Hi Steven,
It looks like conda can’t find a compiler on your system. If you install the package
clangxx_osx-64
Into the Rtest environment then you should be able to continue. If you still have problems compiling, then there are suggestions that running
export CONDA_BUILD_SYSROOT=$(xcrun --show-sdk-path)
before starting R might be necessary.
Hope this helps,
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 29 Apr 2020, at 20:35, Manning, Steven T. <[log in to unmask]> wrote:
>
> Actually, I was able to rewrite permissions I believe, but the next error message I got looked like this:
>
> > install_version("mvtnorm", version="1.0-8")
> Downloading package from url: https://cran.case.edu/src/contrib/Archive/mvtnorm/mvtnorm_1.0-8.tar.gz
> Installing mvtnorm
> '/usr/local/fsl/fslpython/envs/Rtest/lib/R/bin/R' --no-site-file --no-environ \
> --no-save --no-restore --quiet CMD INSTALL \
> '/private/var/folders/lr/1wxwxvpx79vd9nt0_502839h0000gn/T/RtmphKNfGP/devtools6e6f7a1c3863/mvtnorm' \
> --library='/usr/local/fsl/fslpython/envs/Rtest/lib/R/library' \
> --install-tests
>
> * installing *source* package ‘mvtnorm’ ...
> ** package ‘mvtnorm’ successfully unpacked and MD5 sums checked
> ** libs
> x86_64-apple-darwin13.4.0-clang -I/usr/local/fsl/fslpython/envs/Rtest/lib/R/include -DNDEBUG -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/usr/local/fsl/fslpython/envs/Rtest/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/usr/local/fsl/fslpython/envs/Rtest/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
> make: x86_64-apple-darwin13.4.0-clang: No such file or directory
> make: *** [C_FORTRAN_interface.o] Error 1
> ERROR: compilation failed for package ‘mvtnorm’
> * removing ‘/usr/local/fsl/fslpython/envs/Rtest/lib/R/library/mvtnorm’
> Installation failed: Command failed (1)
>
>
> What should I attempt next?
>
> Thanks,
>
> Steven
> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Manning, Steven T. <[log in to unmask]>
> Sent: Wednesday, April 29, 2020 3:28 PM
> To: [log in to unmask] <[log in to unmask]>
> Subject: Re: [FSL] Issue with FIX - trouble downloading R
>
> I am attempting to download the mvtnorm, etc. inside R, and I am getting an error that I do not have permission to install to directory '/usr/local/fsl/fslpython/envs/Rtest/lib/R/library'
>
> How do I bypass this permission?
>
> Thanks,
> Steven
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of Matthew Webster
> Sent: Tuesday, April 21, 2020 12:16 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Issue with FIX - trouble downloading R
>
> Hi Steven,
> Great! The remaining commands need to be run in R itself, if the Rtest environment is active, you should be able just to start R as normal, or you can use the full path
>
> /usr/local/fsl/fslpython/envs/Rtest/bin/R
>
> Kind Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
>
> > On 17 Apr 2020, at 13:55, Manning, Steven T. <[log in to unmask]> wrote:
> >
> > Thank you! That appeared to be successful. Here is the output
> >
> > manning.343$ sudo conda install -n Rtest R=3.4 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 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.
> > Collecting package metadata (repodata.json): done Solving environment:
> > done
> >
> > ## Package Plan ##
> >
> > environment location: /usr/local/fsl/fslpython/envs/Rtest
> >
> > added / updated specs:
> > - r-class=7.3_14
> > - r-devtools
> > - r-e1071=1.6_8
> > - r-kernlab=0.9_25
> > - r-randomforest=4.6_12
> > - r-rocr=1.0_7
> > - r=3.4
> >
> >
> > The following packages will be downloaded:
> >
> > package | build
> > ---------------------------|-----------------
> > curl-7.61.1 | ha441bb4_0 122 KB
> > gsl-2.4 | h1de35cc_4 1.8 MB
> > krb5-1.14.2 | h9a779f2_6 1.0 MB
> > libcurl-7.61.1 | hf30b1f0_0 327 KB
> > libssh2-1.8.0 | h322a93b_4 204 KB
> > ncurses-6.0 | hd04f020_2 699 KB
> > openssl-1.0.2u | h1de35cc_0 2.0 MB
> > r-base-3.4.3 | h9b62496_0 20.8 MB
> > r-bitops-1.0_6 | r343h7f474d2_4 24 KB
> > r-catools-1.17.1 | r343he124285_4 162 KB
> > r-curl-3.1 | r343h7f474d2_0 348 KB
> > r-devtools-1.13.4 | r343he124285_0 417 KB
> > r-digest-0.6.13 | r343h7f474d2_0 114 KB
> > r-e1071-1.6_8 | r343he124285_0 667 KB
> > r-gdata-2.18.0 | r343h889e2dd_0 937 KB
> > r-git2r-0.20.0 | r343h7f474d2_0 852 KB
