af126b8f0cf9ddc553a78869a3c820a4bd4fdc59
braney
  Mon Aug 17 13:36:13 2026 -0700
build: link the browser against zlib-ng instead of the system zlib, refs #38125

Adds zlib-ng as a second git submodule, alongside htslib, and points ZLIB at it.
It is built with --zlib-compat, so the header and the symbol names are the
ordinary zlib ones and no calling code has to change.

Measured over the eight Recommended Track Set pages, hgTracks uses 29 percent
less processor time and 26 percent less wall clock, and the image it produces is
pixel identical. Writing the PNG is about three times faster and reading a
bigBed data block about twice as fast, which is why the gain is larger than the
image work alone would give.

This also makes the platforms agree. x86_64 was linking a static /lib64/libz.a
only because that file happened to be present, the arm64 Docker build fell
through to a shared -lz, and Darwin was taking MacPorts zlib. All three now use
the submodule.

Verified on x86_64 Linux, aarch64 Linux and Apple silicon: zlib-ng builds, its
own test suite passes, the makefiles pick it up, and bigBedToBed output is byte
identical to before the change.

diff --git src/inc/common.mk src/inc/common.mk
index f16671ddcf0..0a78054e177 100644
--- src/inc/common.mk
+++ src/inc/common.mk
@@ -1,584 +1,587 @@
 # if CC is undefined, set it to gcc
 CC?=gcc
 # allow the somewhat more modern C syntax, e.g. 'for (int i=5; i<10, i++)'
 CFLAGS += -std=c99
 # Several long-standing idioms in the tree alias memory through incompatible
 # types (e.g. the dlList sentinel trick in lib/dlist.c, which overlays
 # struct dlNode on struct dlList).  -fstrict-aliasing (on at -O2 and above, but
 # not at -O1) miscompiles these, silently corrupting results.  Disable it so the
 # higher -O levels are safe.  refs #37761
 CFLAGS += -fno-strict-aliasing
 
 # This is required to get the cgiLoader.mk compile target to work.  for some
 # reason, make's %.o: %.c overrides the rule below, cause the compiles to fail
 # due to lack of -I flags in rule.  Running with make -r to not use built-in
 # rules fixes, however MAKEFLAGS += -r doesn't do the trick, this does.
 # make is a very mysterious fellow traveler.
 GNUMAKEFLAGS += -r
 
 # add additional library paths
 L += ${LDFLAGS}
 
 # to build on sundance: CC=gcc -mcpu=v9 -m64
 ifeq (${COPT},)
     COPT=-O3 -g
 endif
 ifeq (${MACHTYPE},)
     MACHTYPE:=$(shell uname -m)
 #    $(info MACHTYPE was empty, set to: ${MACHTYPE})
 endif
 ifneq (,$(findstring -,$(MACHTYPE)))
 #    $(info MACHTYPE has - sign ${MACHTYPE})
     MACHTYPE:=$(shell uname -m)
 #    $(info MACHTYPE has - sign set to: ${MACHTYPE})
 endif
 
 HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
 HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/submodules/htslib
 
 # to check for Mac OSX Darwin specifics:
 UNAME_S := $(shell uname -s)
 # to check for differences in Linux OS version
 KERNEL_REL := $(shell uname -r)
 # to check for builds on hgwdev
 HOSTNAME = $(shell uname -n)
 
 # Semi-static builds, normally done in Docker
 #
 # use make SEMI_STATIC=yes to enable
 #  
 # These use static libraries except for -ldl, -lm, and -lc
 # which must be dynamic.
 #
 ifeq (${SEMI_STATIC},yes)
     # switch to static libraries
     STATIC_PRE = -Wl,-Bstatic
 endif
 L = ${STATIC_PRE}
 
 ifeq (${HOSTNAME},hgwdev)
   IS_HGWDEV = yes
   OURSTUFF = /cluster/software/r9
 else
   ifeq (${HOSTNAME},hgwdev-old.gi.ucsc.edu)
     IS_HGWDEV = yes
     OURSTUFF = /cluster/software
   else
      IS_HGWDEV = no
   endif
 endif
 
