Dear Matthew,
Great, thanks so much for your help.
Have a nice day,
Marta
> On Dec 3, 2019, at 11:30 AM, Matthew Webster <[log in to unmask]> wrote:
>
> Dear Marta,
> The R binary should be the one within the Rtest environment bin folder ( something like $FSLDIR/fslpython/envs/Rtest/bin/R ). The kernlab version looks fine.
>
> Kind Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
>
>> On 2 Dec 2019, at 19:11, Marta Moreno <[log in to unmask]> wrote:
>>
>> Dear Matthew,
>>
>> I was able to run all commands now, thanks a lot.
>>
>> One more question, which R’s path should I put in my path to run hcp_fix now that R3.4 is installed this way?
>>
>> Also, I saw that the version for kernlab I have installed following your commands is r-kernlab=0.9_25 and not 'kernlab' version 0.9.24. Is that OK?
>>
>> Thanks a lot!
>>
>> Marta
>>
>>
>>
>>> On Dec 2, 2019, at 10:55 AM, Matthew Webster <[log in to unmask]> wrote:
>>>
>>> Dear Marta,
>>> Can you check you are running the command as the same user who owns the fsl directory? You can also try using the
>>>
>>> source
>>>
>>> Command instead of a dot, if that is failing for some reason.
>>>
>>> Kind Regards
>>> Matthew
>>>
>>> --------------------------------
>>> Dr Matthew Webster
>>> FMRIB Centre
>>> John Radcliffe Hospital
>>> University of Oxford
>>>
>>>> On 29 Nov 2019, at 17:48, Marta Moreno <[log in to unmask]> wrote:
>>>>
>>>> Dear Matthew,
>>>>
>>>> I am having problems with the (.) followed by a space. I am getting the following error:
>>>>
>>>> . $FSLDIR/fslpython/bin/activate Rtest
>>>> .: Permission denied.
>>>>
>>>> Thanks,
>>>>
>>>> Marta
>>>>
>>>>> On Nov 29, 2019, at 11:54 AM, Matthew Webster <[log in to unmask]> wrote:
>>>>>
>>>>> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> To unsubscribe from the FSL list, click the following link:
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>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
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>>>>>
>>>>>
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