Question: Problem when installing GenomicFeatures on GNU/Linux server
1
gravatar for JunLVI
4.1 years ago by
JunLVI40
Japan
JunLVI40 wrote:

 

 

Hi, I was trying to perform Analysis of RNA-Seq data, ran into problem when installing the GenomicFeatures packages. 

During startup - Warning message:

Setting LC_CTYPE failed, using "C" 

Error in dyn.load(file, DLLpath = DLLpath, ...) : 

  unable to load shared object '/misc/u32/huang/R/lib64/R/library/RCurl/libs/RCurl.so':

  libcurl.so.4: cannot open shared object file: No such file or directory

Error: loading failed

Execution halted

ERROR: loading failed

* removing '/misc/u32/huang/R/lib64/R/library/RCurl'

During startup - Warning message:

Setting LC_CTYPE failed, using "C" 

ERROR: dependency 'RCurl' is not available for package 'rtracklayer'

* removing '/misc/u32/huang/R/lib64/R/library/rtracklayer'

During startup - Warning message:

Setting LC_CTYPE failed, using "C" 

ERROR: dependency 'RCurl' is not available for package 'biomaRt'

* removing '/misc/u32/huang/R/lib64/R/library/biomaRt'

During startup - Warning message:

Setting LC_CTYPE failed, using "C" 

ERROR: dependencies 'rtracklayer', 'biomaRt', 'RCurl' are not available for package 'GenomicFeatures'

* removing '/misc/u32/huang/R/lib64/R/library/GenomicFeatures'


The downloaded source packages are in

    '/tmp/RtmpBE1CMc/downloaded_packages'

Warning messages:

1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :

  installation of package 'RCurl' had non-zero exit status

2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :

  installation of package 'rtracklayer' had non-zero exit status

3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :

  installation of package 'biomaRt' had non-zero exit status

4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :

  installation of package 'GenomicFeatures' had non-zero exit status

 

And I could not load the GenomicFeatures by using

library(GenomicFeatures)

I noticed that packages like "RCurl" was not successfully installed, tried to install "RCurl" first: 

During startup - Warning message:

Setting LC_CTYPE failed, using "C" 

Error in dyn.load(file, DLLpath = DLLpath, ...) : 

  unable to load shared object '/misc/u32/huang/R/lib64/R/library/RCurl/libs/RCurl.so':

  libcurl.so.4: cannot open shared object file: No such file or directory

Error: loading failed

Execution halted

ERROR: loading failed

* removing '/misc/u32/huang/R/lib64/R/library/RCurl'

still could not install "RCurl". 

somebody suggested me to install 

libcurl-devel first

but it turned out that if I want to use sudo yum command as suggested, I need the authoration from the server manager.

https://www.biostars.org/p/162646/

 

I just wanted to know, is there anyway to install the package of my own account, instead of installing the package on the whole server system which would require a lot of fuss. 

BTW, I could install the "GenomicFeatures" package in my Mac and use it without any problem.

That makes my believe that  R version is NOT the problem, as suggested when I tried to install "RCurl" with install.packages():

> install.packages("RCurl")

--- Please select a CRAN mirror for use in this session ---

Error in download.file(url, destfile = f, quiet = TRUE) : 

  unsupported URL scheme

HTTPS CRAN mirror 


 1: 0-Cloud [https]             2: Austria [https]          

 3: China (Beijing 4) [https]   4: China (Hefei) [https]    

 5: Colombia (Cali) [https]     6: France (Lyon 2) [https]  

 7: Iceland [https]             8: Russia (Moscow 1) [https]

 9: Switzerland [https]        10: UK (Bristol) [https]     

11: UK (Cambridge) [https]     12: USA (CA 1) [https]       

13: USA (KS) [https]           14: USA (MI 1) [https]       

15: USA (TN) [https]           16: USA (TX) [https]         

17: USA (WA) [https]           18: (HTTP mirrors)           



Selection: 12

Warning: unable to access index for repository https://cran.cnr.Berkeley.edu/src/contrib

Warning message:

package 'RCurl' is not available (for R version 3.2.2)

> sessionInfo()

R version 3.2.2 (2015-08-14)

Platform: x86_64-pc-linux-gnu (64-bit)


locale:

[1] C


attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     


other attached packages:

[1] BiocInstaller_1.16.5


loaded via a namespace (and not attached):

[1] tools_3.2.2
edger genomicfeatures • 1.4k views
ADD COMMENTlink modified 4.1 years ago by James W. MacDonald51k • written 4.1 years ago by JunLVI40

This line and the referenced to RCurl in (your?) personal library path

unable to load shared object '/misc/u32/huang/R/lib64/R/library/RCurl/libs/RCurl.so'

suggests that you have RCurl installed, but that the libcurl library that was available when it was installed is no longer available. Maybe you tried to copy an RCurl folder from one computer to another? You should never do that.

At the end you choose the Berkely repository. Unfortunately and in my opinion, this repository often seems to be incomplete, and in your case it says that RCurl is not available. Further, the 'unsupported URL scheme' is probably trying to say that you do not have support for https, only http. So choose the option that corresponds to (HTTP mirrors) (number 18 in your example above, but the number of the entry might change) and then choose the http version of a reliable mirror, particularly 0-cloud or Austria or UK (Cambridge).

It might be (probably will be?) that RCurl will again fail to install, and then James MacDonald's approach (especially asking your system administrator to install the 'devel' version of libcurl, or simply RCurl and let them sweat through the heavy stuff) is appropriate.

ADD REPLYlink written 4.1 years ago by Martin Morgan ♦♦ 24k
Answer: Problem when installing GenomicFeatures on GNU/Linux server
0
gravatar for James W. MacDonald
4.1 years ago by
United States
James W. MacDonald51k wrote:

You can install the libcurl sources in your own directory and add to your path. I imagine a well crafted google search would help you find some instructions. But isn't it easier to ask your sysadmin to install the libcurl headers for you?

ADD COMMENTlink written 4.1 years ago by James W. MacDonald51k
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