Thanks, Tim! I followed your advice and I am almost there… How did you install
randomForest' version 4.6.12? I am getting the following error:
install_version("randomForest", version = "4.6-12", repos =
"http://cran.us.r-project.org”)
(…)
/var/tmp//ccP5LbYW.s:2671:2: error: unknown directive
.stabn 224,0,0,LBE141
^
/var/tmp//ccP5LbYW.s:2673:9: error: unsupported directive '.stabs'
.stabs "",36,0,0,Lscope8-LFBB8
^
/var/tmp//ccP5LbYW.s:2697:9: error: unsupported directive '.stabs'
.stabs "",100,0,0,Letext0
^
/var/tmp//ccP5LbYW.s:2835:11: warning: section "__textcoal_nt" is deprecated
.section __TEXT,__textcoal_nt,coalesced,pure_instructions
^ ~~~~~~~~~~~~~
/var/tmp//ccP5LbYW.s:2835:11: note: change section name to "__text"
.section __TEXT,__textcoal_nt,coalesced,pure_instructions
^ ~~~~~~~~~~~~~
make: *** [rfsub.o] Error 1
ERROR: compilation failed for package ‘randomForest’
* removing
‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/randomForest’
Installation failed: Command failed (1)
Thanks!
-L
> On May 27, 2018, at 9:12 PM, Timothy Coalson <[email protected]> wrote:
>
> The way I solved this was to use the very latest R version (cran mirrors
> contain debian and ubuntu packages, see
> http://cran.wustl.edu/bin/linux/ubuntu/
> <http://cran.wustl.edu/bin/linux/ubuntu/> , and they also have OS X binaries:
> http://cran.wustl.edu/bin/macosx/ <http://cran.wustl.edu/bin/macosx/> ), then
> install devtools (this is the main reason for installing the latest R, as
> getting devtools installed in older R is an even bigger pain), and then use
> "install_version":
> https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages
>
> <https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages>
>
> Tim
>
>
> On Sun, May 27, 2018 at 3:32 PM, Marta Moreno <[email protected]
> <mailto:[email protected]>> wrote:
> I am using workbench v1.3. I have used R v3.3, R v3.4.and R v3.5. None of
> them allowed me to install specified software packages versions required to
> run hcp_fix: ('kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071'
> version 1.6.7 or 'randomForest' version 4.6.12), so I guess the error I am
> getting now is regarding this issue. I have pasted the error below:
>
> Error in ctreefit(object = object, controls = controls, weights = weights, :
> no slot of name "remove_weights" for this object of class "TreeGrowControl"
> Calls: eval -> eval -> <Anonymous> -> ctreefit
> Execution halted
>
> Please advice on which R version should I have installed to make it to work.
> I have downloaded software packages and installing them in R as root as
> follow:
> > install.packages('/Users/alayar/Downloads/kernlab_0.9-24.tar',
> > dependencies=TRUE)
> Warning message:
> package ‘/Users/alayar/Downloads/kernlab_0.9-24.tar’ is not available (for R
> version 3.3.3)
>
> Thanks!
>
> -L
>
>> On May 27, 2018, at 4:24 PM, Glasser, Matthew <[email protected]
>> <mailto:[email protected]>> wrote:
>>
>> There is no relationship between R and Workbench (or R and matlab). As to a
>> Workbench/matlab incompatibility, we would need to know what version of
>> Workbench and matlab to debug this.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Marta Moreno <[email protected]
>> <mailto:[email protected]>>
>> Date: Sunday, May 27, 2018 at 3:22 PM
>> To: "[email protected] <mailto:[email protected]>"
>> <[email protected] <mailto:[email protected]>>
>> Cc: Matt Glasser <[email protected] <mailto:[email protected]>>, HCP Users
>> <[email protected] <mailto:[email protected]>>
>> Subject: Re: [HCP-Users] error running hcp_fix
>>
>> Thanks, but with newer versions is not working either because R software
>> packages such as 'kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071'
>> version 1.6.7 or 'randomForest' version 4.6.12, are incompatible with R 3.3
>> or 3.5. At least based on my experience. So could you please let me know
>> which is the R version I need to install to have it compatible with
>> workbench and also compatible with R software packages listed above that are
>> needed to run hcp_fix? I am using a MAC pro, with workbench v1.3.