+# zlib comes from the zlib-ng submodule in submodules/zlib-ng, built in
+# zlib-compat mode so the header and the symbols are the ordinary zlib ones, and
+# linked statically the way htslib is.  zlib-ng writes a PNG about three times
+# faster and reads a bigBed block about twice as fast, and its output is ordinary
+# deflate that any zlib can read.  Building it here also makes the platforms
+# agree: before this, x86_64 happened to find a static /lib64/libz.a while the
+# arm64 build fell through to a shared -lz.  Override on the make command line
+# with ZLIB=... to link some other zlib.  refs #38125
 ifeq (${ZLIB},)
-  ifneq ($(wildcard /lib64/libz.a),)
-    ZLIB=/lib64/libz.a
-  else
-    ZLIB=-lz
-  endif
+  ZLIB=$(kentSrc)/submodules/zlib-ng/libz.a
 endif
 
 # for Darwin (Mac OSX), use static libs when they can be found
 ifeq ($(UNAME_S),Darwin)
   ifneq ($(wildcard /opt/local/include/openssl/ssl.h),)
     HG_INC += -I/opt/local/include
   endif
   # on M1, the directory changed
   ifneq ($(wildcard /opt/homebrew/include/openssl/ssl.h),)
     HG_INC += -I/opt/homebrew/include
     L += -L/opt/homebrew/lib/
   endif
-  ifneq ($(wildcard /opt/local/lib/libz.a),)
-    ZLIB = /opt/local/lib/libz.a
-  endif
+  # no ZLIB line here: Darwin uses the zlib-ng submodule like every other
+  # platform.  refs #38125
   ifneq ($(wildcard /opt/local/lib/libpng.a),)
     PNGLIB = /opt/local/lib/libpng.a
   endif
   ifeq (${BZ2LIB},)
     ifneq ($(wildcard /opt/local/lib/libbz2.a),)
       BZ2LIB=/opt/local/lib/libbz2.a
     endif
   endif
   ifneq ($(wildcard /opt/local/lib/libfreetype.a),)
     FREETYPELIBS = /opt/local/lib/libfreetype.a
   endif
   ifneq ($(wildcard /opt/local/lib/libbrotlidec.a),)
     FREETYPELIBS += /opt/local/lib/libbrotlidec.a /opt/local/lib/libbrotlicommon.a
   else
     ifneq ($(wildcard /usr/local/Cellar/brotli/1.1.0/lib/libbrotlidec.a),)
       FREETYPELIBS += /usr/local/Cellar/brotli/1.1.0/lib/libbrotlidec.a /usr/local/Cellar/brotli/1.1.0/lib/libbrotlicommon.a
     endif
   endif
   ifneq ($(wildcard /usr/local/opt/openssl@3/lib/libssl.a),)
     SSLLIB = /usr/local/opt/openssl@3/lib/libssl.a
   else
     ifneq ($(wildcard /opt/local/libexec/openssl3/lib/libssl.a),)
       SSLLIB = /opt/local/libexec/openssl3/lib/libssl.a
     endif
   endif
   ifneq ($(wildcard /usr/local/opt/openssl@3/lib/libcrypto.a),)
     CRYPTOLIB = /usr/local/opt/openssl@3/lib/libcrypto.a
   else
     ifneq ($(wildcard /opt/local/libexec/openssl3/lib/libcrypto.a),)
       CRYPTOLIB = /opt/local/libexec/openssl3/lib/libcrypto.a
     endif
   endif
   ifneq ($(wildcard /opt/local/lib/libiconv.a),)
     ICONVLIB = /opt/local/lib/libiconv.a
   endif
   ifneq ($(wildcard /usr/local/Cellar/mariadb/11.6.2/lib/libmariadbclient.a),)
       MYSQLLIBS = /usr/local/Cellar/mariadb/11.6.2/lib/libmariadbclient.a
   else
     ifneq ($(wildcard /opt/homebrew/lib/libmysqlclient.a),)
       MYSQLLIBS = /opt/homebrew/lib/libmysqlclient.a
     endif
   endif
 endif
 
 ifeq (${HOSTNAME},cirm-01)
   FULLWARN = yes
   ifeq (${MYSQLLIBS},)
     ifneq ($(wildcard /data/home/galt/lib64/libmariadb.a),)
       MYSQLLIBS = /data/home/galt/lib64/libmariadb.a
     endif
   endif
   ifeq (${SSLLIB},)
     ifneq ($(wildcard /data/home/galt/lib64/libssl.a),)
       SSLLIB = /data/home/galt/lib64/libssl.a
     endif
   endif
   ifeq (${CRYPTOLIB},)
     ifneq ($(wildcard /data/home/galt//lib64/libcrypto.a),)
       CRYPTOLIB = /data/home/galt/lib64/libcrypto.a
     endif
   endif
   HG_INC += -I/data/home/galt/include
   HG_INC += -I/data/home/galt/include/mariadb
 endif
 
 ifeq (${SSLLIB},)
   ifneq ($(wildcard /usr/lib64/libssl.a),)
     SSLLIB = /usr/lib64/libssl.a
   endif
 endif
 ifeq (${CRYPTOLIB},)
   ifneq ($(wildcard /usr/lib64/libcrypto.a),)
     CRYPTOLIB = /usr/lib64/libcrypto.a
   endif
 endif
 
