Dear Marta,
It’s quite important to make sure that the correct commands are called - can you try the following commands specifically ( from the previous link )
$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
The dot (.) followed by a space in the activate line is very important, so that the subsequent commands work with the new environment.
If the installation works with no errors, you should then be able to start R and run the remaining installs ( require(devtools) etc… )
Hope this helps,
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 29 Nov 2019, at 16:46, Marta Moreno <[log in to unmask]> wrote:
>
> Dear Matthew,
>
> I am not familiar with this method so I am not sure. I am in /usr/local/fsl/fslpython/bin and running all commands form there (conda create -n Rtest, activate Rtest, conda install R=3.4, etc.) Please advice.
>
> Thanks,
>
> Marta
>
>
>> On Nov 29, 2019, at 11:38 AM, Matthew Webster <[log in to unmask]> wrote:
>>
>> Dear Marta,
>> Can you confirm that you’re installing into the activated Rtest environment that you created in the previous steps?
>>
>> Kind Regards
>> Matthew
>> --------------------------------
>> Dr Matthew Webster
>> FMRIB Centre
>> John Radcliffe Hospital
>> University of Oxford
>>
>>> On 29 Nov 2019, at 15:25, Marta Moreno <[log in to unmask]> wrote:
>>>
>>> Dear Mathew,
>>>
>>> I followed the instructions from the link you gave me but I am getting the following errors. Please advise.
>>>
>>> Thanks,
>>>
>>> Marta
>>>
>>>
>>> Error here:
>>>
>>> Leahs-iMac-Pro:bin root# 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.
>>> failed
>>>
>>> UnsatisfiableError: The following specifications were found to be incompatible with each other:
>>>
>>>
>>>
>>> Package r-base conflicts for:
>>> r-class=7.3_14 -> r-base[version='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']
>>> 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-rocr=1.0_7 -> 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-randomforest=4.6_12 -> r-base[version='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']
>>> r-kernlab=0.9_25 -> r-base[version='>=3.4.2,<3.4.3a0|>=3.4.3,<3.4.4.0a0|>=3.5.0,<3.5.1.0a0']
>>> r-e1071=1.6_8 -> r-base[version='3.4.1.*|>=3.4.2,<3.4.3a0|>=3.4.3,<3.4.4.0a0|>=3.5.0,<3.5.1.0a0']
>>> Package r-pkgbuild conflicts for:
>>> r-devtools -> r-pkgbuild[version='>=1.0.2']
>>> Package ncurses conflicts for:
>>> python=3.7 -> ncurses[version='>=6.1,<7.0a0']
>>> Package libcxx conflicts for:
>>> r-devtools -> libcxx[version='>=4.0.1']
>>> python=3.7 -> libcxx[version='>=4.0.1']
>>> r-e1071=1.6_8 -> libcxx[version='>=4.0.1']
>>> r-kernlab=0.9_25 -> libcxx[version='>=4.0.1']
>>> Package r-git2r conflicts for:
>>> r-devtools -> r-git2r[version='>=0.11.0|>=0.23.0']
>>> Package r-curl conflicts for:
>>> r-devtools -> r-curl[version='>=0.9']
>>> Package r-digest conflicts for:
>>> r-devtools -> r-digest
>>> Package _r-mutex conflicts for:
>>> r-e1071=1.6_8 -> _r-mutex=1[build=anacondar_1]
>>> r-class=7.3_14 -> _r-mutex=1[build='anacondar_1|mro_2']
>>> r-rocr=1.0_7 -> _r-mutex=1[build=anacondar_1]
>>> r-kernlab=0.9_25 -> _r-mutex=1[build=anacondar_1]
>>> r-randomforest=4.6_12 -> _r-mutex=1[build=anacondar_1]
>>> r-devtools -> _r-mutex=1[build=anacondar_1]
>>> Package sqlite conflicts for:
>>> python=3.7 -> sqlite[version='>=3.24.0,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.27.2,<4.0a0|>=3.29.0,<4.0a0|>=3.30.1,<4.0a0']
>>> Package r-sessioninfo conflicts for:
>>> r-devtools -> r-sessioninfo
>>> Package libgcc conflicts for:
>>> r-e1071=1.6_8 -> libgcc
>>> r-randomforest=4.6_12 -> libgcc
>>> r-devtools -> libgcc
>>> r-class=7.3_14 -> libgcc
>>> Package r-callr conflicts for:
>>> r-devtools -> r-callr
>>> Package r-rstudioapi conflicts for:
>>> r-devtools -> r-rstudioapi[version='>=0.2.0|>=0.6.0.9000']
>>> Package r-roxygen2 conflicts for:
