12cbc1fdde9c30c87616b8bb86dbbad764a55129
hiram
  Mon Jan 13 09:19:55 2025 -0800
clean up the duplicated -lm and use static zlib and bz2lib when available refs #35048

diff --git src/inc/common.mk src/inc/common.mk
index 0c9afd8..36a3753 100644
--- src/inc/common.mk
+++ src/inc/common.mk
@@ -1,489 +1,499 @@
 # 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
 
 # add additional library paths
 L += ${LDFLAGS}
 
 # to build on sundance: CC=gcc -mcpu=v9 -m64
 ifeq (${COPT},)
     COPT=-O -g
 endif
 ifeq (${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)/htslib
 
 # to check for Mac OSX Darwin specifics:
 UNAME_S := $(shell uname -s)
 # to check for builds on hgwdev
 HOSTNAME = $(shell uname -n)
 
 ifeq (${HOSTNAME},hgwdev-new)
   IS_HGWDEV = yes
   OURSTUFF = /cluster/software/r9
 else
   ifeq (${HOSTNAME},hgwdev)
     IS_HGWDEV = yes
     OURSTUFF = /cluster/software
   else
      IS_HGWDEV = no
   endif
 endif
 
+ifeq (${ZLIB},)
+  ifneq ($(wildcard /lib64/libz.a),)
+    ZLIB=/lib64/libz.a
+  else
+    ZLIB=-lz
+  endif
+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
   ifneq ($(wildcard /opt/local/lib/libz.a),)
     ZLIB = /opt/local/lib/libz.a
   endif
   ifneq ($(wildcard /opt/local/lib/libpng.a),)
     PNGLIB = /opt/local/lib/libpng.a
   endif
   ifneq ($(wildcard /opt/local/lib/libfreetype.a),)
     FREETYPELIBS = /opt/local/lib/libfreetype.a /opt/local/lib/libbz2.a /opt/local/lib/libbrotlidec.a /opt/local/lib/libbrotlicommon.a
   endif
   ifneq ($(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 /opt/homebrew/lib/libmysqlclient.a),)
     MYSQLLIBS = /opt/homebrew/lib/libmysqlclient.a
   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}
 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 ${HDF5LIBS} -lz
+    HALLIBS=${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-new)
         HALLIBS += ${OURSTUFF}/lib/libcurl.a /usr/lib/gcc/x86_64-redhat-linux/11/libstdc++.a
     else
       ifeq (${HOSTNAME},hgwdev)
           HALLIBS += ${OURSTUFF}/lib/libcurl.a /usr/lib/gcc/x86_64-redhat-linux/4.8.5/libstdc++.a
       else
           HALLIBS += -lcurl -lstdc++
       endif
     endif
     HG_DEFS+=-DUSE_HAL
     HG_INC+=-I${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 libm is installed
 ifeq (${MLIB},)
   MLIB=-lm
 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},)
     MYSQLINC := $(shell mysql_config --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},)
       MYSQLLIBS := $(shell mysql_config --libs || 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 (${ZLIB},)
-  ZLIB=-lz
+ifeq (${BZ2LIB},)
+  ifneq ($(wildcard /lib64/libbz2.a),)
+    BZ2LIB=/lib64/libbz2.a
+  else
+    BZ2LIB=-lbz2
+  endif
 endif
 
 # on hgwdev, use the static libraries
 ifeq (${IS_HGWDEV},yes)
    HG_INC += -I${OURSTUFF}/include
    HG_INC += -I${OURSTUFF}/include/mariadb 
    FULLWARN = yes
    L+=/hive/groups/browser/freetype/freetype-2.10.0/objs/.libs/libfreetype.a
    L+=${OURSTUFF}/lib64/libssl.a ${OURSTUFF}/lib64/libcrypto.a -ldl
 
    ifeq (${HOSTNAME},hgwdev-new)
        PNGLIB=${OURSTUFF}/lib/libpng.a
        PNGINCL=-I${OURSTUFF}/include/libpng16
-       L += /lib64/libbz2.a
    else
        PNGLIB=/usr/lib64/libpng.a
        PNGINCL=-I/usr/include/libpng15
-       L += -lbz2
    endif
 
    MYSQLINC=/usr/include/mysql
-   MYSQLLIBS=${OURSTUFF}/lib64/libmariadbclient.a ${OURSTUFF}/lib64/libssl.a ${OURSTUFF}/lib64/libcrypto.a -ldl -lz
+   MYSQLLIBS=${OURSTUFF}/lib64/libmariadbclient.a ${OURSTUFF}/lib64/libssl.a ${OURSTUFF}/lib64/libcrypto.a -ldl ${ZLIB}
 
    ifeq (${HOSTNAME},hgwdev-new)
        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
    ifeq (${CONDA_BUILD},1)
        L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl
    else
        ifneq (${SSLLIB},)
           L+=${SSLLIB}
        else
           L+=-lssl
        endif
        ifneq (${CRYPTOLIB},)
           L+=${CRYPTOLIB}
        else
           L+=-lcrypto -ldl
        endif
        ifeq (${DLLIB},)
           L+=-ldl
        endif
    endif
 endif
 
 #global external libraries
 L += $(kentSrc)/htslib/libhts.a
 
-L+=${PNGLIB} ${MLIB} ${ZLIB} ${ICONVLIB}
+L+=${PNGLIB} ${MLIB} ${ZLIB} ${BZ2LIB} ${ICONVLIB}
 HG_INC+=${PNGINCL}
 
 # 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 (${NODEBIN},)
     NODEBIN = /cluster/software/src/node-v0.10.24-linux-x64/bin
     ifeq ($(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