Opened 7 years ago

Closed 7 years ago

#35063 closed defect (fixed)

tophat: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'?

Reported by: richard.zuerner@… Owned by: haroldpimentel@…
Priority: Normal Milestone:
Component: ports Version: 2.1.1
Keywords: lion Cc:
Port: tophat

Description

I tried running macports to install tophat on Lion but failed. I already have cufflinks and bowtie loaded via macports and would like to continue with this install using macports as well. I found the errors in the log file (attached), but not sure how to work around them. Any help would be appreciated. Thanks!

Attachments (3)

main.log (10.3 KB) - added by richard.zuerner@… 7 years ago.
main log of tophat installation. Clearly shows errors leading to problem.
main2cleaninstall.log (27.0 KB) - added by richard.zuerner@… 7 years ago.
log file of second run
cleantophatrun.rtf (1.1 KB) - added by richard.zuerner@… 7 years ago.
screen output of run

Download all attachments as: .zip

Change History (6)

Changed 7 years ago by richard.zuerner@…

Attachment: main.log added

main log of tophat installation. Clearly shows errors leading to problem.

comment:1 Changed 7 years ago by ryandesign (Ryan Schmidt)

Keywords: lion added; RNA sequence software removed
Owner: changed from macports-tickets@… to haroldpimentel@…
Summary: tophat error on liontophat: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'?

The error I see in your log is:

:info:build GFaSeqGet.cpp:62:17: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'?

However this was not a clean attempt, so please "sudo port clean tophat", then try again; if it fails again, attach the new main.log.

Changed 7 years ago by richard.zuerner@…

Attachment: main2cleaninstall.log added

log file of second run

Changed 7 years ago by richard.zuerner@…

Attachment: cleantophatrun.rtf added

screen output of run

comment:2 Changed 7 years ago by richard.zuerner@…

Hi, Thanks for the quick response. I ran the clean and install commands, but with same result. The new log file and screen output are attached as files. Thanks!

comment:3 Changed 7 years ago by jmroot (Joshua Root)

Resolution: fixed
Status: newclosed
Note: See TracTickets for help on using tickets.