make fails for ubuntu 12.04 running on Amazon EC2

[Gabriel]

Hello all,

First, apologies if I come off as a total newbie -- that is in fact
what I am, so please feel free to correct whatever misunderstandings
or incorrect assumptions I may be bringing to this question. I am
trying to install migrate-n version 3.3.2 on Ubuntu 12.04 running on
an Amazon EC2 instance. I seem to be able to get ./configure to run
properly but when I attempt to run make I get an error and the compile
aborts. I'll first post the error and then I'll post full logs for my
configure and make runs. I don't know what other information to give
so I'm sorry for asking people to dig through those logs but they're
all I have.

****Error:

gcc: error: /usr/local/lib/libz.1.dylib: No such file or directory
gcc: error: 1: No such file or directory
gcc: error: 1.2.5: No such file or directory
gcc: error: unrecognized option â-compatibility_versionâ
gcc: error: unrecognized option â-current_versionâ
make[2]: *** [libz.1.2.5.dylib] Error 1
make[2]: Leaving directory `/home/ubuntu/migrate/migrate-3.3.2/src/
zlib'
make[1]: *** [zlib] Error 2
make[1]: Leaving directory `/home/ubuntu/migrate/migrate-3.3.2/src'
make: *** [intro] Error 2
ubuntu@ip-10-28-93-250:~/migrate/migrate-3.3.2/src$ ^C
ubuntu@ip-10-28-93-250:~/migrate/migrate-3.3.2/src$ version
version: command not found


_______________________________________________________________________________________
_______________________________________________________________________________________
****Configure Log:

ubuntu@ip-10-28-93-250:~/migrate-3.3.2/src$ ./configure
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for gmake... make
=======================================================================
Migrate subversion:
Hardware: unknown
System OS: linux-gnu Linux
System CPU: x86_64
-----------------------------------------------------------------------
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... no
checking for xlC... no
checking for cxx... no
checking for cc++... no
checking for aCC... no
checking for c++... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
C-compiler: gcc
C++-compiler:g++
CFLAGS: -O3 -funroll-loops -fomit-frame-pointer -falign-loops=16 -
Dx86_64
=======================================================================
checking for a BSD-compatible install... /usr/bin/install -c
checking for pthread_create in -lpthread... yes
checking for MPI_Init in -lmpi... no
checking for exp in -lm... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for strings.h... (cached) yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for int... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for inline... inline
checking return type of signal handlers... void
checking for strftime... yes
checking for strcspn... yes
checking for strsep... yes
checking for lgamma... yes
checking which zlib implementation to use... autodetect
checking for main in -lz... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating conf.h
config.status: conf.h is unchanged

MIGRATE-N is now setup
to compile the program you need to type one of the
commands below (ordered by preference):

SINGLE CPU machines
make # with PDF output support
# this might fail on first attempt,
# if the make fails, please let me know
# often linking fails because the C++ pdf library
# and the core migrate parts (C) mismatch
# check the Makefile line for STDLIB= -lstdc++

SMP machines more than 1 CPU in machine
make thread # uses the thread library if present
make # on macs running macos 10.6+ using GrandCentral

PARALLEL Computers, Clusters with MPI software
make mpis # each cpu-core can be treated as a node
make mpis-thread # experimental, may increase load per node!
------------------------------------------------------------------------
SPEED and other TESTING
the migrate website contains a testsuite.tar.gz that has
many tests for single, parallel and thread compilations
the tests are driven by a python script rt (see the README
in the testsuite) and a submit script that allows to streamline
submissions to a batch queue system, currently supported systems
are SUN/ORACLE GRIDENGINE, TORQUE/MOAB, and NONE
------------------------------------------------------------------------
In case there are problems with the compile send a message to the
migrate...@google.com usergroup, include a log of
./configure
make
=======================================================================

_________________________________________________________________________________________
_________________________________________________________________________________________
****Make Log:

ubuntu@ip-10-28-93-250:~/migrate-3.3.2/src$ make
-----------------------------------------------------
Migrate 3.3.2
please **read** the documentation
this Makefile will produce an executable: migrate-n
or migrate-n-mpi for the parallel version
For more Makefile options type make help

