[Bioc-devel] HiCBricks Bioc 3.11 Mac build is failing

. Koustav Pal, PhD Post-Doctoral Fellow in Genome Architecture, Computational Genomics Group, IFOM - The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano, Italy. Phone: +393441130157 E-mail: koustav@ifom.eu [[alternative HTML version deleted

[Bioc-devel] Forking out modules from existing packages as new packages

? Is it then possible to create a suite-like package, similar to tidyverse, where users say BiocManager::install(“Set_of_bla_bla_packages”)? Koustav Pal, PhD Post-Doctoral Fellow in Genome Architecture, Computational Genomics Group, IFOM - The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano

Re: [Bioc-devel] HiCBricks build error

Hi Bioconductor team, can you please help with this issue? Koustav Pal, PhD Post-Doctoral Fellow in Genome Architecture, Computational Genomics Group, IFOM - The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano, Italy. Phone: +393441130157 E-mail: koustav@ifom.eu

[Bioc-devel] HiCBricks build error

> Missing filters: deflate > --- failed re-building ‘IntroductionToHiCBricks.rmd’ > > SUMMARY: processing the following file failed: > ‘IntroductionToHiCBricks.rmd’ > > Error: Vignette re-building failed. > Execution halted Koustav Pal, PhD Post-Doctoral Fellow in Genome Architectur

[Bioc-devel] Problem downloading files with GenomicDataCommons

en there, this cryptic error message is found in the examples. Please note, that I am well-aware that I can provide the manifest to the gdc-client and I will not have to worry about it. Still, I would like to get to the bottom of this issue. Can someone please provide some help/insights? Koustav

Re: [Bioc-devel] Possible need for a GenomicIntersection package

intersections against the genomic coordinates associated to a Hi-C matrix. Koustav Pal, PhD Post-Doctoral Fellow in Genome Architecture, Computational Genomics Group, IFOM - The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano, Italy. Phone: +393441130157 E-mail: koustav@ifom.eu

Re: [Bioc-devel] What is Bioconductor's position on allowing users to create files in the working directory without an explicit path definition in the filename

. Even then, a few users have expressed distress regarding this implementation as this is a non-standard one. Standard in this context would typically be how we handle files in shell. Can you provide additional suggestions regarding procedures that may alleviate user confusion? Koustav Pal

[Bioc-devel] What is Bioconductor's position on allowing users to create files in the working directory without an explicit path definition in the filename

sition and this is only a requirement when the package is being build by the builder? Koustav Pal, Post-Doctoral Fellow in Genome Architecture, Computational Genomics Group, IFOM - The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano, Italy. Phone: +393441130157 E-mail: k

Re: [Bioc-devel] Bioconductor build still has not completed

Hi Lori, The package name is HiCLegos. It is on the single package builder going through the submission process. It finished building about a minute ago. Still it would be helpful to know why it took such a long time. Thanks. Koustav Pal, PhD Student in Genome Architecture, Computational

[Bioc-devel] Bioconductor build still has not completed

minor bugs. Are the build machines down? Is this happening to any other package? Is there a way I can access the build machine logs? Koustav Pal, PhD Student in Genome Architecture, Computational Genomics Group, IFOM - The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano