Error in installation S4Vectors package
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Entering edit mode
jial2 • 0
@jial2-7016
Last seen 4.7 years ago
United States

Hello,

I met an error message when I installed s4vectors into R. I could not find how to fix by searching online. Here are the messages as below.

> biocLite("S4Vectors")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.1 (2015-06-18).
Installing package(s) ‘S4Vectors’

  There is a binary version available but the source version is later:
          binary source needs_compilation
S4Vectors  0.8.1  0.8.3             FALSE

installing the source package ‘S4Vectors’

trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/S4Vectors_0.8.3.tar.gz'
Content type 'application/x-gzip' length 202692 bytes (197 KB)
==================================================
downloaded 197 KB

* installing *source* package ‘S4Vectors’ ...
** libs
sh: make: command not found
ERROR: compilation failed for package ‘S4Vectors’
* removing ‘/Users/jial2/Library/R/3.2/library/S4Vectors’

The sessionInfo is

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.8.5 (Mountain Lion)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] BiocInstaller_1.20.1 devtools_1.9.1       RCurl_1.95-4.7       bitops_1.0-6         zoo_1.7-12          

loaded via a namespace (and not attached):
 [1] lattice_0.20-33 digest_0.6.8    grid_3.2.1      R6_2.1.1        magrittr_1.5    httr_1.0.0      stringi_0.5-5   curl_0.9.1     
 [9] tools_3.2.1     stringr_1.0.0   memoise_0.2.1  


Thanks for the help!

em

 

s4vectors • 2.5k views
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Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 7 months ago
United States

Or you could retry the installation after doing:

options(install.packages.compile.from.source="never")

This will install the binary version of the package which does not need to be compiled, therefore you don't need Xcode or make.

 

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Entering edit mode
@laurent-gatto-5645
Last seen 1 day ago
Belgium

The following line

sh: make: command not found
indicates that you are missing make. You will need to install Xcode and then install make (see for example there).
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