Opened 10 years ago
Closed 5 years ago
#42120 closed update (fixed)
cufflinks: update to 2.1.1
| Reported by: | ryandesign (Ryan Carsten Schmidt) | Owned by: | ryandesign (Ryan Carsten Schmidt) |
|---|---|---|---|
| Priority: | Normal | Milestone: | |
| Component: | ports | Version: | 2.2.1 |
| Keywords: | Cc: | kurthindenburg (Kurt Hindenburg) | |
| Port: | cufflinks |
Description
cufflinks 0.9.3 does not build (#38885, #38969) and should be updated to the latest version.
This patch attempts to do this, however it fails to build.
I have reported this build failure to the cufflinks discussion group for assistance: https://groups.google.com/d/msg/tuxedo-tools-users/84RZcSzeE0o/6HEOlJjAIIgJ
Attachments (2)
Change History (9)
Changed 10 years ago by ryandesign (Ryan Carsten Schmidt)
| Attachment: | cufflinks-2.1.1.diff added |
|---|
comment:2 Changed 9 years ago by kurthindenburg (Kurt Hindenburg)
Maybe https://github.com/Homebrew/homebrew-science/blob/master/cufflinks.rb would be helpful
Also note that the project has moved to github - the below is what I used to test
github.setup cole-trapnell-lab cufflinks 2.2.1 master_sites https://cole-trapnell-lab.github.io/cufflinks/assets/downloads/
Really the software needs fixed when --with-eigen=no to actually work.
comment:3 Changed 9 years ago by ryandesign (Ryan Carsten Schmidt)
I have a portfile for cufflinks 2.2.1 ready to go, but it needs boost 1.58.0, or a patch to be packported to 1.57.0.
comment:4 Changed 9 years ago by ryandesign (Ryan Carsten Schmidt)
I've attached my cufflinks 2.2.1 patch. Even with boost 1.58.0 it does not build. I've asked for clarification from the developers of boost.
Changed 7 years ago by ryandesign (Ryan Carsten Schmidt)
| Attachment: | cufflinks-2.2.1.diff added |
|---|
comment:5 Changed 7 years ago by ryandesign (Ryan Carsten Schmidt)
I refreshed the patch, but it still doesn't build. It's not compatible with the current version of samtools (1.4.1), and maybe not with the current version of boost (1.64.0). Upstream isn't responding to the bug reports filed in the github issue tracker so the software appears to be dead at the moment.
comment:6 Changed 7 years ago by kurthindenburg (Kurt Hindenburg)
| Owner: | haroldpimentel@… deleted |
|---|---|
| Status: | new → assigned |
comment:7 Changed 5 years ago by ryandesign (Ryan Carsten Schmidt)
| Owner: | set to ryandesign |
|---|---|
| Resolution: | → fixed |
| Status: | assigned → closed |
patch which does not work yet