Hi Belinda,
This now looks very close to being complete, if the first two install_version commands ( install_version("mvtnorm", version="1.0-8”) install_version("multcomp", version="1.4-8”) ) appeared to go OK, then can you try:
install_version("coin", version="1.2-2",dependencies=FALSE)
This should make R request manual confirmation to (re-)install the previous packages - select the no/skip/bypass option and hopefully only coin should be downloaded and installed.
Hope this helps,
Kind regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 17 Oct 2020, at 20:04, Lennerz, Belinda <[log in to unmask]> wrote:
>
> Hi Matthew,
> I re-did all steps from root, and am now stuck again where i was before.
> Can you please advise?
> Thank you so much!!
> Belinda
>
> I have performed steps:
> sudo su -
> export FSLDIR=/usr/local/fsl
> $FSLDIR/fslpython/bin/conda create -n fslR
> . $FSLDIR/fslpython/bin/activate fslR
> $FSLDIR/fslpython/bin/conda install -c conda-forge -n fslR R=3.4 r-rocr=1.0_7 r-kernlab=0.9_25 r-randomForest=4.6_12 r-class=7.3_14 r-e1071=1.6_8 r-devtools clangxx_osx-64 clang_osx-64
> export CONDA_BUILD_SYSROOT=$(xcrun --show-sdk-path)
> $FSLDIR/fslpython/envs/fslR/bin/R
> require(devtools)
> chooseCRANmirror()
> install_version("mvtnorm", version="1.0-8")
> install_version("multcomp", version="1.4-8")
>
> When attempting
> install_version("coin", version="1.2-2")
>
> I get the following:
>
> > install_version("coin", version="1.2-2")
> Downloading package from url: https://cran.case.edu/src/contrib/Archive/coin/coin_1.2-2.tar.gz
> Downloading package from url: https://cran.case.edu/src/contrib/Archive/multcomp/multcomp_1.4-8.tar.gz
> Downloading package from url: https://cran.case.edu/src/contrib/Archive/mvtnorm/mvtnorm_1.0-8.tar.gz
> * installing *source* package 'mvtnorm' ...
> ** package 'mvtnorm' successfully unpacked and MD5 sums checked
> ** libs
> clang -I/usr/local/fsl/fslpython/envs/fslR/lib/R/include -DNDEBUG -I/usr/local/fsl/fslpython/envs/fslR/include -fPIC -I/usr/local/fsl/fslpython/envs/fslR/include -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
> clang -I/usr/local/fsl/fslpython/envs/fslR/lib/R/include -DNDEBUG -I/usr/local/fsl/fslpython/envs/fslR/include -fPIC -I/usr/local/fsl/fslpython/envs/fslR/include -c miwa.c -o miwa.o
> gfortran -fPIC -I/usr/local/fsl/fslpython/envs/fslR/include -L/usr/local/fsl/fslpython/envs/fslR/lib -c mvt.f -o mvt.o
> clang -I/usr/local/fsl/fslpython/envs/fslR/lib/R/include -DNDEBUG -I/usr/local/fsl/fslpython/envs/fslR/include -fPIC -I/usr/local/fsl/fslpython/envs/fslR/include -c mvtnorm-init.c -o mvtnorm-init.o
> gfortran -fPIC -I/usr/local/fsl/fslpython/envs/fslR/include -L/usr/local/fsl/fslpython/envs/fslR/lib -c tvpack.f -o tvpack.o
> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/fsl/fslpython/envs/fslR/lib/R/lib -arch x86_64 -L/usr/local/fsl/fslpython/envs/fslR/lib -lgfortran -L/usr/local/fsl/fslpython/envs/fslR -o mvtnorm.so C_FORTRAN_interface.o miwa.o mvt.o mvtnorm-init.o tvpack.o -L/usr/local/fsl/fslpython/envs/fslR/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5 -L/usr/local/fsl/fslpython/envs/fslR/lib/gcc -lgfortran -lquadmath -lm -L/usr/local/fsl/fslpython/envs/fslR/lib/R/lib -lR -lintl -lc -Wl,-framework -Wl,CoreFoundation
> ld: warning: directory not found for option '-L/usr/local/fsl/fslpython/envs/fslR/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5'
> ld: warning: directory not found for option '-L/usr/local/fsl/fslpython/envs/fslR/lib/gcc'
> installing to /usr/local/fsl/fslpython/envs/fslR/lib/R/library/mvtnorm/libs
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (mvtnorm)
> * installing *source* package 'multcomp' ...
> ** package 'multcomp' successfully unpacked and MD5 sums checked
> ** R
> ** data
> *** moving datasets to lazyload DB
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (multcomp)
> Downloading package from url: https://cran.case.edu/src/contrib/Archive/mvtnorm/mvtnorm_1.0-8.tar.gz
> Skipping mvtnorm, it is already being installed
> Error in vapply(remotes, install_remote, ..., FUN.VALUE = character(1)) :
> values must be type 'character',
> but FUN(X[[2]]) result is type 'logical'
> >
>
>
>
> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Matthew Webster <[log in to unmask]>
> Sent: Friday, October 16, 2020 4:14 PM
> To: [log in to unmask]
> Subject: Re: installing R for FIX [EXTERNAL]
>
> * External Email - Caution *
>
> Dear Belinda,
> There seems to a strange issue with dependencies here, it’s possible your system might have a conda config file modifying the default channels.