>>> r-devtools -> r-roxygen2[version='>=4.1.0']
>>> Package openssl conflicts for:
>>> 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']
>>> Package pip conflicts for:
>>> python=3.7 -> pip
>>> Package r-remotes conflicts for:
>>> r-devtools -> r-remotes[version='>=2.0.2']
>>> Package r-withr conflicts for:
>>> r-devtools -> r-withr
>>> Package r-usethis conflicts for:
>>> r-devtools -> r-usethis[version='>=1.4.0']
>>> Package r-httr conflicts for:
>>> r-devtools -> r-httr[version='>=0.4']
>>> Package r-memoise conflicts for:
>>> r-devtools -> r-memoise[version='>=1.0.0']
>>> Package libgfortran conflicts for:
>>> r-randomforest=4.6_12 -> libgfortran[version='>=3.0.1']
>>> r-kernlab=0.9_25 -> libgfortran[version='>=3.0.1']
>>> Package r-rversions conflicts for:
>>> r-devtools -> r-rversions
>>> Package r-gplots conflicts for:
>>> r-rocr=1.0_7 -> r-gplots
>>> Package r-class conflicts for:
>>> r-e1071=1.6_8 -> r-class
>>> Package libopenblas conflicts for:
>>> r-kernlab=0.9_25 -> libopenblas
>>> Package r-jsonlite conflicts for:
>>> r-devtools -> r-jsonlite
>>> Package r-cli conflicts for:
>>> r-devtools -> r-cli
>>> Package r-rcmdcheck conflicts for:
>>> r-devtools -> r-rcmdcheck[version='>=1.3.2']
>>> Package r-whisker conflicts for:
>>> r-devtools -> r-whisker
>>> Package zlib conflicts for:
>>> python=3.7 -> zlib[version='>=1.2.11,<1.3.0a0']
>>> Package readline conflicts for:
>>> python=3.7 -> readline[version='>=7.0,<8.0a0']
>>> Package tk conflicts for:
>>> python=3.7 -> tk[version='>=8.6.7,<8.7.0a0|>=8.6.8,<8.7.0a0']
>>> Package r-mass conflicts for:
>>> r-class=7.3_14 -> r-mass[version='>=7.3.49,<7.3.50.0a0']
>>> Package r-pkgload conflicts for:
>>> r-devtools -> r-pkgload[version='>=1.0.1']
>>> Package libffi conflicts for:
>>> python=3.7 -> libffi[version='>=3.2.1,<4.0a0']
>>> Package r-evaluate conflicts for:
>>> r-devtools -> r-evaluate
>>> Package mro-base conflicts for:
>>> r-class=7.3_14 -> mro-base=3.5.0
>>> Package r-rcurl conflicts for:
>>> r-devtools -> r-rcurl
>>> Package xz conflicts for:
>>> python=3.7 -> xz[version='>=5.2.4,<6.0a0']
>>>
>>>> On Nov 27, 2019, at 8:29 AM, Matthew Webster <[log in to unmask]> wrote:
>>>>
>>>> Dear Marta,
>>>> We currently recommend installing the R dependencies via a conda-based method:
>>>>
>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1910&L=FSL&O=D&P=6293
>>>>
>>>> gives a series of commands that should work with 10.14.6.
>>>>
>>>> Kind Regards
>>>> Matthew
>>>> --------------------------------
>>>> Dr Matthew Webster
>>>> FMRIB Centre
>>>> John Radcliffe Hospital
>>>> University of Oxford
>>>>
>>>>> On 26 Nov 2019, at 21:02, Marta Moreno <[log in to unmask]> wrote:
>>>>>
>>>>> Dear experts,
>>>>>
>>>>> I am experiencing some problems installing these packages (see below) that I need to run ICAFIX. I have tried several R versions, clangs and gfortran versions. This is how I am trying to install them. Which R version do I need? What am I missing?
>>>>>
>>>>> I am using MacOs Mojave version 10.14.6 on iMac Pro 2017. It is being a nightmare so I would really appreciate your help.
>>>>>
>>>>> sudo -i
>>>>> R
>>>>> options(repos = c(CRAN = "https://cran.rstudio.com"))
>>>>> require(devtools)
>>>>>
>>>>> install_version("kernlab", version = "0.9-24", repos = "http://cran.us.r-project.org")
>>>>> install_version("party", version = "1.0-25", repos = "http://cran.us.r-project.org")
>>>>> install_version("e1071", version = "1.6-7", repos = "http://cran.us.r-project.org")
>>>>> install_version("randomForest", version = "4.6-12", repos = "http://cran.us.r-project.org")
>>>>>
>>>>> Thanks a lot,
>>>>>
>>>>> Marta
>>>>>
>>>>>
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>>>>>
>>>>
>>>>
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>>>
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>>
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