I am interested in getting email about any problems.
Please send all compile warning or error messages
to bee...@fsu.edu [Peter Beerli]
----------------------------------------------------
make all
make[1]: Entering directory `/home/ubuntu/migrate-3.3.2/src'
(cd ./haru ; make -f makefile.gcc "CC=g++" "CPP=gcc" "ARCH="
"MACOSVERSION=" "MYCPPFLAGS=-DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib -I../zlib")
make[2]: Entering directory `/home/ubuntu/migrate-3.3.2/src/haru'
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfExceptions.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfList.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfUtils.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfStreams.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfAutoPtrObjects.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfObjects.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfContents.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfPages.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfFonts.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfXref.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfDestinations.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfOutlines.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfBorderStyle.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfAnnotations.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfDoc.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfCatalog.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfInfo.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfEncoding.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfFontDef.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfXObjects.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfFontDef_Courier.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfFontDef_Helvetica.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfFontDef_Times.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfFontDef_Symbol.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfFontDef_ZapfDingbats.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfEncoding_ISO8859.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfEncoding_KOI8.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfEncoding_MSCP.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfMbFonts.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfCMap.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfUnicodeText.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfMbFontDef_Gothic.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfMbFontDef_Mincyo.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfMbFontDef_SimHei.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfMbFontDef_SimSun.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfMbFontDef_Ming.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfMbFontDef_Batang.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfMbFontDef_Dotum.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfCMap_RKSJ.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfCMap_EUC.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfCMap_GB_EUC.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfCMap_ETen_B5.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfCMap_KSCms_UHC.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfCMap_KSC_EUC.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfPngImage.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfJpegImage.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c PdfEncrypt.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c libharuc.cc
libharuc.cc: In function âint
pdf_cid_type2_fontdef_ascent(pdf_cid_type2_fontdef)â:
libharuc.cc:164:69: warning: converting to non-pointer type âlong intâ
from NULL [-Wconversion-null]
