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