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BioC 3.4: INSTALL report for rtracklayer on morelia

This page was generated on 2017-04-15 16:22:42 -0400 (Sat, 15 Apr 2017).

Package 1094/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rtracklayer 1.34.2
Michael Lawrence
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/rtracklayer
Last Changed Rev: 126808 / Revision: 128728
Last Changed Date: 2017-02-17 18:00:59 -0500 (Fri, 17 Feb 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: rtracklayer
Version: 1.34.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rtracklayer
StartedAt: 2017-04-14 15:24:27 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 15:24:57 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 30.2 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rtracklayer
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
* installing *source* package ‘rtracklayer’ ...
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... no
./configure: line 1884: brew: command not found
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_rtracklayer.c -o R_init_rtracklayer.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c readGFF.c -o readGFF.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bigWig.c -o bigWig.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chain_io.c -o chain_io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c twoBit.c -o twoBit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c handlers.c -o handlers.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c utils.c -o utils.o
utils.c:4:8: warning: unused variable 'ans' [-Wunused-variable]
  SEXP ans;
       ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/bbiRead.c -o ucsc/bbiRead.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/cirTree.c -o ucsc/cirTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/common.c -o ucsc/common.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c:496:9: warning: implicit declaration of function 'isAllNt' is invalid in C99 [-Wimplicit-function-declaration]
    if (isAllNt(allele, alLen))
        ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/errAbort.c -o ucsc/errAbort.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/hash.c -o ucsc/hash.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/linefile.c -o ucsc/linefile.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/localmem.c -o ucsc/localmem.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/zlibFace.c -o ucsc/zlibFace.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/dystring.c -o ucsc/dystring.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/hmmstats.c -o ucsc/hmmstats.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/obscure.c -o ucsc/obscure.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/pipeline.c -o ucsc/pipeline.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/rangeTree.c -o ucsc/rangeTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/rbTree.c -o ucsc/rbTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/memalloc.c -o ucsc/memalloc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/dlist.c -o ucsc/dlist.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/udc.c -o ucsc/udc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/net.c -o ucsc/net.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/bits.c -o ucsc/bits.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/twoBit.c -o ucsc/twoBit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/internet.c -o ucsc/internet.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/https.c -o ucsc/https.o
ucsc/https.c:38:16: warning: 'CRYPTO_num_locks' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
int numLocks = CRYPTO_num_locks();
               ^
/usr/include/openssl/crypto.h:415:5: note: 'CRYPTO_num_locks' has been explicitly marked deprecated here
int CRYPTO_num_locks(void) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER; /* return CRYPTO_NUM_LOCKS (shared libs!) */
    ^
ucsc/https.c:42:1: warning: 'CRYPTO_set_id_callback' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
CRYPTO_set_id_callback(openssl_id_callback);
^
/usr/include/openssl/crypto.h:425:6: note: 'CRYPTO_set_id_callback' has been explicitly marked deprecated here
void CRYPTO_set_id_callback(unsigned long (*func)(void)) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
     ^
ucsc/https.c:43:1: warning: 'CRYPTO_set_locking_callback' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
CRYPTO_set_locking_callback(openssl_locking_callback);
^
/usr/include/openssl/crypto.h:417:6: note: 'CRYPTO_set_locking_callback' has been explicitly marked deprecated here
void CRYPTO_set_locking_callback(void (*func)(int mode,int type,
     ^
ucsc/https.c:74:5: warning: 'SSL_library_init' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
    SSL_library_init();
    ^
/usr/include/openssl/ssl.h:1558:5: note: 'SSL_library_init' has been explicitly marked deprecated here
int SSL_library_init(void ) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
    ^
ucsc/https.c:75:5: warning: 'ERR_load_crypto_strings' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
    ERR_load_crypto_strings();
    ^
/usr/include/openssl/err.h:296:6: note: 'ERR_load_crypto_strings' has been explicitly marked deprecated here
void ERR_load_crypto_strings(void) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
     ^
ucsc/https.c:76:5: warning: 'ERR_load_SSL_strings' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
    ERR_load_SSL_strings();
    ^
/usr/include/openssl/ssl.h:1677:6: note: 'ERR_load_SSL_strings' has been explicitly marked deprecated here
void ERR_load_SSL_strings(void) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