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c libharuc_jpfonts.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c libharuc_krfonts.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c libharuc_cnsfonts.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c libharuc_cntfonts.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c libharu_png.cc
gcc -I. -O3 -DNDEBUG -DNOJPEG -DNOPNG -Iharu -DPRETTY -DLETTERPAPER -
Izlib -I../zlib -c libharu_jpeg.cc
ar rc libharu.a PdfExceptions.o PdfList.o PdfUtils.o PdfStreams.o
PdfAutoPtrObjects.o PdfObjects.o PdfContents.o PdfPages.o PdfFonts.o
PdfXref.o PdfDestinations.o PdfOutlines.o PdfBorderStyle.o
PdfAnnotations.o PdfDoc.o PdfCatalog.o PdfInfo.o PdfEncoding.o
PdfFontDef.o PdfXObjects.o PdfFontDef_Courier.o PdfFontDef_Helvetica.o
PdfFontDef_Times.o PdfFontDef_Symbol.o PdfFontDef_ZapfDingbats.o
PdfEncoding_ISO8859.o PdfEncoding_KOI8.o PdfEncoding_MSCP.o
PdfMbFonts.o PdfCMap.o PdfUnicodeText.o PdfMbFontDef_Gothic.o
PdfMbFontDef_Mincyo.o PdfMbFontDef_SimHei.o PdfMbFontDef_SimSun.o
PdfMbFontDef_Ming.o PdfMbFontDef_Batang.o PdfMbFontDef_Dotum.o
PdfCMap_RKSJ.o PdfCMap_EUC.o PdfCMap_GB_EUC.o PdfCMap_ETen_B5.o
PdfCMap_KSCms_UHC.o PdfCMap_KSC_EUC.o PdfPngImage.o PdfJpegImage.o
PdfEncrypt.o libharuc.o libharuc_jpfonts.o libharuc_krfonts.o
libharuc_cnsfonts.o libharuc_cntfonts.o libharu_png.o libharu_jpeg.o
ranlib libharu.a
make[2]: Leaving directory `/home/ubuntu/migrate-3.3.2/src/haru'
(cd ./zlib ; make)
make[2]: Entering directory `/home/ubuntu/migrate-3.3.2/src/zlib'
gcc -O3 -c -o example.o example.c
gcc -O3 -c -o adler32.o adler32.c
gcc -O3 -c -o compress.o compress.c
gcc -O3 -c -o crc32.o crc32.c
gcc -O3 -c -o deflate.o deflate.c
gcc -O3 -c -o gzclose.o gzclose.c
gcc -O3 -c -o gzlib.o gzlib.c
gcc -O3 -c -o gzread.o gzread.c
gcc -O3 -c -o gzwrite.o gzwrite.c
gcc -O3 -c -o infback.o infback.c
gcc -O3 -c -o inffast.o inffast.c
gcc -O3 -c -o inflate.o inflate.c
gcc -O3 -c -o inftrees.o inftrees.c
gcc -O3 -c -o trees.o trees.c
gcc -O3 -c -o uncompr.o uncompr.c
gcc -O3 -c -o zutil.o zutil.c
ar rc libz.a adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o
gzread.o gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o
uncompr.o zutil.o
gcc -O3 -o example example.o -L. libz.a
gcc -O3 -c -o minigzip.o minigzip.c
gcc -O3 -o minigzip minigzip.o -L. libz.a
gcc -O3 -fPIC -DPIC -c -o objs/adler32.o adler32.c
gcc -O3 -fPIC -DPIC -c -o objs/compress.o compress.c
gcc -O3 -fPIC -DPIC -c -o objs/crc32.o crc32.c
gcc -O3 -fPIC -DPIC -c -o objs/deflate.o deflate.c
gcc -O3 -fPIC -DPIC -c -o objs/gzclose.o gzclose.c
gcc -O3 -fPIC -DPIC -c -o objs/gzlib.o gzlib.c
gcc -O3 -fPIC -DPIC -c -o objs/gzread.o gzread.c
gcc -O3 -fPIC -DPIC -c -o objs/gzwrite.o gzwrite.c
gcc -O3 -fPIC -DPIC -c -o objs/infback.o infback.c
gcc -O3 -fPIC -DPIC -c -o objs/inffast.o inffast.c
gcc -O3 -fPIC -DPIC -c -o objs/inflate.o inflate.c
gcc -O3 -fPIC -DPIC -c -o objs/inftrees.o inftrees.c
gcc -O3 -fPIC -DPIC -c -o objs/trees.o trees.c
gcc -O3 -fPIC -DPIC -c -o objs/uncompr.o uncompr.c
gcc -O3 -fPIC -DPIC -c -o objs/zutil.o zutil.c
gcc -dynamiclib -install_name /usr/local/lib/libz.1.dylib -
compatibility_version 1 -current_version 1.2.5 -O3 -fPIC -o libz.
1.2.5.dylib adler32.lo compress.lo crc32.lo deflate.lo gzclose.lo
gzlib.lo gzread.lo gzwrite.lo infback.lo inffast.lo inflate.lo
inftrees.lo trees.lo uncompr.lo zutil.lo -lc -L. libz.a
gcc: error: /usr/local/lib/libz.1.dylib: No such file or directory
gcc: error: 1: No such file or directory
gcc: error: 1.2.5: No such file or directory
gcc: error: unrecognized option â-compatibility_versionâ
gcc: error: unrecognized option â-current_versionâ
make[2]: *** [libz.1.2.5.dylib] Error 1
make[2]: Leaving directory `/home/ubuntu/migrate-3.3.2/src/zlib'
make[1]: *** [zlib] Error 2
make[1]: Leaving directory `/home/ubuntu/migrate-3.3.2/src'
make: *** [intro] Error 2
ubuntu@ip-10-28-93-250:~/migrate-3.3.2/src$

