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:
>>>>>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> To unsubscribe from the FSL list, click the following link:
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>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> To unsubscribe from the FSL list, click the following link:
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>>>>>>>
>>>>>>
>>>>>>
>>>>>> To unsubscribe from the FSL list, click the following link:
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>>>>>>
>>>>>
>>>>>
>>>>> To unsubscribe from the FSL list, click the following link:
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>>>>>
>>>>
>>>>
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