 
 # Skip freetype for conda build; not needed for utils, and the Mac build environment has
 # freetype installed but we don't want to use the system libraries because they can be
 # for a newer OSX version than the conda build target, and can be incompatible.
 ifneq (${CONDA_BUILD},1)
   FREETYPECFLAGS = $(shell freetype-config --cflags  2> /dev/null)
   # Ubuntu does not have freetype-config anymore
   ifeq (${FREETYPEFLAGS},)
      FREETYPECFLAGS =  $(shell pkg-config freetype2 --cflags 2> /dev/null )
   endif
 
   # use the static library on OSX
   ifeq (${IS_HGWDEV},no)
     ifeq (${FREETYPELIBS},)
       ifeq ($(UNAME_S),Darwin)
         FREETYPELIBS =  $(shell freetype-config --libs --static 2> /dev/null )
       else
         FREETYPELIBS =  $(shell freetype-config --libs 2> /dev/null )
         # Ubuntu does not have freetype-config anymore
         ifeq (${FREETYPELIBS},)
           FREETYPELIBS =  $(shell pkg-config freetype2 --libs 2> /dev/null )
         endif
       endif
     endif
   endif
 
   ifneq (${FREETYPECFLAGS},)
   FREETYPECFLAGS += -DUSE_FREETYPE
   endif
 
   HG_INC += ${FREETYPECFLAGS}
   L += ${FREETYPELIBS}
 endif
 
 ifeq (${PTHREADLIB},)
   PTHREADLIB=-lpthread
 endif
 
 ifneq ($(UNAME_S),Darwin)
   L+=${PTHREADLIB}
   ifneq ($(filter 3.%, ${KERNEL_REL}),)
      # older linux needed libconv
     XXXICONVLIB=-liconv
   endif
 else
   ifeq (${ICONVLIB},)
     ICONVLIB=-liconv
   endif
 endif
 
 # autodetect UCSC installation of hal:
 ifeq (${HALDIR},)
     # ONLY on hgwdev, not any other machine here (i.e. hgcompute-01)
     ifeq (${IS_HGWDEV},yes)
       HALDIR = /hive/groups/browser/hal/build/hal.2024-12-12
       #HALDIR = /hive/groups/browser/hal/build/rocky9/hal.2024-12-18
       ifneq ($(wildcard ${HALDIR}),)
         ifeq (${USE_HAL},)
           USE_HAL=1
         endif
       endif
     endif
 endif
 
 ifeq (${USE_HAL},1)
     # force static libraries to keep programs portable
     HDF5DIR=/hive/groups/browser/hal/build/hdf5-1.12.0
     HDF5LIBDIR=${HDF5DIR}/local/lib
     HDF5LIBS=${HDF5LIBDIR}/libhdf5_cpp.a ${HDF5LIBDIR}/libhdf5.a ${HDF5LIBDIR}/libhdf5_hl.a
     HALLIBS=${HALDIR}/hal/lib/libHalBlockViz.a ${HALDIR}/hal/lib/libHalMaf.a ${HALDIR}/hal/lib/libHalLiftover.a ${HALDIR}/hal/lib/libHalLod.a ${HALDIR}/hal/lib/libHal.a ${HALDIR}/sonLib/lib/sonLib.a ${HDF5LIBS} ${ZLIB}
     ifeq (${HOSTNAME},hgwdev)
         HALLIBS += /usr/lib/gcc/x86_64-redhat-linux/11/libstdc++.a
     else
       ifeq (${HOSTNAME},hgwdev-old.gi.ucsc.edu)
           HALLIBS += /usr/lib/gcc/x86_64-redhat-linux/4.8.5/libstdc++.a
       else
           HALLIBS += -lstdc++
       endif
     endif
     HG_DEFS+=-DUSE_HAL
     HG_INC+=-I${HALDIR}/inc -I${HALDIR}/hal/blockViz/inc
 endif
 # on hgwdev, include HAL by defaults
 ifeq (${IS_HGWDEV},yes)
    L+=${HALLIBS}
 endif
 
