Here are some suggestions for Linux. Perhaps they will be helpful on Mac:
https://github.com/Washington-University/HCPpipelines/tree/master/ICAFIX
Matt.
On 5/23/19, 12:08 AM, "FSL - FMRIB's Software Library on behalf of Damion Demeter" <[log in to unmask] on behalf of [log in to unmask]> wrote:
Hello,
I am having all kinds of trouble installing FIX on mac OS Mojave. I've run into some of the same problems in this thread, but more. I've spent the whole day trying to install it, any help would be appreciated! Beyond R telling me that party can't be installed because of other packages (like the error below) I had a lot of other issues I sidestepped. If anyone can help, I'm trying to run hcp scripts that rely on FIX being installed and I'm completely stuck. It looks to me like something needs to be updated with FIX to reflect missing R libraries? I also don't have any clue as to why my fslpython env path is different, unless this readme is for FSL 5 paths? (I downloaded the only link to fix on the official fsl wiki page, not sure the version because the readme, etc. don't specify) https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide
Here's the steps/problems I encountered after activating the fslpython env as per the readme instructions:
1. I followed the instructions exactly in the readme, and for some reason I couldn't get R to install in the specified location ($FSLDIR/fslpython/envs/fslpython/fslpython/bin/R). Instead, it installs here: $FSLDIR/fslpython/bin/R
2. I did the suggestion here for calling fsl's conda, and that worked to install R and the conda installed libraries. For me it was this:
sudo $FSLDIR/fslpython/bin/conda install R=3.3
sudo $FSLDIR/fslpython/bin/conda install r-rocr=1.0_7 r-kernlab=0.9_25 r-randomForest=4.6_12 r-class=7.3_14 r-e1071=1.6_8 r-devtools
3. When I launch R and try for the last step (install party) nothing works. I even tried this conda path I found on the conda search page: conda install -c conda-forge r-party
This was found here: https://anaconda.org/conda-forge/r-party
4. Here's the error I get when I follow the readme instructions to install party (I'll paste the first group of lines, but more packages fail in the same way because the previous dependency failed):
R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require(devtools)
Loading required package: devtools
> install_version("party", version="1.0-25")
--- Please select a CRAN mirror for use in this session ---
Selection:
Enter an item from the menu, or 0 to exit
Selection: 63
Error in package_find_repo(package, repos) :
couldn't find package 'party'
> install_version("party", version="1.0-25")
Downloading package from url: https://ftp.osuosl.org/pub/cran/src/contrib/Archive/party/party_1.0-25.tar.gz
Installing party
trying URL 'https://ftp.osuosl.org/pub/cran/src/contrib/coin_1.3-0.tar.gz'
Content type 'application/x-gzip' length 1827725 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
Installing coin
trying URL 'https://ftp.osuosl.org/pub/cran/src/contrib/libcoin_1.0-4.tar.gz'
Content type 'application/x-gzip' length 757102 bytes (739 KB)
==================================================
downloaded 739 KB
Installing libcoin
'/usr/local/fsl/fslpython/lib/R/bin/R' --no-site-file --no-environ --no-save \
--no-restore --quiet CMD INSTALL \
'/private/tmp/Rtmpiz6SQ2/devtools15510ecd5498/libcoin' \
--library='/usr/local/fsl/fslpython/lib/R/library' --install-tests
* installing *source* package ‘libcoin’ ...
** package ‘libcoin’ successfully unpacked and MD5 sums checked
** libs
x86_64-apple-darwin13.4.0-clang -I/usr/local/fsl/fslpython/lib/R/include -DNDEBUG -I"/usr/local/fsl/fslpython/lib/R/library/mvtnorm/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/usr/local/fsl/fslpython/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/usr/local/fsl/fslpython/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c libcoin-init.c -o libcoin-init.o
In file included from libcoin-init.c:28:
In file included from ./libcoin.h:28:
In file included from ./libcoin_internal.h:30:
/usr/local/fsl/fslpython/lib/R/include/R.h:55:11: fatal error: 'stdlib.h' file not found
# include <stdlib.h> /* Not used by R itself, but widely assumed in packages */
^~~~~~~~~~
1 error generated.
make: *** [libcoin-init.o] Error 1
ERROR: compilation failed for package ‘libcoin’
* removing ‘/usr/local/fsl/fslpython/lib/R/library/libcoin’
Installation failed: Command failed (1)
trying URL 'https://ftp.osuosl.org/pub/cran/src/contrib/matrixStats_0.54.0.tar.gz'
Content type 'application/x-gzip' length 183731 bytes (179 KB)
==================================================
downloaded 179 KB
Installing matrixStats
'/usr/local/fsl/fslpython/lib/R/bin/R' --no-site-file --no-environ --no-save \
--no-restore --quiet CMD INSTALL \
'/private/tmp/Rtmpiz6SQ2/devtools155104ba11d6/matrixStats' \
--library='/usr/local/fsl/fslpython/lib/R/library' --install-tests
* installing *source* package ‘matrixStats’ ...
** package ‘matrixStats’ successfully unpacked and MD5 sums checked
** libs
x86_64-apple-darwin13.4.0-clang -I/usr/local/fsl/fslpython/lib/R/include -DNDEBUG -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/usr/local/fsl/fslpython/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/usr/local/fsl/fslpython/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c 000.init.c -o 000.init.o
In file included from 000.init.c:1:
In file included from /usr/local/fsl/fslpython/lib/R/include/Rdefines.h:37:
/usr/local/fsl/fslpython/lib/R/include/R_ext/RS.h:34:11: fatal error: 'string.h' file not found
# include <string.h> /* for memcpy, memset */
^~~~~~~~~~
1 error generated.
make: *** [000.init.o] Error 1
ERROR: compilation failed for package ‘matrixStats’
* removing ‘/usr/local/fsl/fslpython/lib/R/library/matrixStats’
Installation failed: Command failed (1)
trying URL 'https://ftp.osuosl.org/pub/cran/src/contrib/multcomp_1.4-10.tar.gz'
Content type 'application/x-gzip' length 603161 bytes (589 KB)
==================================================
downloaded 589 KB
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