sv.txt` from the brca_tcga_pan_can_atlas_2018 dataset. Here's a reproducible example in R: ```r ## using pipette package ## https://github.com/acidgenomics/r-pipette con

brca_tcga_pan_can_atlas_2018 is failing with `cBioDataPack`

11

Hi, I'm seeing a parsing error for `brca_tcga_pan_can_atlas_2018`: `utils::read.table` chokes too easily on malformed files -- is it worth considering switching to readr/vroom or data.table here to harden against malformed...

Hi Romain, I'm having trouble getting highlight to install on the Harvard HPC cluster (CentOS): ``` Installing highlight '/home/XXX/miniconda3/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/RtmpKed5AP/devtoolsda844bf8257/romainfrancois-highlight-b888782' \...

Hi, I seem to have hit a bug in S4Vectors for objects that extend `SimpleList`. Attempting to subset the list via `[` extraction is now returning an error in Bioconductor...