 ifeq (${USE_HIC},)
     USE_HIC=1
 endif
 
 ifeq (${USE_HIC},1)
     HG_DEFS+=-DUSE_HIC
 endif
 
 # autodetect where png is installed
 ifeq (${PNGLIB},)
       PNGLIB := $(shell libpng-config --ldflags  || true)
 endif
 ifeq (${PNGLIB},)
   PNGLIB=-lpng
 endif
 ifeq (${PNGINCL},)
   PNGINCL := $(shell libpng-config --I_opts  || true)
 #       $(info using libpng-config to set PNGINCL: ${PNGINCL})
 endif
 
 # autodetect where mysql includes and libraries are installed
 # do not need to do this during 'clean' target (this is very slow for 'clean')
 ifneq ($(MAKECMDGOALS),clean)
 
   # set MYSQL include path
   ifeq (${MYSQLINC},)
     # newer distros do not have the mysql_config symlink anymore
     ifeq (, $(shell which mysql_config))
         MYSQLCONFIG := mariadb_config
     else
         MYSQLCONFIG := mysql_config
     endif
 
     MYSQLINC := $(shell ${MYSQLCONFIG} --include | sed -e 's/-I//' || true)
         # $(info using mysql_config to set MYSQLINC: ${MYSQLINC})
   endif
 
   ifeq (${MYSQLINC},)
     ifneq ($(wildcard /usr/local/mysql/include/mysql.h),)
 	  MYSQLINC=/usr/local/mysql/include
     endif
   endif
   ifeq (${MYSQLINC},)
     ifneq ($(wildcard /usr/include/mysql/mysql.h),)
 	  MYSQLINC=/usr/include/mysql
     endif
   endif
 
   # this does *not* work on Mac OSX with the dynamic libraries
   ifneq ($(UNAME_S),Darwin)
     ifeq (${MYSQLLIBS},)
       # mysql_config --libs includes -lm, however libm must be a dynamic library
       # so to handle SEMI_STATIC it is removed here and will be added at the end
       MYSQLLIBS := $(shell ${MYSQLCONFIG} --libs | sed 's/-lm$$//' || true)
 #        $(info using mysql_config to set MYSQLLIBS: ${MYSQLLIBS})
     endif
   endif
   ifeq ($(findstring src/hg/,${CURDIR}),src/hg/)
     ifeq (${MYSQLINC},)
         $(error can not find installed mysql development system)
     endif
   endif
   ifeq (${MYSQLLIBS},)
     ifneq ($(wildcard /usr/lib64/libmysqlclient.a),)
       MYSQLLIBS = /usr/lib64/libmysqlclient.a
     endif
   endif
     # last resort, hoping the compiler can find it in standard locations
   ifeq (${MYSQLLIBS},)
       MYSQLLIBS="-lmysqlclient"
   endif
 endif
 
 # $(info have MYSQLINC: ${MYSQLINC})
 # $(info have MYSQLLIBS: ${MYSQLLIBS})
 
 # OK to add -lstdc++ to all MYSQLLIBS just in case it is
 #    MySQL version 5.6 libraries, but no 'librt' on Mac OSX
 ifeq (${IS_HGWDEV},no)
   ifeq ($(UNAME_S),Darwin)
     MYSQLLIBS += -lstdc++
   else
     MYSQLLIBS += -lstdc++ -lrt
   endif
 endif
 
 ifeq (${BZ2LIB},)
   ifneq ($(wildcard /lib64/libbz2.a),)
     BZ2LIB=/lib64/libbz2.a
    else
     BZ2LIB=-lbz2
    endif
 endif
 
 # htslib (libhts.a) must come before its dependency libs (-lcurl -llzma, and
 # -lz -lbz2 below) on the link line. With the linker default --as-needed (e.g.
 # Debian/Ubuntu), a dependency listed before libhts.a gets dropped, producing
 # undefined lzma_*/curl_* references when libhts.a is linked. refs #37741
 L += $(kentSrc)/submodules/htslib/libhts.a
 