> > r-gplots-3.0.1 | r343h889e2dd_0 491 KB
> > r-gtools-3.5.0 | r343h7f474d2_4 130 KB
> > r-httr-1.3.1 | r343h889e2dd_0 269 KB
> > r-jsonlite-1.5 | r343h7f474d2_0 583 KB
> > r-kernlab-0.9_25 | r343h9f775be_0 1.6 MB
> > r-memoise-1.1.0 | r343h889e2dd_0 32 KB
> > r-mime-0.5 | r343h7f474d2_0 28 KB
> > r-openssl-0.9.9 | r343h7f474d2_0 510 KB
> > r-r6-2.2.2 | r343h889e2dd_0 230 KB
> > r-randomforest-4.6_12 | r343h883f7c5_4 146 KB
> > r-rocr-1.0_7 | r343h889e2dd_4 152 KB
> > r-rstudioapi-0.7 | r343h889e2dd_0 109 KB
> > r-whisker-0.3_2 | r343h889e2dd_4 48 KB
> > r-withr-2.1.1 | r343h889e2dd_0 121 KB
> > readline-7.0 | hc1231fa_4 314 KB
> > xz-5.2.5 | h1de35cc_0 282 KB
> > ------------------------------------------------------------
> > Total: 35.3 MB
> >
> > The following NEW packages will be INSTALLED:
> >
> > _r-mutex pkgs/r/osx-64::_r-mutex-1.0.0-anacondar_1
> > bwidget pkgs/main/osx-64::bwidget-1.9.11-1
> > bzip2 pkgs/main/osx-64::bzip2-1.0.8-h1de35cc_0
> > ca-certificates pkgs/main/osx-64::ca-certificates-2020.1.1-0
> > cairo pkgs/main/osx-64::cairo-1.14.12-hc4e6be7_4
> > cctools pkgs/main/osx-64::cctools-895-1
> > clang pkgs/main/osx-64::clang-4.0.1-1
> > clang_osx-64 pkgs/main/osx-64::clang_osx-64-4.0.1-h1ce6c1d_18
> > clangxx pkgs/main/osx-64::clangxx-4.0.1-1
> > clangxx_osx-64 pkgs/main/osx-64::clangxx_osx-64-4.0.1-h22b1bf0_18
> > compiler-rt pkgs/main/osx-64::compiler-rt-4.0.1-hcfea43d_1
> > curl pkgs/main/osx-64::curl-7.61.1-ha441bb4_0
> > fontconfig pkgs/main/osx-64::fontconfig-2.13.0-h5d5b041_1
> > freetype pkgs/main/osx-64::freetype-2.9.1-hb4e5f40_0
> > fribidi pkgs/main/osx-64::fribidi-1.0.5-h1de35cc_0
> > gettext pkgs/main/osx-64::gettext-0.19.8.1-h15daf44_3
> > gfortran_osx-64 pkgs/main/osx-64::gfortran_osx-64-4.8.5-h22b1bf0_8
> > glib pkgs/main/osx-64::glib-2.63.1-hd977a24_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-1.8.8-hb8d4a28_0
> > icu pkgs/main/osx-64::icu-58.2-h4b95b61_1
> > jpeg pkgs/main/osx-64::jpeg-9b-he5867d9_2
> > krb5 pkgs/main/osx-64::krb5-1.14.2-h9a779f2_6
> > ld64 pkgs/main/osx-64::ld64-274.2-1
> > libcurl pkgs/main/osx-64::libcurl-7.61.1-hf30b1f0_0
> > libcxx pkgs/main/osx-64::libcxx-4.0.1-hcfea43d_1
> > libcxxabi pkgs/main/osx-64::libcxxabi-4.0.1-hcfea43d_1
> > libffi pkgs/main/osx-64::libffi-3.2.1-h475c297_4
> > libgfortran pkgs/main/osx-64::libgfortran-3.0.1-h93005f0_2
> > libiconv pkgs/main/osx-64::libiconv-1.15-hdd342a3_7
> > libpng pkgs/main/osx-64::libpng-1.6.37-ha441bb4_0
> > libssh2 pkgs/main/osx-64::libssh2-1.8.0-h322a93b_4
> > libtiff pkgs/main/osx-64::libtiff-4.1.0-hcb84e12_0
> > libxml2 pkgs/main/osx-64::libxml2-2.9.9-hf6e021a_1
> > llvm pkgs/main/osx-64::llvm-4.0.1-1
> > llvm-lto-tapi pkgs/main/osx-64::llvm-lto-tapi-4.0.1-1
> > llvm-openmp pkgs/main/osx-64::llvm-openmp-4.0.1-hcfea43d_1
> > ncurses pkgs/main/osx-64::ncurses-6.0-hd04f020_2
> > openssl pkgs/main/osx-64::openssl-1.0.2u-h1de35cc_0
> > pango pkgs/main/osx-64::pango-1.42.4-h060686c_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-bitops pkgs/r/osx-64::r-bitops-1.0_6-r343h7f474d2_4
> > r-boot pkgs/r/osx-64::r-boot-1.3_20-r343h889e2dd_0
> > r-catools pkgs/r/osx-64::r-catools-1.17.1-r343he124285_4
> > 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-curl pkgs/r/osx-64::r-curl-3.1-r343h7f474d2_0
> > r-devtools pkgs/r/osx-64::r-devtools-1.13.4-r343he124285_0
> > r-digest pkgs/r/osx-64::r-digest-0.6.13-r343h7f474d2_0
> > r-e1071 pkgs/r/osx-64::r-e1071-1.6_8-r343he124285_0
> > r-foreign pkgs/r/osx-64::r-foreign-0.8_69-r343h7f474d2_0
> > r-gdata pkgs/r/osx-64::r-gdata-2.18.0-r343h889e2dd_0
> > r-git2r pkgs/r/osx-64::r-git2r-0.20.0-r343h7f474d2_0
> > r-gplots pkgs/r/osx-64::r-gplots-3.0.1-r343h889e2dd_0
> > r-gtools pkgs/r/osx-64::r-gtools-3.5.0-r343h7f474d2_4
> > r-httr pkgs/r/osx-64::r-httr-1.3.1-r343h889e2dd_0
> > r-jsonlite pkgs/r/osx-64::r-jsonlite-1.5-r343h7f474d2_0
> > r-kernlab pkgs/r/osx-64::r-kernlab-0.9_25-r343h9f775be_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-memoise pkgs/r/osx-64::r-memoise-1.1.0-r343h889e2dd_0
> > r-mgcv pkgs/r/osx-64::r-mgcv-1.8_22-r343h7f474d2_0
> > r-mime pkgs/r/osx-64::r-mime-0.5-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-openssl pkgs/r/osx-64::r-openssl-0.9.9-r343h7f474d2_0
> > r-r6 pkgs/r/osx-64::r-r6-2.2.2-r343h889e2dd_0
