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hms-dbmi / scde

R package for analyzing single-cell RNA-seq data
http://pklab.med.harvard.edu/scde
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Install flexmix 2.3-13 for Travis build. #58

Closed jdblischak closed 6 years ago

jdblischak commented 6 years ago

A follow-up PR to handle the consequences of PR #56 (that you noted in https://github.com/hms-dbmi/scde/commit/9b67594ae6fe89730d6117d7e1fee9c2c3917ff9):

I hadn't realized that install.packages only installs the latest version of a CRAN pacakge even though a maximum version is specified (e.g. see the SO question R doesn't respect maximum version when installing package dependencies). Thus if a user doesn't already have flexmix installed, the installation will fail because the latest version of flexmix does not satisfy the dependency requirement. This is why the Travis build failed with the following error:

Package required and available but unsuitable version: ‘flexmix’

Overall this early failure is a good thing because users will know something is wrong from the beginning instead of finding out later when trying to run the code.

I attempted to fix the Travis build by installing flexmix 2.3-13 before the build starts.

jdblischak commented 6 years ago

I was able to get the Travis build working on oldrel and release, but it fails on devel:

No output has been received in the last 10m0s, this potentially indicates a stalled build or something wrong with the build itself. Check the details on how to adjust your build configuration on: https://docs.travis-ci.com/user/common-build-problems/#Build-times-out-because-no-output-was-received