 # on hgwdev, use the static libraries
 ifeq (${IS_HGWDEV},yes)
    HG_INC += -I${OURSTUFF}/include
    HG_INC += -I${OURSTUFF}/include/mariadb 
    FULLWARN = yes
    L+=/hive/groups/browser/freetype/freetype-2.10.0/objs/.libs/libfreetype.a
    L += -lcurl -llzma -lssl -lcrypto
    ifeq (${HOSTNAME},hgwdev)
        PNGLIB=${OURSTUFF}/lib/libpng.a
        PNGINCL=-I${OURSTUFF}/include/libpng16
    else
        PNGLIB=/usr/lib64/libpng.a
        PNGINCL=-I/usr/include/libpng15
    endif
 
    MYSQLINC=/usr/include/mysql
    MYSQLLIBS=${OURSTUFF}/lib64/libmariadbclient.a ${OURSTUFF}/lib64/libssl.a ${OURSTUFF}/lib64/libcrypto.a ${ZLIB}
 
    ifeq (${HOSTNAME},hgwdev)
        MYSQLLIBS += /usr/lib/gcc/x86_64-redhat-linux/11/libstdc++.a /usr/lib64/librt.a
    else
        MYSQLLIBS += /usr/lib/gcc/x86_64-redhat-linux/4.8.5/libstdc++.a /usr/lib64/librt.a
    endif
 
 else
    L+=-lcurl -llzma
    ifeq (${CONDA_BUILD},1)
        L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so
    else
        ifneq (${SSLLIB},)
           L+=${SSLLIB}
        else
           L+=-lssl
        endif
        ifneq (${CRYPTOLIB},)
           L+=${CRYPTOLIB}
        else
           L+=-lcrypto
        endif
    endif
 endif
 
 #global external libraries
 L+=${PNGLIB} ${MLIB} ${ZLIB} ${BZ2LIB} ${ICONVLIB}
 HG_INC+=${PNGINCL}
 
 # NOTE: these must be last libraries and must be dynamic.
 # We switched by to dynamic with SEMI_STATIC
 ifeq (${SEMI_STATIC},yes)
     # switch back to dynamic libraries
     DYNAMIC_PRE = -Wl,-Bdynamic
 endif
 DYNAMIC_LIBS = ${DYNAMIC_PRE} -ldl -lm -lc
 
 L+= ${DYNAMIC_LIBS}
 
 
 # pass through COREDUMP
 ifneq (${COREDUMP},)
     HG_DEFS+=-DCOREDUMP
 endif
 
 # autodetect UCSC additional source code with password for some external tracks on gbib
 GBIBDIR = /hive/groups/browser/gbib/
 ifneq ($(wildcard ${GBIBDIR}/*.c),)
   HG_DEFS+=-DUSE_GBIB_PWD
   HG_INC += -I${GBIBDIR}
 endif
 
 SYS = $(shell uname -s)
 
 ifeq (${HG_WARN},)
   ifeq (${SYS},Darwin)
       HG_WARN = -Wall -Wno-unused-variable -Wno-deprecated-declarations
       HG_WARN_UNINIT=
   else
     ifeq (${SYS},SunOS)
       HG_WARN = -Wall -Wformat -Wimplicit -Wreturn-type
       HG_WARN_UNINIT=-Wuninitialized
     else
       ifeq (${FULLWARN},yes)
         HG_WARN = -Wall -Werror -Wformat -Wformat-security -Wimplicit -Wreturn-type -Wempty-body -Wunused-but-set-variable -fno-common
         HG_WARN_UNINIT=-Wuninitialized
       else
         HG_WARN = -Wall -Wformat -Wimplicit -Wreturn-type
         HG_WARN_UNINIT=-Wuninitialized
       endif
     endif
   endif
   # -Wuninitialized generates a warning without optimization
   ifeq ($(findstring -O,${COPT}),-O)
      HG_WARN += ${HG_WARN_UNINIT}
   endif
 endif
 
 # this is to hack around many make files not including HG_WARN in
 # the link line
 CFLAGS += ${HG_WARN}
 
 ifeq (${SCRIPTS},)
     SCRIPTS=${HOME}/bin/scripts
 endif
 ifeq (${CGI_BIN},)
     CGI_BIN=/usr/local/apache/cgi-bin
 endif
 ifeq (${DOCUMENTROOT},)
     DOCUMENTROOT=/usr/local/apache/htdocs
 endif
 ifeq (${BINDIR},)
     BINDIR = ${HOME}/bin/${MACHTYPE}
 endif
 ifeq (${ENCODE_PIPELINE_BIN},)
     ENCODE_PIPELINE_BIN=/cluster/data/encode/pipeline/bin
 endif
 
 # avoid an extra leading slash when DESTDIR is empty
 ifeq (${DESTDIR},)
   DESTBINDIR=${BINDIR}
 else
   DESTBINDIR=${DESTDIR}/${BINDIR}
 endif
 