> > r-randomforest pkgs/r/osx-64::r-randomforest-4.6_12-r343h883f7c5_4
> > r-recommended pkgs/r/osx-64::r-recommended-3.4.3-r343_0
> > r-rocr pkgs/r/osx-64::r-rocr-1.0_7-r343h889e2dd_4
> > r-rpart pkgs/r/osx-64::r-rpart-4.1_11-r343h7f474d2_0
> > r-rstudioapi pkgs/r/osx-64::r-rstudioapi-0.7-r343h889e2dd_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
> > r-whisker pkgs/r/osx-64::r-whisker-0.3_2-r343h889e2dd_4
> > r-withr pkgs/r/osx-64::r-withr-2.1.1-r343h889e2dd_0
> > readline pkgs/main/osx-64::readline-7.0-hc1231fa_4
> > tk pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
> > tktable pkgs/main/osx-64::tktable-2.10-h1de35cc_0
> > xz pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
> > zlib pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3
> > zstd pkgs/main/osx-64::zstd-1.3.7-h5bba6e5_0
> >
> >
> > Proceed ([y]/n)? y
> >
> >
> > Downloading and Extracting Packages
> > r-mime-0.5 | 28 KB | ##################################### | 100%
> > r-jsonlite-1.5 | 583 KB | ##################################### | 100%
> > gsl-2.4 | 1.8 MB | ##################################### | 100%
> > r-r6-2.2.2 | 230 KB | ##################################### | 100%
> > krb5-1.14.2 | 1.0 MB | ##################################### | 100%
> > r-curl-3.1 | 348 KB | ##################################### | 100%
> > r-openssl-0.9.9 | 510 KB | ##################################### | 100%
> > r-rstudioapi-0.7 | 109 KB | ##################################### | 100%
> > r-withr-2.1.1 | 121 KB | ##################################### | 100%
> > readline-7.0 | 314 KB | ##################################### | 100%
> > r-memoise-1.1.0 | 32 KB | ##################################### | 100%
> > r-catools-1.17.1 | 162 KB | ##################################### | 100%
> > r-gdata-2.18.0 | 937 KB | ##################################### | 100%
> > libcurl-7.61.1 | 327 KB | ##################################### | 100%
> > r-gplots-3.0.1 | 491 KB | ##################################### | 100%
> > r-httr-1.3.1 | 269 KB | ##################################### | 100%
> > r-bitops-1.0_6 | 24 KB | ##################################### | 100%
> > openssl-1.0.2u | 2.0 MB | ##################################### | 100%
> > r-digest-0.6.13 | 114 KB | ##################################### | 100%
> > libssh2-1.8.0 | 204 KB | ##################################### | 100%
> > r-devtools-1.13.4 | 417 KB | ##################################### | 100%
> > r-randomforest-4.6_1 | 146 KB | ##################################### | 100%
> > r-rocr-1.0_7 | 152 KB | ##################################### | 100%
> > r-kernlab-0.9_25 | 1.6 MB | ##################################### | 100%
> > r-e1071-1.6_8 | 667 KB | ##################################### | 100%
> > ncurses-6.0 | 699 KB | ##################################### | 100%
> > curl-7.61.1 | 122 KB | ##################################### | 100%
> > xz-5.2.5 | 282 KB | ##################################### | 100%
> > r-git2r-0.20.0 | 852 KB | ##################################### | 100%
> > r-base-3.4.3 | 20.8 MB | ##################################### | 100%
> > r-gtools-3.5.0 | 130 KB | ##################################### | 100%
> > r-whisker-0.3_2 | 48 KB | ##################################### | 100%
> > Preparing transaction: done
> > Verifying transaction: done
> > Executing transaction: done
> >
> > Apologies for the hesitation, but what is the next step? can I go next in the command line to require(devtools), or is there another step?
> >
> >
> > Thanks!
> >
> > Steven
> > From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of
> > Matthew Webster <[log in to unmask]>
> > Sent: Friday, April 17, 2020 8:39 AM
> > To: [log in to unmask] <[log in to unmask]>
> > Subject: Re: [FSL] Issue with FIX - trouble downloading R
> >
> > Hi Steven,
> > It looks like you might be missing the updated "-n Rtest” option from the conda call - can you double-check the line?
> >
> > Kind Regards
> > Matthew
> > --------------------------------
> > Dr Matthew Webster
> > FMRIB Centre
> > John Radcliffe Hospital
> > University of Oxford
> >
> >> On 17 Apr 2020, at 13:37, Manning, Steven T. <[log in to unmask]> wrote:
> >>
> >> Matthew,
> >>
> >> It appears the error is in the installation of the software packages.
