Package update issue under OSX Sierra
Entering edit mode
Aki Hoji ▴ 10
Last seen 9 months ago
United States

OSX Sierra (BuildVersion:  17B48) broke something but I can't tell. When I try to update multiple packages, compilation fails as below.  I'd really appreciate any pointers and tricks to solve this issue.


Installing package into ‘/Volumes/Documents/Users/akihoji/Library/R/3.x/library’
(as ‘lib’ is unspecified)
trying URL ''
Content type 'application/x-gzip' length 1113799 bytes (1.1 MB)
downloaded 1.1 MB

Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help

All my packages loaded Thu Nov  9 10:17:00 2017
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2017c.1.0/zoneinfo/America/New_York'
* installing *source* package ‘openssl’ ...

** package ‘openssl’ successfully unpacked and MD5 sums checked
Homebrew 1.3.6
Homebrew/homebrew-core (git revision cd116; last commit 2017-11-08)
Using PKG_CFLAGS=-I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/openssl/include
Using PKG_LIBS=-L/usr/local/opt/openssl@1.1/lib -L/usr/local/opt/openssl/lib -lssl -lcrypto
** libs
rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o
clang -I/usr/local/Cellar/r/3.4.2/lib/R/include -DNDEBUG -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/openssl/include  -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include   -fPIC  -g -O2  -c aes.c -o aes.o
In file included from aes.c:1:
/usr/local/Cellar/r/3.4.2/lib/R/include/Rinternals.h:39:11: fatal error: 'stdio.h' file not found
# include <stdio.h>
1 error generated.
make: *** [aes.o] Error 1
ERROR: compilation failed for package ‘openssl’
* removing ‘/Volumes/Documents/Users/akihoji/Library/R/3.x/library/openssl’
* restoring previous ‘/Volumes/Documents/Users/akihoji/Library/R/3.x/library/openssl’
Warning in install.packages :
  installation of package ‘openssl’ had non-zero exit status

Session info ----------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.2 (2017-09-28)
 system   x86_64, darwin16.7.0        
 ui       RStudio (1.0.153)           
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       <NA>                        
 date     2017-11-09                  


compilation error osx • 1.5k views
Entering edit mode
nitesh.turaga ▴ 140
Last seen 2.1 years ago
United States


Did you install XCode? 

Also take a look at for any packages you need as extras. 


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