 # location of interperted version of stringify program
 STRINGIFY = ${kentSrc}/utils/stringify/stringifyEz
 
 MKDIR=mkdir -p
 ifeq (${STRIP},)
    STRIP=true
 endif
 CVS=cvs
 GIT=git
 
 # portable naming of compiled executables: add ".exe" if compiled on
 # Windows (with cygwin).
 ifeq (${OS}, Windows_NT)
   AOUT=a
   EXE=.exe
 else
   AOUT=a.out
   EXE=
 endif
 
 #Lowelab defines
 #The lowelab specific code will be included in compilation if the following conditions are satistied
 LOWELAB_WIKI_DEF=
 LOWELAB_DEF=
 ifdef LOWELAB
     LOWELAB_WIKI=1
     LOWELAB_DEF=-DLOWELAB
 endif
 ifdef LOWELAB_WIKI
     LOWELAB_WIKI_DEF=-DLOWELAB_WIKI
 endif
 LOWELAB_DEFS=${LOWELAB_DEF} ${LOWELAB_WIKI_DEF}
 
 ifdef LOWELAB
     ifeq (${SCRIPTS},/cluster/bin/scripts)
         SCRIPTS=${HOME}/scripts
     endif
     ifeq (${CGI_BIN},/usr/local/apache/cgi-bin)
         CGI_BIN=/www/cgi-bin
     endif
     ifeq (${DOCUMENTROOT},/usr/local/apache/htdocs)
         DOCUMENTROOT=/www/browser-docs
     endif
 endif
 
 #ENCODE COMMON VARIABLES
 CONFIG_FILES = \
 	fields.ra \
 	labs.ra
 CV = cv.ra
 CVDIR=${HOME}/kent/src/hg/makeDb/trackDb/cv/alpha
 PIPELINE_PATH=/hive/groups/encode/dcc/pipeline
 CONFIG_DIR = ${PIPELINE_PATH}/${PIPELINE_DIR}/config
 ENCODEDCC_DIR = ${PIPELINE_PATH}/downloads/encodeDCC
 
 CC_PROG_OPTS = ${COPT} ${CFLAGS} ${HG_DEFS} ${LOWELAB_DEFS} ${HG_WARN} ${HG_INC} ${XINC}
 %.o: %.c
 	${CC} ${CC_PROG_OPTS} -o $@ -c $<
 
 # autodetect UCSC installation of node.js:
 ifeq (${NODEBIN},)
     NODEBIN = /cluster/software/src/node-v22.19.0-linux-x64/bin
     ifeq ($(wildcard ${NODEBIN}),)
 	NODEBIN=
     endif
 endif
 
 # node.js tools: jshint, jsx, jsxhint, uglifyjs, ...
 ifeq (${JSHINT},)
     JSHINT=${NODEBIN}/jshint
     ifeq ($(wildcard ${JSHINT}),)
 	    JSHINT=true
     endif
 endif
 ifeq (${JSXHINT},)
     JSXHINT=${NODEBIN}/jsxhint
     ifeq ($(wildcard ${JSXHINT}),)
         JSXHINT=true
     endif
 endif
 ifeq (${JSX},)
     JSX=${NODEBIN}/jsx
     ifeq ($(wildcard ${JSX}),)
         JSX=true
     endif
 endif
 ifeq (${UGLIFYJS},)
     UGLIFYJS=${NODEBIN}/uglifyjs
     ifeq ($(wildcard ${UGLIFYJS}),)
         UGLIFYJS=true
     endif
 endif
 
 # OSX does not have the --remove-destination option. 
 # We use this option to make sure that the username and date of files lets us figure out
 # who was the one that built the current version of a file
 ifeq ($(UNAME_S),Darwin)
     CPREMDESTOPT=-f
 else
     CPREMDESTOPT=--remove-destination
 endif
 
 ifeq (${LOWELAB}, 1)
   O += lowelabPfamHit.o lowelabArkinOperonScore.o lowelabTIGROperonScore.o loweutils.o \
   geneTree.o cogsxra.o jgiGene.o snoRNAs.o sargassoSeaXra.o minGeneInfo.o gbRNAs.o easyGene.o arcogdesc.o arCOGs.o cddDesc.o cddInfo.o \
   megablastInfo.o alignInfo.o ec.o codeBlastScore.o ecAttribute.o tRNAs.o
 endif