___________________________________________________________________________________________
___________________________________________________________________________________________

I realize that that's a lot to throw at you folks and I appreciate
your patience. If you need me to help you narrow things down or
provide some other information then just let me know. I don't know a
lot about what I'm doing here so thank you again for bearing with me.

[Peter Beerli]

Gabriel,
could you try to:

cd zlib
configure
make
cd ..
make

if this leads to the same error, let me know
Peter (beerli at fsu dot edu)

> --
> You received this message because you are subscribed to the Google Groups "migrate-support" group.
> To post to this group, send email to migrate...@googlegroups.com.
> To unsubscribe from this group, send email to migrate-suppo...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/migrate-support?hl=en.
>

[Gabriel]

Well, that helped! The program seems to have compiled without error.
However, all is not yet well. When I run "make install" I get the
following log:

ubuntu@ip-10-28-8-160:~/migrate-3.3.2/src$ make install

(cd ./haru ; make -f makefile.gcc "CC=g++" "CPP=gcc" "ARCH="
"MACOSVERSION=" "MYCPPFLAGS=-DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib -I../zlib")

make[1]: Entering directory `/home/ubuntu/migrate-3.3.2/src/haru'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ubuntu/migrate-3.3.2/src/haru'
(cd ./zlib ; make)
make[1]: Entering directory `/home/ubuntu/migrate-3.3.2/src/zlib'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ubuntu/migrate-3.3.2/src/zlib'
make migrate-n "CFLAGS = -O3 -funroll-loops -fomit-frame-pointer -
falign-loops=16 -Dx86_64 -DNEWVERSION -DBFDEBUG -DNEXUSTREE -
DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -
DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION=\"\\\"\\\"\" -
DMIGRATEVERSION=\"\\\"3.3.2\\\"\" -DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib" "LIBS = -Lharu -lharu -lstdc++ -Lzlib -lz -lm "
"LDFLAGS = -fexceptions"

make[1]: Entering directory `/home/ubuntu/migrate-3.3.2/src'

make[1]: `migrate-n' is up to date.

make[1]: Leaving directory `/home/ubuntu/migrate-3.3.2/src'

/usr/bin/install -c migrate-n /usr/local/bin
/usr/bin/install: cannot remove `/usr/local/bin/migrate-n': Permission
denied
make: *** [install] Error 1



I tried running "sudo make install" in a blind hope that this would
resolve the "permission denied" error, but no dice. Here is everything
I have from the make run (the rest of it scrolled off the screen):


