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frazer-lab / cluster

Repo for cluster issues.
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R-3.4.2 #218

Closed hirokomatsui closed 7 years ago

hirokomatsui commented 7 years ago

We are trying to install R-3.4.2 on flh2 and having an error during configure: configure: error: libcurl >= 7.22.0 library and headers are required with support for https

Although I see libcurl and devel version 7.29.0 are installed. Can you check.

tatarsky commented 7 years ago

Where is your source tree so I can look at the config.log?

tatarsky commented 7 years ago

As usually that error is caused by something else....I've seen it before in several distros.

s041629 commented 7 years ago

/home/matteo/software/R-3.4.2

I tried also with the older version (R-3.4.1) in the same software folder, but I get the same error

tatarsky commented 7 years ago

Grabbing tar ball and will look later today.

tatarsky commented 7 years ago

I had no issues with configure. Do you perhaps have a module loaded that I do not @s041629 ?

Please provide the output of "module load" as your account or I can su to you.

In particular I've seen issues when older gcc is used....

s041629 commented 7 years ago

I don't have any module loaded. I have "export PATH=/frazer01/home/matteo/software/R-3.2.2/bin:$PATH " in my .bashrc. Does it influence the installation?

tatarsky commented 7 years ago

I'm taking a look as you. I have reproduced the error as you and am seeing if I can spot what causes it for you.

It might actually be you appear to have an anaconda curl-config which is then taken precedence from the system curl-config and may be missing something causing the config to exit.

checking for curl-config... /frazer01/home/matteo/anaconda2/bin/curl-config
checking libcurl version ... 7.49.0
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking if libcurl is version 7 and >= 7.22.0... no
configure: error: libcurl >= 7.22.0 library and headers are required with support for https

Can you perhaps place the system paths first and see if you get further?

s041629 commented 7 years ago

I commented everything in my .bashrc and now I can install. I will wait for the installation to be over before closing this thread

tatarsky commented 7 years ago

It might be because your personal curl is too new. I hit that somewhere and I'd have to check my notes what I did about it.

tatarsky commented 7 years ago

Happy also BTW to make a global module for this version. I had built I think a R/3.4.0 module but its not the default. We should review as part of this process the module versions v.s. system versions and adjust defaults appropriately.

s041629 commented 7 years ago

Installation is over and R works fine. I have always had my private R version because I always install tons of packages

tatarsky commented 7 years ago

Completely understand. Enjoy your R!

tatarsky commented 7 years ago

Believed resolved. Re-open if not.