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 | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rtracklayer_1.34.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/rtracklayer.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rtracklayer/DESCRIPTION’ ... OK
* this is package ‘rtracklayer’ version ‘1.34.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rtracklayer’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
Artistic-2.0 + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::testPackage’ ‘GenomicRanges:::INVALID.GR.COLNAMES’
‘S4Vectors:::labeledLine’
‘S4Vectors:::make_XYZxyz_to_XxYyZz_subscript’
‘S4Vectors:::new_SimpleList_from_list’ ‘XVector:::open_input_files’
‘XVector:::rewind_filexp’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
import,BEDFile-ANY-ANY: warning in rgb(cols[1, ], cols[2, ], cols[3, ],
max = 255): partial argument match of 'max' to 'maxColorValue'
asGTF,GRangesList : processFeatures: no visible binding for global
variable ‘tx_id’
asGTF,GRangesList: no visible global function definition for
‘pmapFromTranscripts’
asGTF,GRangesList: no visible global function definition for
‘rectifyDataFrame’
export,GAlignmentPairs-BamFile-ANY : getMateAttribute: no visible
global function definition for ‘last’
export,GenomicRanges-GFFFile-ANY: no visible global function definition
for ‘package.version’
getSeq,TwoBitFile: no visible binding for global variable ‘con’
import,BEDPEFile-ANY-ANY: no visible binding for global variable
‘chrom2’
import,BEDPEFile-ANY-ANY: no visible binding for global variable
‘start2’
import,BEDPEFile-ANY-ANY: no visible binding for global variable ‘end2’
import,BEDPEFile-ANY-ANY: no visible binding for global variable
‘strand2’
import,BamFile-ANY-ANY: no visible global function definition for
‘readGAlignmentPairs’
intersectTrack<-,UCSCTableQuery: possible error in normArgTrack(value,
x, TRUE): unused argument (TRUE)
Undefined global functions or variables:
chrom2 con end2 last package.version pmapFromTranscripts
readGAlignmentPairs rectifyDataFrame start2 strand2 tx_id
* checking Rd files ... NOTE
prepare_Rd: readGFF.Rd:52-53: Dropping empty section \details
prepare_Rd: readGFF.Rd:55-56: Dropping empty section \value
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘cleanupBigWigCache’ ‘readGFFAsGRanges’ ‘readGFFPragmas’
‘sniffGFFVersion’
Undocumented S4 classes:
‘RTLFileList’
Undocumented S4 methods:
generic '[' and siglist 'UCSCTrackModes,ANY,ANY,ANY'
generic 'as.character' and siglist 'RTLFile'
generic 'export' and siglist 'ANY,BEDPEFile,ANY'
generic 'export' and siglist 'GRangesList,GTFFile,ANY'
generic 'export' and siglist 'Pairs,BEDPEFile,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work. If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
src/Makevars.in
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File ‘rtracklayer/libs/rtracklayer.so’:
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Objects: ‘ucsc/errAbort.o’, ‘ucsc/obscure.o’, ‘ucsc/pipeline.o’,
‘ucsc/net.o’, ‘ucsc/https.o’, ‘ucsc/verbose.o’, ‘ucsc/os.o’
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Objects: ‘ucsc/common.o’, ‘ucsc/errAbort.o’, ‘ucsc/net.o’,
‘ucsc/https.o’, ‘ucsc/verbose.o’, ‘ucsc/os.o’
Found ‘__exit’, possibly from ‘_exit’ (C)
Object: ‘ucsc/os.o’
Found ‘_abort’, possibly from ‘abort’ (C)
Object: ‘ucsc/errAbort.o’
Found ‘_exit’, possibly from ‘exit’ (C)
Objects: ‘ucsc/errAbort.o’, ‘ucsc/pipeline.o’
Found ‘_printf’, possibly from ‘printf’ (C)
Objects: ‘ucsc/common.o’, ‘ucsc/pipeline.o’
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Object: ‘ucsc/pipeline.o’
Found ‘_rand’, possibly from ‘rand’ (C)
Object: ‘ucsc/obscure.o’
File ‘rtracklayer/libs/rtracklayer.so’:
Found non-API calls to R: ‘R_ignore_SIGPIPE’, ‘getConnection’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BigWigFile 7.070 1.982 9.058
BEDFile-class 2.303 0.136 14.692
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘rtracklayer_unit_tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.
* 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 /Users/biocbuild/bbs-3.4-bioc/meat/rtracklayer.Rcheck/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)