Dependency

Compiling with libxml in MacOS Catalina

The problem When compiling Emacs 28.05, make bootstrap failed with fatal error: 'libxml/tree.h' file not found while autogen.sh and configure were successfully executed. Troubleshooting The error message pointed out the culprit, libxml.

Dependency issue: In Conda, with SCENIC

I’ve been working with pySCENIC in the recent couples of months. It’s a tool that is meant to uncover gene sets that are controlled by transcription factors and suggests the underlying logic of how genes are regulated.

psutil, python, and icc

I used to dislike dependency management because there are so many things that require root or are mysteriously incompatible with each other. However, I recently came to realize that the existence of dependency itself is a delicate and elegant system despite being messy at times.

Dealing with dependency without sudo like a dummy (again)

The more I work with Linux, the more I encounter dependency issues. This is of course not too big a surprise, but it can be painful especially when you aren’t sudo, so the most obvious solution does not work for you.

Following up library dependency in R package compilation

Hello there. I had not anticipated to encounter this problem again so soon, but I did when I was installing yet another package on my own laptop. ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.

Run Seurat (an R Package) in a notebook interface on a server without root

After a while of playing around, I’ll say the best way to use R with a Notebook-style interface on a server where you are no superuser would be using Anaconda, and then run R inside Anaconda to get whatever package you need.