RPAPER -Izlib -c sequence.c
gcc -O3 -funroll-loops -fomit-frame-pointer -falign-loops=16 -
Dx86_64 -DNEWVERSION -DBFDEBUG -DNEXUSTREE -DHAVE_ZLIB -DZNZ -
DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -
DMEXP=19937 -DMIGRATESUBVERSION="\"\"" -
DMIGRATEVERSION="\"3.3.2\"" -DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib -c sighandler.c
gcc -O3 -funroll-loops -fomit-frame-pointer -falign-loops=16 -
Dx86_64 -DNEWVERSION -DBFDEBUG -DNEXUSTREE -DHAVE_ZLIB -DZNZ -
DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -
DMEXP=19937 -DMIGRATESUBVERSION="\"\"" -
DMIGRATEVERSION="\"3.3.2\"" -DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib -c slice.c
gcc -O3 -funroll-loops -fomit-frame-pointer -falign-loops=16 -
Dx86_64 -DNEWVERSION -DBFDEBUG -DNEXUSTREE -DHAVE_ZLIB -DZNZ -
DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -
DMEXP=19937 -DMIGRATESUBVERSION="\"\"" -
DMIGRATEVERSION="\"3.3.2\"" -DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib -c sort.c
gcc -O3 -funroll-loops -fomit-frame-pointer -falign-loops=16 -
Dx86_64 -DNEWVERSION -DBFDEBUG -DNEXUSTREE -DHAVE_ZLIB -DZNZ -
DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -
DMEXP=19937 -DMIGRATESUBVERSION="\"\"" -
DMIGRATEVERSION="\"3.3.2\"" -DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib -c uep.c
gcc -O3 -funroll-loops -fomit-frame-pointer -falign-loops=16 -
Dx86_64 -DNEWVERSION -DBFDEBUG -DNEXUSTREE -DHAVE_ZLIB -DZNZ -
DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -
DMEXP=19937 -DMIGRATESUBVERSION="\"\"" -
DMIGRATEVERSION="\"3.3.2\"" -DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib -c world.c
gcc -O3 -funroll-loops -fomit-frame-pointer -falign-loops=16 -
Dx86_64 -DNEWVERSION -DBFDEBUG -DNEXUSTREE -DHAVE_ZLIB -DZNZ -
DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -
DMEXP=19937 -DMIGRATESUBVERSION="\"\"" -
DMIGRATEVERSION="\"3.3.2\"" -DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib -c pretty.c
gcc -O3 -funroll-loops -fomit-frame-pointer -falign-loops=16 -
Dx86_64 -DNEWVERSION -DBFDEBUG -DNEXUSTREE -DHAVE_ZLIB -DZNZ -
DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -
DMEXP=19937 -DMIGRATESUBVERSION="\"\"" -
DMIGRATEVERSION="\"3.3.2\"" -DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib -c skyline.c
gcc -O3 -funroll-loops -fomit-frame-pointer -falign-loops=16 -
Dx86_64 -DNEWVERSION -DBFDEBUG -DNEXUSTREE -DHAVE_ZLIB -DZNZ -
DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -
DMEXP=19937 -DMIGRATESUBVERSION="\"\"" -
DMIGRATEVERSION="\"3.3.2\"" -DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib -c watterson.c
gcc -O3 -funroll-loops -fomit-frame-pointer -falign-loops=16 -
Dx86_64 -DNEWVERSION -DBFDEBUG -DNEXUSTREE -DHAVE_ZLIB -DZNZ -
DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -
DMEXP=19937 -DMIGRATESUBVERSION="\"\"" -
DMIGRATEVERSION="\"3.3.2\"" -DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib -c znzlib.c
gcc -O3 -funroll-loops -fomit-frame-pointer -falign-loops=16 -
Dx86_64 -DNEWVERSION -DBFDEBUG -DNEXUSTREE -DHAVE_ZLIB -DZNZ -
DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -
DMEXP=19937 -DMIGRATESUBVERSION="\"\"" -
DMIGRATEVERSION="\"3.3.2\"" -DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib -c pretty-win32.cpp
gcc -O3 -funroll-loops -fomit-frame-pointer -falign-loops=16 -
Dx86_64 -DNEWVERSION -DBFDEBUG -DNEXUSTREE -DHAVE_ZLIB -DZNZ -
DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -
DMEXP=19937 -DMIGRATESUBVERSION="\"\"" -
DMIGRATEVERSION="\"3.3.2\"" -DNOJPEG -DNOPNG -Iharu -DPRETTY -
DLETTERPAPER -Izlib -fexceptions -o migrate-n aic.o altivec.o
autotune.o bayes.o broyden.o calculator.o combroyden2.o data.o
correlation.o gammalike.o fst.o heating.o histogram.o inthp.o joint-
chains.o laguerre.o lrt.o main.o migrate_mpi.o mutationmodel.o mcmc1.o
mcmc2.o menu.o migevents.o options.o profile.o random.o reporter.o
spline.o tools.o tree.o sequence.o sighandler.o slice.o sort.o uep.o
world.o pretty.o skyline.o watterson.o znzlib.o pretty-win32.o -Lharu
-lharu -lstdc++ -Lzlib -lz -lm ;
make[2]: Leaving directory `/home/ubuntu/migrate-3.3.2/src'

make[1]: Leaving directory `/home/ubuntu/migrate-3.3.2/src'

Seems OK to me, right? So what's the problem with the installation?
Thanks for the continued support.