> >> Here is the output, but based on my interpretation, the needed R
> >> software packages aren't being installed
> >>
> >> (Rtest) Stevens-MBP:~ manning.343$ sudo 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 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.
> >> Collecting package metadata (repodata.json): done Solving
> >> environment: failed with initial frozen solve. Retrying with flexible solve.
> >> Solving environment: -
> >> Found conflicts! Looking for incompatible packages.
> >> This can take several minutes. Press CTRL-C to abort.
> >> Examining conflict for r-devtools r-rocr r-kernlab python r-e1071 r-randomforestExamining conflict for r-devtools r-rocr r-kernlab r-e1071 r-randomforest r-clasExamining conflict for r-devtools r-rocr r-kernlab r-e1071 r-randomforest r-clasExamining conflict for r-devtools r-rocr r-kernlab r-e1071 r-class: 25%|▎| 2/8 Examining conflict for r-devtools r-rocr r-kernlab r-e1071 r-class: 38%|▍| 3/8 Examining conflict for r-e1071 r-kernlab r-devtools python: 38%|▍| 3/8 [00:05<0Examining conflict for r-e1071 r-kernlab r-devtools python: 50%|▌| 4/8 [00:05<0Examining conflict for r-devtools python: 50%|█▌ | 4/8 [00:05<00:04, 1.20s/it]Examining conflict for r-e1071 r-class r-devtools: 75%|▊| 6/8 [00:05<00:01, 1.Examining conflict for r-devtools r-rocr r-e1071 r-randomforest r-class: 88%|▉|Examining conflict for r-devtools r-rocr r-e1071 r-randomforest r-class: 100%|█| failed
> >>
> >> UnsatisfiableError: The following specifications were found to be incompatible with each other:
> >>
> >> Output in format: Requested package -> Available versions
> >>
> >> Package mro-base conflicts for:
> >> r-class=7.3_14 -> mro-base=3.5.0
> >> r-devtools -> r-jsonlite -> mro-base=3.5.0
> >> r-e1071=1.6_8 -> r-class -> mro-base=3.5.0
> >>
> >> Package r-class conflicts for:
> >> r-class=7.3_14
> >> r-e1071=1.6_8 -> r-class
> >>
> >> Package r-base conflicts for:
> >> r-devtools ->
> >> r-base[version='3.2.0.*|3.2.1.*|3.2.2.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4
> >> .2,<3.4.3a0|>=3.4.3,<3.4.4.0a0|>=3.5.0,<3.5.1.0a0|>=3.5.1,<3.5.2.0a0|
> >> >=3.6,<3.7.0a0'] r-devtools -> r-jsonlite -> r-base=3.1.3
> >>
> >> Package curl conflicts for:
> >> r-kernlab=0.9_25 -> r-base[version='>=3.5.0,<3.5.1.0a0'] -> curl
> >> r-class=7.3_14 -> r-base[version='>=3.5.1,<3.5.2.0a0'] ->
> >> curl[version='>=7.58.0']
> >> r-rocr=1.0_7 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> curl
> >> r-randomforest=4.6_12 -> r-base[version='>=3.4.3,<3.4.4.0a0'] -> curl
> >> r-devtools -> r-base[version='>=3.6,<3.7.0a0'] -> curl
> >> r-e1071=1.6_8 -> r-base[version='>=3.5.0,<3.5.1.0a0'] -> curl
> >>
> >> Package libopenblas conflicts for:
> >> r-kernlab=0.9_25 -> libopenblas
> >> r-class=7.3_14 -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> libopenblas[version='>=0.2.20,<0.2.21.0a0']
> >> r-devtools -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> libopenblas[version='>=0.2.20,<0.2.21.0a0']
> >> r-kernlab=0.9_25 -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> libopenblas[version='>=0.2.20,<0.2.21.0a0']
> >> r-e1071=1.6_8 -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> libopenblas[version='>=0.2.20,<0.2.21.0a0']
> >> r-rocr=1.0_7 -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> libopenblas[version='>=0.2.20,<0.2.21.0a0']
> >>
> >> Package libcxxabi conflicts for:
> >> r-e1071=1.6_8 -> libcxx[version='>=4.0.1'] ->
> >> libcxxabi==4.0.1[build='hcfea43d_1|hebd6815_0']
> >> python=3.7 -> libcxx[version='>=4.0.1'] ->
> >> libcxxabi==4.0.1[build='hcfea43d_1|hebd6815_0']
> >> r-kernlab=0.9_25 -> libcxx[version='>=4.0.1'] ->
> >> libcxxabi==4.0.1[build='hcfea43d_1|hebd6815_0']
> >> r-devtools -> libcxx[version='>=4.0.1'] ->
> >> libcxxabi==4.0.1[build='hcfea43d_1|hebd6815_0']
> >>
> >> Package ncurses conflicts for:
> >> r-e1071=1.6_8 -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> ncurses[version='5.9.*|6.0.*|>=6.1,<7.0a0|>=6.0,<7.0a0']
> >> r-kernlab=0.9_25 -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> ncurses[version='6.0.*|>=6.1,<7.0a0|>=6.0,<7.0a0']
> >> python=3.7 -> ncurses[version='>=6.1,<7.0a0|>=6.2,<7.0a0']
> >> r-devtools -> r-base[version='>=3.6,<3.7.0a0'] ->
> >> ncurses[version='5.9.*|6.0.*|>=6.1,<7.0a0|>=6.0,<7.0a0|>=5.9*']