     ^
ucsc/https.c:77:5: warning: 'OPENSSL_add_all_algorithms_noconf' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
    OpenSSL_add_all_algorithms();
    ^
/usr/include/openssl/evp.h:829:3: note: expanded from macro 'OpenSSL_add_all_algorithms'
                OPENSSL_add_all_algorithms_noconf()
                ^
/usr/include/openssl/evp.h:821:6: note: 'OPENSSL_add_all_algorithms_noconf' has been explicitly marked deprecated here
void OPENSSL_add_all_algorithms_noconf(void) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
     ^
ucsc/https.c:104:7: warning: 'SSL_CTX_new' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
ctx = SSL_CTX_new(SSLv23_client_method());
      ^
/usr/include/openssl/ssl.h:1351:10: note: 'SSL_CTX_new' has been explicitly marked deprecated here
SSL_CTX *SSL_CTX_new(SSL_METHOD *meth) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
         ^
ucsc/https.c:104:19: warning: 'SSLv23_client_method' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
ctx = SSL_CTX_new(SSLv23_client_method());
                  ^
/usr/include/openssl/ssl.h:1522:13: note: 'SSLv23_client_method' has been explicitly marked deprecated here
SSL_METHOD *SSLv23_client_method(void) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;   /* SSLv3 but can rollback to v2 */
            ^
ucsc/https.c:129:8: warning: 'BIO_new_ssl_connect' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
sbio = BIO_new_ssl_connect(ctx);
       ^
/usr/include/openssl/ssl.h:1343:6: note: 'BIO_new_ssl_connect' has been explicitly marked deprecated here
BIO *BIO_new_ssl_connect(SSL_CTX *ctx) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
     ^
ucsc/https.c:131:1: warning: 'BIO_ctrl' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
BIO_get_ssl(sbio, &ssl);
^
/usr/include/openssl/bio.h:492:29: note: expanded from macro 'BIO_get_ssl'
#define BIO_get_ssl(b,sslp)     BIO_ctrl(b,BIO_C_GET_SSL,0,(char *)sslp)
                                ^
/usr/include/openssl/bio.h:600:6: note: 'BIO_ctrl' has been explicitly marked deprecated here
long    BIO_ctrl(BIO *bp,int cmd,long larg,void *parg) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
        ^
ucsc/https.c:143:1: warning: 'BIO_ctrl' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
BIO_set_conn_hostname(sbio, hostnameProto);
^
/usr/include/openssl/bio.h:416:39: note: expanded from macro 'BIO_set_conn_hostname'
#define BIO_set_conn_hostname(b,name) BIO_ctrl(b,BIO_C_SET_CONNECT,0,(char *)name)
                                      ^
/usr/include/openssl/bio.h:600:6: note: 'BIO_ctrl' has been explicitly marked deprecated here
long    BIO_ctrl(BIO *bp,int cmd,long larg,void *parg) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
        ^
ucsc/https.c:145:1: warning: 'BIO_ctrl' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
BIO_set_nbio(sbio, 1);     /* non-blocking mode */
^
/usr/include/openssl/bio.h:426:27: note: expanded from macro 'BIO_set_nbio'
#define BIO_set_nbio(b,n)       BIO_ctrl(b,BIO_C_SET_NBIO,(n),NULL)
                                ^
/usr/include/openssl/bio.h:600:6: note: 'BIO_ctrl' has been explicitly marked deprecated here
long    BIO_ctrl(BIO *bp,int cmd,long larg,void *parg) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
        ^
ucsc/https.c:149:9: warning: 'BIO_ctrl' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
    if (BIO_do_connect(sbio) == 1) 
        ^
/usr/include/openssl/bio.h:441:27: note: expanded from macro 'BIO_do_connect'
#define BIO_do_connect(b)       BIO_do_handshake(b)
                                ^
/usr/include/openssl/bio.h:443:29: note: expanded from macro 'BIO_do_handshake'
#define BIO_do_handshake(b)     BIO_ctrl(b,BIO_C_DO_STATE_MACHINE,0,NULL)
                                ^
/usr/include/openssl/bio.h:600:6: note: 'BIO_ctrl' has been explicitly marked deprecated here
long    BIO_ctrl(BIO *bp,int cmd,long larg,void *parg) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
        ^
ucsc/https.c:153:11: warning: 'BIO_test_flags' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
    if (! BIO_should_retry(sbio)) 
          ^
/usr/include/openssl/bio.h:231:30: note: expanded from macro 'BIO_should_retry'
#define BIO_should_retry(a)             BIO_test_flags(a, BIO_FLAGS_SHOULD_RETRY)
                                        ^
/usr/include/openssl/bio.h:209:6: note: 'BIO_test_flags' has been explicitly marked deprecated here
int  BIO_test_flags(const BIO *b, int flags) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
     ^
ucsc/https.c:157:38: warning: 'ERR_reason_error_string' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
        safef(s, sizeof s, "SSL error: %s", ERR_reason_error_string(ERR_get_error()));
                                            ^
/usr/include/openssl/err.h:283:13: note: 'ERR_reason_error_string' has been explicitly marked deprecated here
const char *ERR_reason_error_string(unsigned long e) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
            ^
ucsc/https.c:157:62: warning: 'ERR_get_error' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
        safef(s, sizeof s, "SSL error: %s", ERR_reason_error_string(ERR_get_error()));
                                                                    ^
/usr/include/openssl/err.h:266:15: note: 'ERR_get_error' has been explicitly marked deprecated here
unsigned long ERR_get_error(void) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
              ^
ucsc/https.c:162:10: warning: 'BIO_ctrl' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
    fd = BIO_get_fd(sbio, NULL);
         ^
/usr/include/openssl/bio.h:461:26: note: expanded from macro 'BIO_get_fd'