On Oct 1, 3:31 pm, Peter Beerli <beerli.pe...@gmail.com> wrote:
> Gabriel,
> could you try to:
>
> cd zlib
> configure
> make
> cd ..
> make
>
> if this leads to the same error, let me know
> Peter (beerli at fsu dot edu)
>

> > migrate-supp...@google.com usergroup, include a log of

> ...
>
> read more »

[Peter Beerli]

Gabriel,

sudo make install

should work or you seem to have a funny installation (this has nothing to do with migrate per se)

could it be that there is already a migrate-n in /usr/local/bin as suggested by

/usr/bin/install: cannot remove `/usr/local/bin/migrate-n': Permission

denied

cd /usr/local/bin

check out whether there is migrate-n (ls -la migrate*)

and remove that copy

and then try again

sudo make install 

or simply (assuming that you are in the migrate source directory)

sudo cp migrate-n /usr/local/bin/

in any case, it should work even if it is not in the /usr/local/bin, try

cd example

../migrate-n parmfile.testbayes

now the more exciting part to compile migrate for multiple cores

make thread

and (even better) for parallel processing using multiple cores/cpus.

using 

make mpis

but that will need installation of openmpi (Iam sure there is a ubuntu package for that)

Peter

[Bruno P. Kinoshita]

Hi Gabriel, 

Looks like the user you are using to compile migrate has no rights to write to /usr/local/bin. Do you have root access? 

If not, maybe you can use ./configure --prefix=$HOME/migrate or some other directory. 

HTH,
 
Bruno P. Kinoshita
http://kinoshita.eti.br
http://tupilabs.com

[Gabriel]

Well we're definitely getting somewhere. I chose $HOME/ubuntu/migrate
since Amazon seems to want me to do everything in home/ubuntu. However
now when I go to migrate-3.3.2/src/zlib and run make, I get the
following error:

ubuntu@ip-10-28-8-160:~/migrate-3.3.2/src/zlib$ make

gcc -dynamiclib -install_name /usr/local/lib/libz.1.dylib -
compatibility_version 1 -current_version 1.2.5 -O3 -fPIC -o libz.
1.2.5.dylib adler32.lo compress.lo crc32.lo deflate.lo gzclose.lo
gzlib.lo gzread.lo gzwrite.lo infback.lo inffast.lo inflate.lo
inftrees.lo trees.lo uncompr.lo zutil.lo -lc -L. libz.a

gcc: error: /usr/local/lib/libz.1.dylib: No such file or directory
gcc: error: 1: No such file or directory
gcc: error: 1.2.5: No such file or directory
gcc: error: unrecognized option â-compatibility_versionâ
gcc: error: unrecognized option â-current_versionâ

make: *** [libz.1.2.5.dylib] Error 1

If I run make from migrate-3.3.2/src I get the same set of errors as I
got before. I think what I need to do is to convince migrate to
install itself inside of Amazon's sandbox, but it looks to my naive
eyes like there are multiple parts of its auto-configuration that want
to install in more standard directories that I don't have access to.
How can I get around these problems?

On Oct 1, 9:22 pm, "Bruno P. Kinoshita" <brunodepau...@yahoo.com.br>
wrote:

> Hi Gabriel,
>
> Looks like the user you are using to compile migrate has no rights to write to /usr/local/bin. Do you have root access?
>
> If not, maybe you can use ./configure --prefix=$HOME/migrate or some other directory.
>
> HTH,
>

> Bruno P. Kinoshitahttp://kinoshita.eti.brhttp://tupilabs.com

> ...
>
> read more »

[Peter Beerli]

this will be more tricky because of th missing zlib in your standard system (this is weird because I bet that zlib is available on ubuntu systems), if you go back to the slip directory

configure --PREFIX=$HOME/ubuntu/migrate/lib
make clean
make
make install

I assume you use the bash shell: then change in your .bashrc or wherever you get your $PATH etc from
add
export LD_LIBRARY_PATH=$HOME/ubuntu/migrate/lib:$LD_LIBRARY_PATH
get a new terminal (this may mean logout/login -- try to do that while the first shell is open
because if you made a mistake in .bashrc file this could hang and lock you out;
this should allow to find the libraries for zlib.

Peter