>
> Can you ( in a sudo’d terminal session ) deactivate and then remove the fslR env:
>
> $FSLDIR/fslpython/bin/conda deactivate
> $FSLDIR/fslpython/bin/conda env remove -n fslR
>
> recreate and reactivate with:
>
> $FSLDIR/fslpython/bin/conda create -n fslR
> . $FSLDIR/fslpython/bin/activate fslR
>
> And then try the all-in-one install:
>
> $FSLDIR/fslpython/bin/conda install -c defaults -n fslR 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 clangxx_osx-64 clang_osx-64
>
> If that doesn’t work, then delete/recreate fslR again and try:
>
> $FSLDIR/fslpython/bin/conda install -c conda-forge -n fslR R=3.4 r-rocr=1.0_7 r-kernlab=0.9_25 r-randomForest=4.6_12 r-class=7.3_14 r-e1071=1.6_8 r-devtools clangxx_osx-64 clang_osx-64
>
> If one of these works ( both work on my test system ), then you should be fine to proceed from the "export CONDA_BUILD_SYSROOT=$(xcrun --show-sdk-path)” line in the instructions.
>
> Hope this helps,
> Kind Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
>
>> On 16 Oct 2020, at 17:53, Belinda Lennerz <[log in to unmask]> wrote:
>>
>> Dear Matthew,
>> Thank you so much for this suggestion. Unfortunately, I am running into the same issues with package installations (copied below). I checked X-Code, and it seems to give the expected readout:
>>
>> Last login: Fri Oct 16 12:25:07 on ttys000
>> xcrun --show-sdk-path% (base) blennerz@x86_64-apple-darwin13 ~ % xcrun --show-sdk-path
>> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
>> (base) blennerz@x86_64-apple-darwin13 ~ %
>>
>> Do you have any additional thoughts?
>> Thank you for your support!!
>> Belinda
>>
>> Last login: Fri Oct 16 12:23:34 on ttys001
>> (base) blennerz@x86_64-apple-darwin13 ~ % conda deactivate
>> blennerz@x86_64-apple-darwin13 ~ % sudo su -
>> Password:
>> belindas-macbook-pro:~ root# export FSLDIR=/usr/local/fsl
>> belindas-macbook-pro:~ root# $FSLDIR/fslpython/bin/conda create -n fslR
>> Collecting package metadata (current_repodata.json): done
>> Solving environment: done
>>
>> ## Package Plan ##
>>
>> environment location: /usr/local/fsl/fslpython/envs/fslR
>>
>>
>>
>> Proceed ([y]/n)? y
>>
>> Preparing transaction: done
>> Verifying transaction: done
>> Executing transaction: done
>> #
>> # To activate this environment, use
>> #
>> # $ conda activate fslR
>> #
>> # To deactivate an active environment, use
>> #
>> # $ conda deactivate
>>
>> belindas-macbook-pro:~ root# . $FSLDIR/fslpython/bin/activate fslR
>> (fslR) belindas-macbook-pro:~ root# $FSLDIR/fslpython/bin/conda install -n fslR R=3.4
>> 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/fslR
>>
>> added / updated specs:
>> - r=3.4
>>
>>
>> The following NEW packages will be INSTALLED:
>>
>> _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1
>> c-ares conda-forge/osx-64::c-ares-1.16.1-haf1e3a3_3
>> ca-certificates conda-forge/osx-64::ca-certificates-2020.6.20-hecda079_0
>> cairo conda-forge/osx-64::cairo-1.14.12-he6fea26_5
>> curl conda-forge/osx-64::curl-7.71.1-hcb81553_8
>> fontconfig conda-forge/osx-64::fontconfig-2.13.1-h1e4e890_1000
>> freetype conda-forge/osx-64::freetype-2.9.1-h5a5313f_1004
>> gettext conda-forge/osx-64::gettext-0.19.8.1-h46ab8bc_1002
>> glib conda-forge/osx-64::glib-2.55.0-h464dc38_2
>> graphite2 conda-forge/osx-64::graphite2-1.3.13-h12caacf_1001
>> gsl conda-forge/osx-64::gsl-2.6-ha2d443c_0
>> harfbuzz conda-forge/osx-64::harfbuzz-1.9.0-h08d66d9_0
>> icu conda-forge/osx-64::icu-58.2-h0a44026_1000
>> jpeg conda-forge/osx-64::jpeg-9d-h0b31af3_0
>> krb5 conda-forge/osx-64::krb5-1.17.1-h1752a42_0
