Question: Package update issue under OSX Sierra
gravatar for Aki Hoji
23 months ago by
Aki Hoji10
Aki Hoji10 wrote:

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 • 815 views
ADD COMMENTlink modified 23 months ago by nitesh.turaga140 • written 23 months ago by Aki Hoji10
Answer: Package update issue under OSX Sierra
gravatar for nitesh.turaga
23 months ago by
United States
nitesh.turaga140 wrote:


Did you install XCode? 

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

ADD COMMENTlink written 23 months ago by nitesh.turaga140
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 133 users visited in the last hour