> >> r-rocr=1.0_7 -> r-base[version='>=3.5.1,<3.5.2.0a0'] ->
> >> ncurses[version='5.9.*|6.0.*|>=6.1,<7.0a0|>=6.0,<7.0a0|>=5.9*']
> >> python=3.7 -> readline[version='>=7.0,<8.0a0'] ->
> >> ncurses[version='6.0.*|>=6.0,<7.0a0']
> >> r-class=7.3_14 -> r-base[version='>=3.5.1,<3.5.2.0a0'] ->
> >> ncurses[version='5.9.*|6.0.*|>=6.1,<7.0a0|>=6.0,<7.0a0|>=5.9*']
> >> r-randomforest=4.6_12 -> r-base[version='>=3.4.3,<3.4.4.0a0'] ->
> >> ncurses[version='5.9.*|6.0.*|>=6.0,<7.0a0|>=5.9*']
> >>
> >> Package libgcc conflicts for:
> >> r-e1071=1.6_8 -> libgcc
> >> r-rocr=1.0_7 -> r-base=3.2.2 -> libgcc r-devtools -> libgcc
> >> r-randomforest=4.6_12 -> libgcc
> >> r-class=7.3_14 -> libgcc
> >>
> >> Package _r-mutex conflicts for:
> >> r-devtools -> _r-mutex=1[build=anacondar_1] r-devtools -> r-jsonlite
> >> -> _r-mutex=1[build=mro_2]
> >>
> >> Package openssl conflicts for:
> >> r-devtools -> r-git2r[version='>=0.23.0'] ->
> >> openssl[version='>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>
> >> =1.1.1b,<1.1.2a']
> >> python=3.7 ->
> >> openssl[version='>=1.0.2o,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>
> >> =1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a']
> >> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf
> >> of Matthew Webster <[log in to unmask]>
> >> Sent: Friday, April 17, 2020 8:31 AM
> >> To: [log in to unmask] <[log in to unmask]>
> >> Subject: Re: [FSL] Issue with FIX - trouble downloading R
> >>
> >> Hi,
> >> Is the error message the one about "/Users/manning.343/.conda/envs/.conda_envs_dir_test”? If so, then a recursive chown to make /Users/manning.343/.conda globally writeable might fix things ( assuming it’s not a shared system ). Also does it look like the actual install worked ( conda install -n Rtest R=3.4 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 ) or is the error occurring before installation?
> >>
> >> Kind Regards
> >> Matthew
> >>
> >> --------------------------------
> >> Dr Matthew Webster
> >> FMRIB Centre
> >> John Radcliffe Hospital
> >> University of Oxford
> >>
> >> > On 17 Apr 2020, at 12:52, Manning, Steven T. <[log in to unmask]> wrote:
> >> >
> >> > Hello,
> >> >
> >> > I apologize for reaching out again, but I’m not sure how else to proceed as I have been continuing to run into problems. I would love to be able to run this analysis, but I cannot seem to run without errors. How should I proceed?
> >> >
> >> > Thank you,
> >> >
> >> > Steven
> >> >
> >> >
> >> > From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of Manning, Steven T.
> >> > Sent: Wednesday, April 15, 2020 8:46 PM
> >> > To: [log in to unmask]
> >> > Subject: Re: [FSL] Issue with FIX - trouble downloading R
> >> >
> >> > Matthew,
> >> >
> >> > Thanks for your reply. If I've tried running your code through the terminal and still ran into the same problem discussed below, what should I do next?
> >> >
> >> > Thanks,
> >> >
> >> > Steven
> >> > From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf
> >> > of Matthew Webster <[log in to unmask]>
> >> > Sent: Friday, April 10, 2020 12:02 PM
> >> > To: [log in to unmask] <[log in to unmask]>
> >> > Subject: Re: [FSL] Issue with FIX - trouble downloading R
> >> >
> >> > Hi Steven,
> >> > Apologies - all the conda commands should be run with sudo ( to match the main FSL install ).
> >> >
> >> > Kind Regards
> >> > Matthew
> >> > --------------------------------
> >> > Dr Matthew Webster
> >> > FMRIB Centre
> >> > John Radcliffe Hospital
> >> > University of Oxford
> >> >
> >> >
> >> > On 10 Apr 2020, at 13:11, Manning, Steven T. <[log in to unmask]> wrote:
> >> >
> >> > Matthew,
> >> >
> >> > I try and run conda without sudo, and it doesn't allow me to use conda without sudo. Is there a way I can override?
> >> >
> >> > NotWritableError: The current user does not have write permissions to a required path.
> >> > path: /Users/manning.343/.conda/envs/.conda_envs_dir_test
> >> > uid: 501
> >> > gid: 20
> >> >
> >> > If you feel that permissions on this path are set incorrectly, you
> >> > can manually change them by executing
> >> >
> >> > $ sudo chown 501:20
> >> > /Users/manning.343/.conda/envs/.conda_envs_dir_test
> >> >
> >> > In general, it's not advisable to use 'sudo conda'.
