Hi Jolyon,
You have gcc available, but not the other compilers ( e.g. g++, cc1plus are not found as well as ginstall ). You want to make sure you have installed the full compiler suite - you may need to run something like
sudo apt-get install --reinstall g++-4.8
To make sure everything is installed. You probably also need to modify the config to use install rather than ginstall - but check first what your FSLMACHTYPE is now considered to be.
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 16 Apr 2019, at 11:00, Matthew Webster <[log in to unmask]> wrote:
>
> Hi Jolyon,
> Looking at BUILD_LOG_2, you will also need to modify lines 32/39 in libxml++/io/ostreamoutputbuffer.cc
> From
> return output_;
> To
> return bool(output_);
>
> However if you follow Paul’s email, this may not be necessary.
>
> Kind Regards
> Matthew
>
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
>
>> On 16 Apr 2019, at 09:44, paul mccarthy <[log in to unmask]> wrote:
>>
>> Hi Jolyon,
>>
>> Try with gcc-4.8 again, but before running ./build, edit the files
>> inside the $FSLDIR/config/$FSLMACHTYPE to suit your platform.
>>
>> Cheers,
>>
>> Paul
>>
>> On Tue, 16 Apr 2019 at 09:23, Jolyon Jones <[log in to unmask]> wrote:
>>>
>>> Hi Matthew,
>>>
>>> Thanks very much for your reply. I did as instructed, however, the build failed again.
>>> I have taken a number of steps to try and rectify the problem since yesterday. The full process is below but see the lines below (----//-----) for the modifications after your suggestion yesterday. Any light you may be able to shed on the matter would go a long way.
>>> Thanks in advance. Kind regards, Jolyon.
>>>
>>> (i've attached the build logs to this onedrive account;
>>> https://universityofcambridgecloud-my.sharepoint.com/:f:/g/personal/jaj58_cam_ac_uk/En7Agw9wbfJKrSqw2F_Le4UBP5vvBLXfYu8WiDcGWBa_gw?e=OFCgpn
>>>
>>> I am running Ubuntu 18.04.2 LTS (bionic) in an oracle virtual box.
>>>
>>> sudo apt-get update
>>> sudo apt-get upgrade
>>> sudo apt get install build-essential
>>> gcc -v
>>> make -v
>>> sudo apt-get install expat
>>> sudo apt-get install libexpat1-dev
>>> sudo apt-get install libx11-dev
>>> sudo apt-get install libx11-6
>>> sudo apt-get install libgl-dev which was (libgl1-mesa-dev)
>>> sudo apt-get install zlib1g
>>> sudo apt-get install zlib1g-dev
>>>
>>> Installation checked with command apt-cache policy ""
>>>
>>> 1)Downloaded and unpacked FSL tar file into /fslbuild
>>>
>>> 2)cd'd into fsl/etc/fslconf and opened fsl.sh
>>>
>>> 3) Removed the "#" on the lines below and saved
>>> FSLCONFDIR=$FSLDIR/config
>>> FSLMACHTYPE=`$FSLDIR/etc/fslconf/fslmachtype.sh`
>>> export FSLCONFDIR FSLMACHTYPE
>>>
>>> 4) Created .bash_profile in home/Userjaj directory using gedit with these lines;
>>> #!/bin/bash
>>> FSLDIR=/fslbuild/fsl
>>> . ${FSLDIR}/etc/fslconf/fsl.sh
>>> PATH=${FSLDIR}/bin:${PATH}
>>> export FSLDIR PATH
>>>
>>> 5) From directory /fslbuild
>>> export FSLDIR=`pwd`/fsl
>>> executed first the the below command executed secondly;
>>> . ${FSLDIR}/etc/fslconf/fsl.sh
>>>
>>> 6) From directory /fslbuild
>>> ls $FSLDIR/config/$FSLMACHTYPE
>>> I get this error message:
>>> ls: cannot access ' /fslbuild/fsl/config/gnu_64-gcc7. ': No such file or directory
>>>
>>> 7) As instructed cd'd into fslbuild/fsl/config
>>> cp -r $FSLDIR/config/linux_64-gcc4.8 $FSLDIR/config/$FSLMACHTYPE
>>>
>>> 8) ls $FSLDIR/config/$FSLMACHTYPE
>>> output:
>>> externallibs.mk systemvars.mk
>>>
>>> 9) cd into /fslbuild/fsl
>>> sudo ./build
>>> BUILD_LOG_1
>>>
>>> -----------------------------------------------------------------//-------------------------------------------------------------------------------------------------------------------
>>>
>>> -- didn't compile properly, therefore as instructed by Matthew Webster ([log in to unmask]);
>>> Changed $FSLIR/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc:42
>>> from return input_;
>>> to
>>> return bool(input_); and saved/opened new terminal
>>>
>>> repeat
>>> 9) cd into /fslbuild/fsl
>>> sudo ./build
>>> BUILD_LOG_2
>>> --failed--
>>>
>>> sudo apt-et remove gcc g++
>>> removing build-essential
>>> removing g++
>>> removing gcc
>>>
>>> Download gcc-4.0 (suggested in email from Paul Mccarthy)
>>> sudo add-apt-repository ppa:ubunutu-toolchain-r/test
>>> sudo apt-get update
>>> sudo apt-get install g++-4.9
>>> sudo apt-get install g++-4.0
>>> make -v = GNU Make 4.1
>>>
>>> sudo apt install gcc-4.8
>>> (apparently the version you can get on the newest ubuntu: https://askubuntu.com/questions/1084930/install-gcc-4-4-7-on-ubuntu-18-04)
>>>
>>> apt-cahce policy gcc-4.8 -> installed
>>>
>>> repeat
>>> 9) cd into /fslbuild/fsl
>>> sudo ./build
>>> BUILD_LOG_3
>>> --failed--
>>>
>>> In the previous step I removed gcc-7.3.0. As this build failed I re-updated so that gcc-7.3.0 was now available for use. Checked with the following. It appears that both gcc 7.3.0 and gc-4.8 is installed.
>>>
>>> make -v = GNU Make 4.1
>>> gcc --version = gcc 7.3.0
>>> apt-cache policy gcc-4.8 = installed
>>>
>>> - I then attempted to download gcc-4.4 from a mirror service (detailed below), however I am having trouble installing this, and as such it remains just a downloaded file (no action has been taken). I've read about symbolic links and thought this may be the way to go (having both gcc-7.3.0 & gcc-4.4 installed).
>>> Downloaded 4.4 from
>>> ftp://ftp.mirrorservice.org/sites/sourceware.org/pub/gcc/snapshots/
>>> created new folder gcc_build and transferred tar file to this folder. No furhter action taken.
>>>
>>> repeat
>>> 9) cd into /fslbuild/fsl
>>> sudo ./build
>>> BUILD_LOG_4
>>> --failed--
>>>
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