#define BIO_get_fd(b,c)         BIO_ctrl(b,BIO_C_GET_FD,0,(char *)c)
                                ^
/usr/include/openssl/bio.h:600:6: note: 'BIO_ctrl' has been explicitly marked deprecated here
long    BIO_ctrl(BIO *bp,int cmd,long larg,void *parg) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
        ^
ucsc/https.c:170:9: warning: 'BIO_test_flags' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
    if (BIO_should_read(sbio)) 
        ^
/usr/include/openssl/bio.h:227:29: note: expanded from macro 'BIO_should_read'
#define BIO_should_read(a)              BIO_test_flags(a, BIO_FLAGS_READ)
                                        ^
/usr/include/openssl/bio.h:209:6: note: 'BIO_test_flags' has been explicitly marked deprecated here
int  BIO_test_flags(const BIO *b, int flags) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
     ^
ucsc/https.c:174:14: warning: 'BIO_test_flags' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
    else if (BIO_should_write(sbio)) 
             ^
/usr/include/openssl/bio.h:228:30: note: expanded from macro 'BIO_should_write'
#define BIO_should_write(a)             BIO_test_flags(a, BIO_FLAGS_WRITE)
                                        ^
/usr/include/openssl/bio.h:209:6: note: 'BIO_test_flags' has been explicitly marked deprecated here
int  BIO_test_flags(const BIO *b, int flags) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
     ^
ucsc/https.c:226:10: warning: 'BIO_ctrl' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
    fd = BIO_get_fd(sbio, NULL);
         ^
/usr/include/openssl/bio.h:461:26: note: expanded from macro 'BIO_get_fd'
#define BIO_get_fd(b,c)         BIO_ctrl(b,BIO_C_GET_FD,0,(char *)c)
                                ^
/usr/include/openssl/bio.h:600:6: note: 'BIO_ctrl' has been explicitly marked deprecated here
long    BIO_ctrl(BIO *bp,int cmd,long larg,void *parg) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
        ^
ucsc/https.c:280:17: warning: 'BIO_write' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
            int swtx = BIO_write(sbio, sbuf+swt, srd-swt);
                       ^
/usr/include/openssl/bio.h:597:5: note: 'BIO_write' has been explicitly marked deprecated here
int     BIO_write(BIO *b, const void *data, int len) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
        ^
ucsc/https.c:283:8: warning: 'BIO_test_flags' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
                if (!BIO_should_write(sbio))
                     ^
/usr/include/openssl/bio.h:228:30: note: expanded from macro 'BIO_should_write'
#define BIO_should_write(a)             BIO_test_flags(a, BIO_FLAGS_WRITE)
                                        ^
/usr/include/openssl/bio.h:209:6: note: 'BIO_test_flags' has been explicitly marked deprecated here
int  BIO_test_flags(const BIO *b, int flags) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
     ^
ucsc/https.c:285:7: warning: 'ERR_print_errors_fp' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
                    ERR_print_errors_fp(stderr);
                    ^
/usr/include/openssl/err.h:287:6: note: 'ERR_print_errors_fp' has been explicitly marked deprecated here
void ERR_print_errors_fp(FILE *fp) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
     ^
ucsc/https.c:304:12: warning: 'BIO_read' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
            brd = BIO_read(sbio, bbuf, 32768);
                  ^
/usr/include/openssl/bio.h:595:5: note: 'BIO_read' has been explicitly marked deprecated here
int     BIO_read(BIO *b, void *data, int len) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
        ^
ucsc/https.c:308:7: warning: 'BIO_test_flags' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
                if (BIO_should_read(sbio))
                    ^
/usr/include/openssl/bio.h:227:29: note: expanded from macro 'BIO_should_read'
#define BIO_should_read(a)              BIO_test_flags(a, BIO_FLAGS_READ)
                                        ^
/usr/include/openssl/bio.h:209:6: note: 'BIO_test_flags' has been explicitly marked deprecated here
int  BIO_test_flags(const BIO *b, int flags) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
     ^
ucsc/https.c:316:7: warning: 'ERR_print_errors_fp' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
                    ERR_print_errors_fp(stderr);
                    ^
/usr/include/openssl/err.h:287:6: note: 'ERR_print_errors_fp' has been explicitly marked deprecated here
void ERR_print_errors_fp(FILE *fp) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
     ^
ucsc/https.c:342:1: warning: 'BIO_free_all' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations]
BIO_free_all(sbio);
^
/usr/include/openssl/bio.h:606:6: note: 'BIO_free_all' has been explicitly marked deprecated here
void    BIO_free_all(BIO *a) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER;
        ^
28 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/base64.c -o ucsc/base64.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/verbose.c -o ucsc/verbose.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/os.c -o ucsc/os.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/openssl/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -L/opt/openssl/lib -lssl -lcrypto -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
ld: warning: directory not found for option '-L/opt/openssl/lib'
installing to /Library/Frameworks/R.framework/Versions/3.3/Resources/library/rtracklayer/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
Creating a generic function from function ‘uri’ in package ‘rtracklayer’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rtracklayer)