> >> >
> >> > Thanks
> >> > From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf
> >> > of Matthew Webster <[log in to unmask]>
> >> > Sent: Friday, April 10, 2020 5:12 AM
> >> > To: [log in to unmask] <[log in to unmask]>
> >> > Subject: Re: [FSL] Issue with FIX - trouble downloading R
> >> >
> >> > Hi Steven,
> >> > Looking at the conda side of things, sudo changes things a bit, can you retry with the following commands:
> >> >
> >> >
> >> > $FSLDIR/fslpython/bin/conda create -n Rtest. ****Should already be
> >> > done**** conda install -n Rtest R=3.4 r-rocr=1.0_7 r-kernlab=0.9_25
> >> > r-randomForest=4.6_12 r-class=7.3_14 r-e1071=1.6_8 r-devtools
> >> >
> >> > *****from within R*******
> >> > require(devtools)
> >> > chooseCRANmirror()
> >> > install_version("mvtnorm", version="1.0-8”)
> >> > install_version("multcomp", version="1.4-8”)
> >> > install_version("coin", version="1.2-2”) install_version("party",
> >> > version="1.0-25”)
> >> > ***************************
> >> >
> >> > I’m not sure about the Matlab error, but it’s worth seeing if we can get the conda installation sorted first.
> >> >
> >> > Kind Regards
> >> > Matthew
> >> > --------------------------------
> >> > Dr Matthew Webster
> >> > FMRIB Centre
> >> > John Radcliffe Hospital
> >> > University of Oxford
> >> >
> >> >
> >> > On 9 Apr 2020, at 22:06, Manning, Steven T. <[log in to unmask]> wrote:
> >> >
> >> > Matthew,
> >> >
> >> > Thank you for your suggestions. Unfortunately, your suggestion on how to download R from the terminal did not seem to work. Here is what the output said:
> >> > tevens-MBP:~ manning.343$ sudo $FSLDIR/fslpython/bin/conda create
> >> > -n Rtest
> >> > Password:
> >> > Collecting package metadata (current_repodata.json): done Solving
> >> > environment: done
> >> >
> >> > ## Package Plan ##
> >> >
> >> > environment location: /usr/local/fsl/fslpython/envs/Rtest
> >> >
> >> >
> >> >
> >> > Proceed ([y]/n)? y
> >> >
> >> > Preparing transaction: done
> >> > Verifying transaction: done
> >> > Executing transaction: done
> >> > #
> >> > # To activate this environment, use #
> >> > # $ conda activate Rtest
> >> > #
> >> > # To deactivate an active environment, use #
> >> > # $ conda deactivate
> >> >
> >> > Stevens-MBP:~ manning.343$ . $FSLDIR/fslpython/bin/activate Rtest
> >> > (Rtest) Stevens-MBP:~ manning.343$ conda install R=3.4 Collecting
> >> > package metadata (current_repodata.json): failed
> >> >
> >> > NotWritableError: The current user does not have write permissions to a required path.
> >> > path: /Users/manning.343/.conda/pkgs/urls.txt
> >> > uid: 501
> >> > gid: 20
> >> >
> >> > If you feel that permissions on this path are set incorrectly, you
> >> > can manually change them by executing
> >> >
> >> > $ sudo chown 501:20 /Users/manning.343/.conda/pkgs/urls.txt
> >> >
> >> > In general, it's not advisable to use 'sudo conda'.
> >> >
> >> >
> >> > (Rtest) Stevens-MBP:~ manning.343$ sudo conda install R=3.4
> >> > Collecting package metadata (current_repodata.json): done Solving
> >> > environment: done
> >> >
> >> > # All requested packages already installed.
> >> >
> >> > (Rtest) Stevens-MBP:~ manning.343$ sudo 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 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.
> >> > Collecting package metadata (repodata.json): done Solving
> >> > environment: failed with initial frozen solve. Retrying with flexible solve.
> >> > Solving environment: -
> >> > Found conflicts! Looking for incompatible packages.
> >> > This can take several minutes. Press CTRL-C to abort.
> >> > Examining conflict for r-devtools r-rocr r-kernlab python r-e1071 r-randomforestExamining conflict for r-devtools r-rocr r-kernlab r-e1071 r-randomforest r-clasExamining conflict for r-devtools r-rocr r-kernlab r-e1071 r-randomforest r-clasExamining conflict for r-devtools r-rocr r-kernlab r-e1071 r-class: 25%|▎| 2/8 Examining conflict for r-devtools r-rocr r-kernlab r-e1071 r-class: 38%|▍| 3/8 Examining conflict for r-e1071 r-kernlab r-devtools python: 38%|▍| 3/8 [00:05<0Examining conflict for r-e1071 r-kernlab r-devtools python: 50%|▌| 4/8 [00:05<0Examining conflict for r-devtools python: 50%|█▌ | 4/8 [00:05<00:04, 1.20s/it]Examining conflict for r-e1071 r-class r-devtools: 75%|▊| 6/8 [00:05<00:01, 1.Examining conflict for r-devtools r-rocr r-e1071 r-randomforest r-class: 88%|▉|Examining conflict for r-devtools r-rocr r-e1071 r-randomforest r-class: 100%|█| failed
> >> >
> >> > UnsatisfiableError: The following specifications were found to be incompatible with each other:
> >> >
> >> > Output in format: Requested package -> Available versions
> >> >
> >> > Package mro-base conflicts for:
> >> > r-class=7.3_14 -> mro-base=3.5.0
> >> > r-devtools -> r-jsonlite -> mro-base=3.5.0
> >> > r-e1071=1.6_8 -> r-class -> mro-base=3.5.0
> >> >
> >> > Package r-class conflicts for:
> >> > r-class=7.3_14
> >> > r-e1071=1.6_8 -> r-class
> >> >
> >> > Package r-base conflicts for:
> >> > r-devtools ->
> >> > r-base[version='3.2.0.*|3.2.1.*|3.2.2.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3
> >> > .4.2,<3.4.3a0|>=3.4.3,<3.4.4.0a0|>=3.5.0,<3.5.1.0a0|>=3.5.1,<3.5.2.
