apastore commented 9 years ago

would be possible to install on hal libcurl and a R 3.2?

Thanks! Alessandro

tatarsky commented 9 years ago

The libcurl RPMS are installed:

rpm -qa|grep curl
python-pycurl-7.19.0-8.el6.x86_64
curl-7.19.7-37.el6_4.x86_64
libcurl-7.19.7-37.el6_4.x86_64
libcurl-devel-7.19.7-37.el6_4.x86_64

I'll look into R 3.2 as a module.

apastore commented 9 years ago

Thanks !

I got this error message…. and I thought it was missing…

trying URL 'http://iis.stat.wright.edu/CRAN/src/contrib/curl_0.9.3.tar.gz' Content type 'application/x-gzip' length 245303 bytes (239 Kb)

opened URL

downloaded 239 Kb

installing source package ‘curl’ ... \ package ‘curl’ successfully unpacked and MD5 sums checked Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containinglibcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Using PKG_CFLAGS= Using PKG_LIBS=-lcurl ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libcurl was not found. Try installing:
- deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
- rpm: libcurl-devel (Fedora, CentOS, RHEL)
- csw: libcurl_dev (Solaris) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
  
  ERROR: configuration failed for package ‘curl’
removing ‘/cbio/cslab/nobackup/pastore/bcbio/lib/R/curl’

The downloaded source packages are in ‘/scratch/5489298.mskcc-fe1.local/RtmpV7BBP7/downloaded_packages’ Warning message: In install.packages("curl") : installation of package ‘curl’ had non-zero exit status

On Sep 8, 2015, at 4:53 PM, tatarsky notifications@github.com wrote:

The libcurl RPMS are installed:

rpm -qa|grep curl python-pycurl-7.19.0-8.el6.x86_64 curl-7.19.7-37.el6_4.x86_64 libcurl-7.19.7-37.el6_4.x86_64 libcurl-devel-7.19.7-37.el6_4.x86_64 I'll look into R 3.2 as a module.

— Reply to this email directly or view it on GitHub https://github.com/cBio/cbio-cluster/issues/313#issuecomment-138696761.

tatarsky commented 9 years ago

Where is the above command being run? Looks like on a node. My rpm output for the devel environment assumed the head node for compilation (mskcc-ln1).

We don't load all devel packages on nodes unless its really needed.

apastore commented 9 years ago

Yes you are right!! sorry!

On Sep 8, 2015, at 5:00 PM, tatarsky notifications@github.com wrote:

Where is the above command being run? Looks like on a node. My rpm output for the devel environment assumed the head node for compilation (mskcc-ln1).

We don't load all devel packages on nodes unless its really needed.

— Reply to this email directly or view it on GitHub https://github.com/cBio/cbio-cluster/issues/313#issuecomment-138698432.

tatarsky commented 9 years ago

To be clear: runtime for libcurl is on all the nodes. The development rpm (includes and such) is not unless asked for due to needing to compile on nodes for some reason. If you need to compile on the nodes its a quick add, I just try to keep it simple on them.

tatarsky commented 9 years ago

R 3.2.2 is compiling with default options. When done I'll install it for test and make a module for its use. I will not clobber the existing R 3.1.1 which predates our support.

apastore commented 9 years ago

Thanks!

I am also happy with libcurl on head node

Best, Alessandro

On Sep 8, 2015, at 5:08 PM, tatarsky notifications@github.com wrote:

R 3.2.2 is compiling with default options. When done I'll install it for test and make a module for its use. I will not clobber the existing R 3.1.1 which predates our support.

— Reply to this email directly or view it on GitHub https://github.com/cBio/cbio-cluster/issues/313#issuecomment-138700108.

tatarsky commented 9 years ago

Cool. Again, no big deal to toss devel on the nodes. R is doing its fortran based compile ;)

tatarsky commented 9 years ago

For test purposes, on the head node only (mskcc-ln1 aka hal):

$ module load R/3.2.2
$ R

R version 3.2.2 (2015-08-14) -- "Fire Safety"

I've not added anything to that R tree that isn't in the default source.

If it works, the module and those items will be replicated to all nodes. Note the default R module remains 3.1.1 as I don't recall who uses R and without a module be aware the RPM R is 3.0.1.

We should probably "clean up" at some point but it requires knowing if people are using older versions and whats been added to them if anything.

tatarsky commented 9 years ago

Checking if the R was working well enough for you to push to nodes.

apastore commented 9 years ago

Yes thanks! I have test it and compile both some CRAN and biocoductor package with out problem

On Sep 10, 2015, at 11:07 AM, tatarsky notifications@github.com wrote:

Checking if the R was working well enough for you to push to nodes.

— Reply to this email directly or view it on GitHub https://github.com/cBio/cbio-cluster/issues/313#issuecomment-139274470.

tatarsky commented 9 years ago

Awesome. I will push it out then and consider this resolved!

apastore commented 9 years ago

sorry one question I still get this error when installing Rcurl (both3.2 and 3.1) do you have any suggestion on what I am doing wrong?

thanks!

installing source package ‘RCurl’ ... \ package ‘RCurl’ successfully unpacked and MD5 sums checked checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ‘RCurl’
removing ‘/cbio/cslab/nobackup/pastore/bcbio/lib/R/site-library/RCurl’

The downloaded source packages are in ‘/tmp/Rtmp4bcASJ/downloaded_packages’ Warning message: In install.packages("RCurl") : installation of package ‘RCurl’ had non-zero exit status

q() Save workspace image? [y/n/c]: n -bash-4.1$ locate 'curl-config' /opt/Anaconda/1.6.0/bin/curl-config /opt/Anaconda/1.6.0/pkgs/curl-7.30.0-0/bin/curl-config /opt/Anaconda/1.6.0/pkgs/curl-7.30.0-0/share/man/man1/curl-config.1 /opt/Anaconda/1.6.0/share/man/man1/curl-config.1

tatarsky commented 9 years ago

I show curl config in the standard path.

$ which curl-config
/usr/bin/curl-config

What is your output of this command?

And always please provide a hostname.

tatarsky commented 9 years ago

curl-config BTW is again a libcurl-devel item. And as noted before the libcurl-devel is loaded on the head node only. Are you on the head node?

apastore commented 9 years ago

Sorry! I did it again I start an interactive session for compile a package!! May fault!

Sent from my iPhone

On Sep 10, 2015, at 8:23 PM, tatarsky notifications@github.com wrote:

I show curl config in the standard path.

$ which curl-config /usr/bin/curl-config What is your output of this command?

And always please provide a hostname.

— Reply to this email directly or view it on GitHub.

tatarsky commented 9 years ago

No prob. But I've loaded libcurl-devel on the nodes. Its 381KB ;)

apastore commented 9 years ago

Thanks! And sorry again!

Sent from my iPhone

On Sep 10, 2015, at 8:28 PM, tatarsky notifications@github.com wrote:

No prob. But I've loaded libcurl-devel on the nodes. Its 381KB ;)

— Reply to this email directly or view it on GitHub.

cBio / cbio-cluster

R 3.2 module and libcurl #313

opened URL

csw: libcurl_dev (Solaris) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'