>> libblas conda-forge/osx-64::libblas-3.8.0-17_openblas
>> libcblas conda-forge/osx-64::libcblas-3.8.0-17_openblas
>> libcurl conda-forge/osx-64::libcurl-7.71.1-h9bf37e3_8
>> libcxx conda-forge/osx-64::libcxx-11.0.0-h439d374_0
>> libedit conda-forge/osx-64::libedit-3.1.20170329-0
>> libev conda-forge/osx-64::libev-4.33-haf1e3a3_1
>> libffi conda-forge/osx-64::libffi-3.2.1-hb1e8313_1007
>> libgcc conda-forge/osx-64::libgcc-4.8.5-1
>> libgfortran conda-forge/osx-64::libgfortran-5.0.0-h7cc5361_12
>> libgfortran5 conda-forge/osx-64::libgfortran5-9.3.0-h7cc5361_12
>> libiconv conda-forge/osx-64::libiconv-1.16-haf1e3a3_0
>> libnghttp2 conda-forge/osx-64::libnghttp2-1.41.0-h7580e61_2
>> libopenblas conda-forge/osx-64::libopenblas-0.3.10-openmp_h54245bb_5
>> libpng conda-forge/osx-64::libpng-1.6.34-ha92aebf_2
>> libssh2 conda-forge/osx-64::libssh2-1.9.0-h8a08a2b_5
>> libtiff conda-forge/osx-64::libtiff-4.0.9-h79f4b77_1002
>> libxml2 conda-forge/osx-64::libxml2-2.9.9-hd80cff7_2
>> llvm-openmp conda-forge/osx-64::llvm-openmp-11.0.0-h73239a0_1
>> ncurses conda-forge/osx-64::ncurses-5.9-10
>> openssl conda-forge/osx-64::openssl-1.1.1h-haf1e3a3_0
>> pango conda-forge/osx-64::pango-1.40.14-h1401c9d_1002
>> pcre conda-forge/osx-64::pcre-8.39-0
>> pixman conda-forge/osx-64::pixman-0.34.0-h1de35cc_1003
>> r conda-forge/osx-64::r-3.4.1-r3.4.1_0
>> r-base conda-forge/osx-64::r-base-3.4.1-4
>> r-boot conda-forge/osx-64::r-boot-1.3_20-r341_0
>> r-class conda-forge/osx-64::r-class-7.3_14-r341hc070d10_2
>> r-cluster conda-forge/osx-64::r-cluster-2.0.6-r3.4.1_0
>> r-codetools conda-forge/osx-64::r-codetools-0.2_15-r341h6115d3f_1
>> r-foreign conda-forge/osx-64::r-foreign-0.8_71-r341hc070d10_2
>> r-kernsmooth conda-forge/osx-64::r-kernsmooth-2.23_15-r3.4.1_0
>> r-lattice conda-forge/osx-64::r-lattice-0.20_35-r341hc070d10_0
>> r-mass conda-forge/osx-64::r-mass-7.3_50-r341hc070d10_2
>> r-matrix conda-forge/osx-64::r-matrix-1.2_14-r341hc070d10_2
>> r-mgcv conda-forge/osx-64::r-mgcv-1.8_24-r341hc070d10_2
>> r-nlme conda-forge/osx-64::r-nlme-3.1_131-r3.4.1_0
>> r-nnet conda-forge/osx-64::r-nnet-7.3_12-r341hc070d10_2
>> r-recommended conda-forge/osx-64::r-recommended-3.4.1-r3.4.1_0
>> r-rpart conda-forge/osx-64::r-rpart-4.1_13-r341hc070d10_2
>> r-spatial conda-forge/osx-64::r-spatial-7.3_11-r341hc070d10_2
>> r-survival conda-forge/osx-64::r-survival-2.42_6-r341hc070d10_1
>> readline conda-forge/osx-64::readline-7.0-0
>> tk conda-forge/osx-64::tk-8.6.10-hb0a8c7a_1
>> xz conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
>> zlib conda-forge/osx-64::zlib-1.2.11-h7795811_1010
>>
>>
>> Proceed ([y]/n)? y
>>
>> Preparing transaction: done
>> Verifying transaction: done
>> Executing transaction: done
>> (fslR) belindas-macbook-pro:~ root# $FSLDIR/fslpython/bin/conda install -n fslR 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 clangxx_osx-64 clang_osx-64
>> 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-kernsmooth libblas gsl r-matrix r-base r-mgcv libcblas:Examining conflict for libblas gsl r-base: : 73it [02:16, 3.81it/s] Examining conflict for clang_osx-64 clangxx_osx-64 r-base: : 75it [02:17, 2.05iExamining conflict for clang_osx-64 clangxx_osx-64 r-base: : 76it [02:17, 1.92iExamining conflict for libev libcurl libnghttp2: : 76it [02:18, 1.92it/s] failed |
>>
>> UnsatisfiableError: The following specifications were found to be incompatible with each other:
>>
>> Output in format: Requested package -> Available versions
>>
>>
>
>
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