> >> > 0a0|>=3.6,<3.7.0a0'] r-devtools -> r-jsonlite -> r-base=3.1.3
> >> >
> >> > Package curl conflicts for:
> >> > r-kernlab=0.9_25 -> r-base[version='>=3.5.0,<3.5.1.0a0'] -> curl
> >> > r-class=7.3_14 -> r-base[version='>=3.5.1,<3.5.2.0a0'] ->
> >> > curl[version='>=7.58.0']
> >> > r-rocr=1.0_7 -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> curl
> >> > r-randomforest=4.6_12 -> r-base[version='>=3.4.3,<3.4.4.0a0'] ->
> >> > curl r-devtools -> r-base[version='>=3.6,<3.7.0a0'] -> curl
> >> > r-e1071=1.6_8 -> r-base[version='>=3.5.0,<3.5.1.0a0'] -> curl
> >> >
> >> > Package libopenblas conflicts for:
> >> > r-kernlab=0.9_25 -> libopenblas
> >> > r-class=7.3_14 -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> > libopenblas[version='>=0.2.20,<0.2.21.0a0']
> >> > r-devtools -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> > libopenblas[version='>=0.2.20,<0.2.21.0a0']
> >> > r-kernlab=0.9_25 -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> > libopenblas[version='>=0.2.20,<0.2.21.0a0']
> >> > r-e1071=1.6_8 -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> > libopenblas[version='>=0.2.20,<0.2.21.0a0']
> >> > r-rocr=1.0_7 -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> > libopenblas[version='>=0.2.20,<0.2.21.0a0']
> >> >
> >> > Package libcxxabi conflicts for:
> >> > r-e1071=1.6_8 -> libcxx[version='>=4.0.1'] ->
> >> > libcxxabi==4.0.1[build='hcfea43d_1|hebd6815_0']
> >> > python=3.7 -> libcxx[version='>=4.0.1'] ->
> >> > libcxxabi==4.0.1[build='hcfea43d_1|hebd6815_0']
> >> > r-kernlab=0.9_25 -> libcxx[version='>=4.0.1'] ->
> >> > libcxxabi==4.0.1[build='hcfea43d_1|hebd6815_0']
> >> > r-devtools -> libcxx[version='>=4.0.1'] ->
> >> > libcxxabi==4.0.1[build='hcfea43d_1|hebd6815_0']
> >> >
> >> > Package ncurses conflicts for:
> >> > r-e1071=1.6_8 -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> > ncurses[version='5.9.*|6.0.*|>=6.1,<7.0a0|>=6.0,<7.0a0']
> >> > r-kernlab=0.9_25 -> r-base[version='>=3.5.0,<3.5.1.0a0'] ->
> >> > ncurses[version='6.0.*|>=6.1,<7.0a0|>=6.0,<7.0a0']
> >> > python=3.7 -> ncurses[version='>=6.1,<7.0a0|>=6.2,<7.0a0']
> >> > r-devtools -> r-base[version='>=3.6,<3.7.0a0'] ->
> >> > ncurses[version='5.9.*|6.0.*|>=6.1,<7.0a0|>=6.0,<7.0a0|>=5.9*']
> >> > r-rocr=1.0_7 -> r-base[version='>=3.5.1,<3.5.2.0a0'] ->
> >> > ncurses[version='5.9.*|6.0.*|>=6.1,<7.0a0|>=6.0,<7.0a0|>=5.9*']
> >> > python=3.7 -> readline[version='>=7.0,<8.0a0'] ->
> >> > ncurses[version='6.0.*|>=6.0,<7.0a0']
> >> > r-class=7.3_14 -> r-base[version='>=3.5.1,<3.5.2.0a0'] ->
> >> > ncurses[version='5.9.*|6.0.*|>=6.1,<7.0a0|>=6.0,<7.0a0|>=5.9*']
> >> > r-randomforest=4.6_12 -> r-base[version='>=3.4.3,<3.4.4.0a0'] ->
> >> > ncurses[version='5.9.*|6.0.*|>=6.0,<7.0a0|>=5.9*']
> >> >
> >> > Package libgcc conflicts for:
> >> > r-e1071=1.6_8 -> libgcc
> >> > r-rocr=1.0_7 -> r-base=3.2.2 -> libgcc r-devtools -> libgcc
> >> > r-randomforest=4.6_12 -> libgcc
> >> > r-class=7.3_14 -> libgcc
> >> >
> >> > Package _r-mutex conflicts for:
> >> > r-devtools -> _r-mutex=1[build=anacondar_1] r-devtools ->
> >> > r-jsonlite -> _r-mutex=1[build=mro_2]
> >> >
> >> > Package openssl conflicts for:
> >> > r-devtools -> r-git2r[version='>=0.23.0'] ->
> >> > openssl[version='>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a
> >> > |>=1.1.1b,<1.1.2a']
> >> > python=3.7 ->
> >> > openssl[version='>=1.0.2o,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a
> >> > |>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a']
> >> >
> >> >
> >> >
> >> >
> >> > I tried to download R as an application, download the necessary packages, and try to run fix again. Here is what the logMatlab.txt file said:
> >> > ------------------------------------------
> >> > Setting up environment variables
> >> > ---
> >> > DYLD_LIBRARY_PATH is
> >> > .:/Applications/MATLAB/MATLAB_Runtime/v96/runtime/maci64:/Applicati
> >> > ons/MATLAB/MATLAB_Runtime/v96/bin/maci64:/Applications/MATLAB/MATLA
> >> > B_Runtime/v96/sys/os/maci64
> >> > /Users/manning.343/Desktop/FSL/1002NA/NiFTI/DOG_run1_MELODICPreProc.Prox.feat/
> >> > 62 1
> >> >
> >> > /bin/sh -c '. /usr/local/fsl/etc/fslconf/fsl.sh; fslmaths
> >> > /Users/manning.343/Desktop/FSL/1002NA/NiFTI/DOG_run1_MELODICPreProc
> >> > .Prox.feat/fix/dummy -abs
> >> > /Users/manning.343/Desktop/FSL/1002NA/NiFTI/DOG_run1_MELODICPreProc
> >> > .Prox.feat/fix/dummyabs': Aborted Error Time: 04/09/2020 16:56:48
> >> > Error using call_fsl (line 36) FSL call (/bin/sh -c '.
