Hi Duncan,
Sorry for the delay.
I am running OSX 10.13.5 High Sierra
I ran '. $FSLDIR/fslpython/bin/activate $FSLDIR/fslpython/envs/fslpython'.
I then ran 'conda env list', and indeed the asterisk indicated I was in the right environment.
Next, I ran '$FSLDIR/fslpython/bin/conda install R=3.4'. The output is below.
I tried to launch 'R' with '$FSLDIR/fslpython/envs/fslpython/bin/R', but it was not available in that directory.
Hmmm,
C
#### Install output
Collecting package metadata: - WARNING conda.models.version:get_matcher(528): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 2.*, but conda is ignoring the .* and treating it as 2
done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.6.7
latest version: 4.6.8
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /usr/local/fsl/fslpython/envs/fslpython
added / updated specs:
- r=3.4
The following packages will be downloaded:
package | build
---------------------------|-----------------
certifi-2019.3.9 | py36_0 155 KB
pcre-8.43 | h0a44026_0 227 KB
pixman-0.38.0 | h1de35cc_0 611 KB
------------------------------------------------------------
Total: 993 KB
The following NEW packages will be INSTALLED:
_r-mutex pkgs/r/osx-64::_r-mutex-1.0.0-anacondar_1
blas pkgs/main/osx-64::blas-1.0-mkl
bwidget pkgs/main/osx-64::bwidget-1.9.11-1
bzip2 pkgs/main/osx-64::bzip2-1.0.6-h1de35cc_5
cairo pkgs/main/osx-64::cairo-1.14.12-he60d9cb_2
cctools pkgs/main/osx-64::cctools-895-h7512d6f_0
clang pkgs/main/osx-64::clang-4.0.1-h662ec87_0
clang_osx-64 pkgs/main/osx-64::clang_osx-64-4.0.1-h1ce6c1d_11
clangxx pkgs/main/osx-64::clangxx-4.0.1-hc9b4283_0
clangxx_osx-64 pkgs/main/osx-64::clangxx_osx-64-4.0.1-h22b1bf0_11
compiler-rt pkgs/main/osx-64::compiler-rt-4.0.1-h5487866_0
curl pkgs/main/osx-64::curl-7.61.1-ha441bb4_0
fontconfig pkgs/main/osx-64::fontconfig-2.12.6-h9850fc5_0
gfortran_osx-64 pkgs/main/osx-64::gfortran_osx-64-4.8.5-h22b1bf0_8
glib pkgs/main/osx-64::glib-2.56.2-hd9629dc_0
graphite2 pkgs/main/osx-64::graphite2-1.3.13-h2098e52_0
gsl pkgs/main/osx-64::gsl-2.4-h1de35cc_4
harfbuzz pkgs/main/osx-64::harfbuzz-1.7.6-h171471c_1
krb5 pkgs/main/osx-64::krb5-1.14.2-h9a779f2_6
ld64 pkgs/main/osx-64::ld64-274.2-h7c2db76_0
libcurl pkgs/main/osx-64::libcurl-7.61.1-hf30b1f0_0
libssh2 pkgs/main/osx-64::libssh2-1.8.0-h322a93b_4
llvm pkgs/main/osx-64::llvm-4.0.1-hc748206_0
llvm-lto-tapi pkgs/main/osx-64::llvm-lto-tapi-4.0.1-h6701bc3_0
llvm-openmp pkgs/main/osx-64::llvm-openmp-4.0.1-hcfea43d_1
pango pkgs/main/osx-64::pango-1.41.0-h3bae10e_0
pcre pkgs/main/osx-64::pcre-8.43-h0a44026_0
pixman pkgs/main/osx-64::pixman-0.38.0-h1de35cc_0
r pkgs/r/osx-64::r-3.4.3-r343_0
r-base pkgs/r/osx-64::r-base-3.4.3-h9b62496_0
r-boot pkgs/r/osx-64::r-boot-1.3_20-r343h889e2dd_0
r-class pkgs/r/osx-64::r-class-7.3_14-r343h7f474d2_4
r-cluster pkgs/r/osx-64::r-cluster-2.0.6-r343h883f7c5_0
r-codetools pkgs/r/osx-64::r-codetools-0.2_15-r343h889e2dd_0
r-foreign pkgs/r/osx-64::r-foreign-0.8_69-r343h7f474d2_0
r-kernsmooth pkgs/r/osx-64::r-kernsmooth-2.23_15-r343h883f7c5_4
r-lattice pkgs/r/osx-64::r-lattice-0.20_35-r343h7f474d2_0
r-mass pkgs/r/osx-64::r-mass-7.3_48-r343h7f474d2_0
r-matrix pkgs/r/osx-64::r-matrix-1.2_12-r343h7f474d2_0
r-mgcv pkgs/r/osx-64::r-mgcv-1.8_22-r343h7f474d2_0
r-nlme pkgs/r/osx-64::r-nlme-3.1_131-r343h883f7c5_0
r-nnet pkgs/r/osx-64::r-nnet-7.3_12-r343h7f474d2_0
r-recommended pkgs/r/osx-64::r-recommended-3.4.3-r343_0
r-rpart pkgs/r/osx-64::r-rpart-4.1_11-r343h7f474d2_0
r-spatial pkgs/r/osx-64::r-spatial-7.3_11-r343h7f474d2_4
r-survival pkgs/r/osx-64::r-survival-2.41_3-r343h7f474d2_0
tktable pkgs/main/osx-64::tktable-2.10-h1de35cc_0
The following packages will be UPDATED:
ca-certificates 2018.03.07-0 --> 2019.1.23-0
certifi 2018.4.16-py36_0 --> 2019.3.9-py36_0
openssl 1.0.2o-h26aff7b_0 --> 1.0.2r-h1de35cc_0
The following packages will be DOWNGRADED:
libedit 3.1.20170329-hb402a30_2 --> 3.1-hb4e282d_0
ncurses 6.1-h0a44026_0 --> 6.0-hd04f020_2
sqlite 3.24.0-ha441bb4_0 --> 3.23.1-hf1716c9_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
pcre-8.43 | 227 KB | ############################################################################################################################################## | 100%
pixman-0.38.0 | 611 KB | ############################################################################################################################################## | 100%
certifi-2019.3.9 | 155 KB | ############################################################################################################################################## | 100%
Preparing transaction: done
Verifying transaction: failed
EnvironmentNotWritableError: The current user does not have write permissions to the target environment.
environment location: /usr/local/fsl/fslpython/envs/fslpython
uid: 502
gid: 20
(fslpython) Conrads-iMac-Pro:~ conradlaptop$ sudo $FSLDIR/fslpython/bin/conda install R=3.4
Password:
Collecting package metadata: done
Solving environment: done
## Package Plan ##
environment location: /usr/local/fsl/fslpython
added / updated specs:
- r=3.4
The following packages will be downloaded:
package | build
---------------------------|-----------------
conda-4.6.8 | py36_0 1.7 MB
------------------------------------------------------------
Total: 1.7 MB
The following packages will be UPDATED:
certifi 2018.11.29-py36_0 --> 2019.3.9-py36_0
conda 4.6.7-py36_0 --> 4.6.8-py36_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
conda-4.6.8 | 1.7 MB | ############################################################################################################################################## | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
########################################################################
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