Question: Installation of RCurl
gravatar for Haiying.Kong
5 months ago by
Haiying.Kong110 wrote:

I am trying to install RCurl package on R 3.5.0.

Toward end, I get the error message:

** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘RCurl’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/icgc/dkfzlsdf/analysis/B240/kong/lib/R/3.5.0/RCurl/libs/': cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/icgc/dkfzlsdf/analysis/B240/kong/lib/R/3.5.0/RCurl’
Warning message:
In install.packages("RCurl_1.95-4.11.tar.gz", lib = "/dkfz/analysis/B240/kong/lib/R/3.5.0") :
  installation of package ‘RCurl_1.95-4.11.tar.gz’ had non-zero exit status


> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE 13.1 (Bottle) (x86_64)

Matrix products: default
BLAS: /usr/lib64/blas/
LAPACK: /usr/lib64/lapack/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.5.0


Could someone please help me?



package installation • 516 views
ADD COMMENTlink modified 5 months ago by Martin Morgan ♦♦ 23k • written 5 months ago by Haiying.Kong110
Answer: Installation of RCurl
gravatar for Martin Morgan
5 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

I downloaded and installed RCurl in two stages

> download.packages("RCurl", "/tmp", repos = BiocInstaller::biocinstallRepos())
> q()
$ cd /tmp
$ tar xzf RCurl_1.95-4.11.tar.gz

At the very and of the build I saw

gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -lcurl -L/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -Wl,-framework -Wl,CoreFoundation

where -licucore is I guess providing the same functionality as the missing library. I looked at the src/Makevars to see where this library is coming from. I don't see explicit mention of it, but I do see

PKG_LIBS=$(CURL_LIBS) $(shell xml2-config --libs)

and when I execute the shell command

$ xml2-config --libs
-L/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm

I see where the library is coming from. From this I infer that your missing library is due to a mis-configured libxml2, and that you should use your system package manager to re-install libxml2.

I include the details above as possible guidance for trouble-shooting your particular installation.

ADD COMMENTlink written 5 months ago by Martin Morgan ♦♦ 23k
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