> >> > /usr/local/fsl/etc/fslconf/fsl.sh; fslmaths
> >> > /Users/manning.343/Desktop/FSL/1002NA/NiFTI/DOG_run1_MELODICPreProc
> >> > .Prox.feat/fix/dummy -abs
> >> > /Users/manning.343/Desktop/FSL/1002NA/NiFTI/DOG_run1_MELODICPreProc
> >> > .Prox.feat/fix/dummyabs') failed, Image Exception : #63 :: No image
> >> > files match:
> >> > /Users/manning.343/Desktop/FSL/1002NA/NiFTI/DOG_run1_MELODICPreProc
> >> > .Prox.feat/fix/dummy
> >> > libc++abi.dylib: terminating with uncaught exception of type
> >> > libc++std::runtime_error: No image files match:
> >> > libc++/Users/manning.343/Desktop/FSL/1002NA/NiFTI/DOG_run1_MELODICP
> >> > libc++reProc.Prox.feat/fix/dummy
> >> > /bin/sh: line 1: 16059 Abort trap: 6 fslmaths /Users/manning.343/Desktop/FSL/1002NA/NiFTI/DOG_run1_MELODICPreProc.Prox.feat/fix/dummy -abs /Users/manning.343/Desktop/FSL/1002NA/NiFTI/DOG_run1_MELODICPreProc.Prox.feat/fix/dummyabs
> >> >
> >> > Thanks for your help
> >> >
> >> > From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf
> >> > of Matthew Webster <[log in to unmask]>
> >> > Sent: Thursday, April 9, 2020 10:52 AM
> >> > To: [log in to unmask] <[log in to unmask]>
> >> > Subject: Re: [FSL] Issue with FIX - trouble downloading R
> >> >
> >> > Hi,
> >> > You can try downloading R separately and updating the FIX settings
> >> > to use that, although I did notice from your log that you’re
> >> > installing into the root conda environment, which may potentially
> >> > be an issue. On OSX 10.14.6, the following works for me
> >> >
> >> > $FSLDIR/fslpython/bin/conda create -n Rtest .
> >> > $FSLDIR/fslpython/bin/activate Rtest conda install R=3.4 conda
> >> > install r-rocr=1.0_7 r-kernlab=0.9_25 r-randomForest=4.6_12
> >> > r-class=7.3_14 r-e1071=1.6_8 r-devtools
> >> >
> >> > require(devtools)
> >> > chooseCRANmirror()
> >> > install_version("mvtnorm", version="1.0-8”)
> >> > install_version("multcomp", version="1.4-8”)
> >> > install_version("coin", version="1.2-2”) install_version("party",
> >> > version="1.0-25”)
> >> >
> >> > Note that this method creates a new environment, rather than using fslpython, to speed up the install process ( and allowing it to be cleanly removed ).
> >> >
> >> > Hope this helps,
> >> > Kind Regards,
> >> > Matthew
> >> > --------------------------------
> >> > Dr Matthew Webster
> >> > FMRIB Centre
> >> > John Radcliffe Hospital
> >> > University of Oxford
> >> >
> >> >
> >> > On 9 Apr 2020, at 15:45, Manning, Steven T. <[log in to unmask]> wrote:
> >> >
> >> > Hello experts,
> >> >
> >> > I am attempting to work through FIX and continuing to run into trouble. The latest error appears to be a combination of an issue with the call_fsl line as I am performing features extraction, as well as I don’t believe I have successfully downloaded the needed R packages to perform the analysis. I have attached a couple documents: the logMatlab.txt file detailing the errors and the output from trying to download the needed R packages.
> >> >
> >> > Can I download R separately, install the needed packages through the R software itself, then direct the FIX pipeline to find those files? I’m continually running into errors, and unfortunately have little computer coding experience.
> >> >
> >> > Thank you very much!
> >> >
> >> > Steven Manning
> >> >
> >> >
> >> >
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> >> > FXCVSHgE6rvmfPDE0TaWYZ6W-uygg3Na7xRaKnqzjYA$
> >> > <Output from attempting to download R and necessary
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