I agree with you re using -k. I only did it after make was terminating
with an error in order to try and reveal any more errors. But I appreciate
the hazards in so doing. Thanks for the reminder.
I have now rerun `make all` to completion without error. I now believe the
compile errors stemmed from my previously trying to perform a parallel
build with `-j 6`
Thanks for coming to my assistance. I do have a new problem but I'll raise
that in a new email.
~Malcolm
Following are a few notes that might be useful to the next centos 7
installer:
# libs for centos7
sudo yum install -y gd-devel
sudo yum install -y libpng-devel
sudo yum install -y bzip2-devel
sudo yum install -y subversion
sudo yum install -y build-essential
sudo yum install -y perl
sudo yum install -y zlib-devel
sudo yum install -y libghc-bzlib-devel
sudo yum install -y gnuplot
sudo yum install -y unzip
sudo yum install -y expat
sudo yum install -y expat-devel #-devel
sudo yum install -y libgd-devel
sudo yum install -y r-base
## extra libs not mentioned in Ubuntu recipe or BUILD_LINUX
sudo yum install -y devtoolset-9 # use newer build chain
sudo yum install -y glibc-devel
sudo yum install -y glibc-static # without which `g++ Comet.o -o comet.exe
-static ...` (and others) fail with "cannot find {-lpthread,-lm,-lc} "
sudo yum install -y fann-devel
## more libs from taken from
release_6-1-0/installer_linux/install-prerequisites-centos-5_2.sh - unclear
if actually needed in centos 7 but hey
sudo yum install -y mcrypt
sudo yum install -y swig
## you will want to make in an environment with:
export LD_LIBRARY_PATH=/usr/lib64:${LD_LIBRARY_PATH} ## for libc and libm
else error:
"/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: cannot
find -lc"
source /opt/rh/devtoolset-9/enable # use newer build chain
# make install should presumably be called by root
sudo make install
# need to pipe yes into the build of XML::Twig
yes | sudo cpan install XML::Twig
restarting apache is performed with `sudo apachectl restart`
On Wednesday, June 8, 2022 at 8:21:28 AM UTC-5 David Shteynberg wrote:
> Also, I wouldn't recommend using make -k because then you get errors with
> linking of the sort you are seeing because prerequisite dependencies are
> not being built properly so downstream linking of applications to
> dependencies fails.
>
> Can you send the actual errors that are generated when you run make all
> for the first time on a fresh source tree as those are likely to hold
> additional clues? Also if you are able to provide access to the machine,
> or a cloud machine with the same configuration and compilation problem, so
> I can log in that would help me troubleshoot the issue.
>
> Thanks!
> -David
>
> On Tue, Jun 7, 2022 at 9:02 PM Malcolm Cook <[email protected]> wrote:
>
>> Hi,
>>
>> I am following & adapting TPP 6.1.0: Installing on Ubuntu 20.04 LTS
>> <http://tools.proteomecenter.org/wiki/index.php?title=TPP_6.1.0:_Installing_on_Ubuntu_20.04_LTS>
>>
>> for our centos 7 environment.
>>
>> Here are some notes and problems I've encountered so far.
>>
>> I am building as non privileged user, proceeding as follows:
>>
>> # create environment for building
>> export LD_LIBRARY_PATH=/usr/lib64:${LD_LIBRARY_PATH} ## for
>> {libc,libm,libpthreads} else error: "ld: cannot find -lc"
>>
>> source /opt/rh/devtoolset-9/enable # enable RED HAT DEVELOPER TOOLSET
>> 9.1
>> <https://access.redhat.com/documentation/en-us/red_hat_developer_toolset/9/html-single/user_guide/index>
>>
>> I am compiling with:
>>
>> make info
>> ARCH = x86_64
>> VENDOR = redhat
>> SYSTEM = linux
>> OS = Linux
>>
>> TPP_VERSION = 6.1.0
>> TPP_RELEASE = Parhelion
>> TPP_BUILDID = TPP v6.1.0 Parhelion, Build 202206071204-exported
>> (Linux-x86_64)
>>
>> SRC_DIR = /n/sci/SCI-004255-ZFPROT/tpp/svn/trans_proteomic_pipeline
>> BUILD_DIR =
>> /n/sci/SCI-004255-ZFPROT/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64-release
>> INSTALL_DIR = /usr/local/tpp
>>
>> TPP_HOME = /usr/local/tpp
>> TPP_DATADIR = /data/tpp
>> TPP_BASEURL = /tpp
>> TPP_DATAURL = /tpp/data
>>
>> MZ5_SUPPORT is not enabled
>>
>> I found as advised that I had to call `make all` many times....
>>
>> The first time created some directories and touch some files and them
>> terminated with error:
>>
>> make: *** No rule to make target
>> '/n/sci/SCI-004255-ZFPROT/tpp/release_6-1-0/build/linux-x86_64-release/html/',
>>
>> needed by 'd3'. Stop.
>>
>> The second time halted without an error without compiling anything,
>> finally printing:
>>
>> ### ...done unpacking Boost source
>>
>> The 3rd through 6th time compile successively more, though it produced a
>> few warnings which were proceeded past, each of the form:
>>
>> /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
>> -I.. -g -O2 -MT rowcol.lo -MD -MP -MF .deps/rowcol.Tpo -c -o rowcol.lo
>> rowcol.c
>> warning: On gcc, DLLs can not be built with '<runtime-link>static'.
>> warning: It is suggested to use '<runtime-link>static' together with
>> '<link>static'.
>>
>> The 7th time terminated with error:
>>
>> /bin/sh ./libtool --silent --mode=link gcc -I./lib -I. -g -O2 -Wall
>> -Wmissing-prototypes -Wstrict-prototypes -fexceptions
>> -DHAVE_EXPAT_CONFIG_H -no-undefined -version-info 6:2:5 -rpath
>> /n/sci/SCI-004255-ZFPROT/tpp/release_6-1-0/build/linux-x86_64-release/lib
>> -o libexpat.la lib/xmlparse.lo lib/xmltok.lo lib/xmlrole.lo
>> libtool: link: `lib/xmlparse.lo' is not a valid libtool object
>>
>> I called make an 8th time, this time as `make -k all` to "keep going"
>> past errors and build as many targets as possible. Many more programs were
>> compiled successfully, though a few additional errors were picked up:
>>
>> /bin/sh ../libtool --mode=link gcc -D_REENTRANT -g -O2 -version-info
>> 2:0:0 -o libfloatfann.la -rpath
>> /n/sci/SCI-004255-ZFPROT/tpp/release_6-1-0/build/linux-x86_64-release/lib
>> floatfann.lo
>> libtool: link: `floatfann.lo' is not a valid libtool object
>>
>> I'd be much obliged if anyone with more experience with tpp and gcc could
>> comment or make any suggestions on moving forward with how to address any
>> of the above errors.
>>
>> Thanks,
>>
>> Malcolm
>>
>> --
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