>>
>> This is becoming a nightmare so I would really appreciate your help.
>>
>> Thanks!,
>>
>> -L
>>
>>> On May 27, 2018, at 3:04 AM, [email protected]
>>> <mailto:[email protected]> wrote:
>>>
>>> Hi - we've seen this in the past with specific combinations of matlab
>>> version and workbench version. I'm not quite sure if the very latest
>>> versions of both have the issue or not.
>>> Cheers.
>>>
>>>
>>>> On 27 May 2018, at 02:32, Marta Moreno <[email protected]
>>>> <mailto:[email protected]>> wrote:
>>>>
>>>> I found the following error, please advice: (before is giving me some
>>>> warnings about different functions that has same name as a Matlab builtin,
>>>> I have pasted the output from last warning and first error).
>>>>
>>>> Which are the files that needs to be included in ‘CIFTIMatlabReaderWriter’
>>>> for the settings.sh?
>>>>
>>>> Warning: Function subsref has the same name as a MATLAB builtin. We
>>>> suggest you
>>>> rename the function to avoid a potential name conflict.
>>>> > In path (line 109)
>>>> In fix_3_clean (line 45)
>>>> /bin/bash: /usr/local/workbench/bin_macosx64: is a directory
>>>> Error using read_gifti_file_standalone (line 20)
>>>> [GIFTI] Loading of XML file
>>>> /private/var/folders/j2/__433pcd02l1cw9qkydkqs5h0000gn/T/tp6555679429695603.gii
>>>> failed.
>>>>
>>>> Error in gifti (line 71)
>>>> this = read_gifti_file_standalone(varargin{1},giftistruct);
>>>>
>>>> Error in ciftiopen (line 31)
>>>> cifti = gifti([tmpfile '.gii']);
>>>>
>>>> Error in fix_3_clean (line 46)
>>>> BO=ciftiopen('Atlas.dtseries.nii',WBC);
>>>>
>>>> Thanks!
>>>>
>>>> -L
>>>>
>>>>
>>>>> On May 26, 2018, at 6:55 PM, Marta Moreno <[email protected]
>>>>> <mailto:[email protected]>> wrote:
>>>>>
>>>>> You were right, now the problem is gone but still cannot find my
>>>>> clean.dtseries
>>>>>
>>>>> Here is the output, I could not find any error in .ica folder:
>>>>> hcp_fix RS_fMRI_1.nii.gz 2000
>>>>> processing FMRI file RS_fMRI_1 with highpass 2000
>>>>> running highpass
>>>>> running MELODIC
>>>>> running FIX
>>>>> FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica
>>>>> create edge masks
>>>>> run FAST
>>>>> registration of standard space masks
>>>>> extract features
>>>>> FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica
>>>>> using training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData
>>>>> and threshold 10
>>>>> FIX Applying cleanup using cleanup file:
>>>>> RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup
>>>>> set to 1
>>>>>
>>>>> Please advice.
>>>>>
>>>>> Thanks!
>>>>>
>>>>> -L
>>>>>
>>>>>
>>>>>> On May 26, 2018, at 2:52 PM, Glasser, Matthew <[email protected]
>>>>>> <mailto:[email protected]>> wrote:
>>>>>>
>>>>>> Perhaps you are running out of memory.
>>>>>>
>>>>>> Peace,
>>>>>>
>>>>>> Matt.
>>>>>>
>>>>>> From: <[email protected]
>>>>>> <mailto:[email protected]>> on behalf of Marta
>>>>>> Moreno <[email protected] <mailto:[email protected]>>
>>>>>> Date: Saturday, May 26, 2018 at 1:50 PM
>>>>>> To: HCP Users <[email protected]
>>>>>> <mailto:[email protected]>>
>>>>>> Subject: [HCP-Users] error running hcp_fix
>>>>>>
>>>>>> Dear experts,
>>>>>>
>>>>>> I am getting the following error. Please advice:
>>>>>>
>>>>>> hcp_fix RS_fMRI_1.nii.gz 2000
>>>>>> processing FMRI file RS_fMRI_1 with highpass 2000
>>>>>> running highpass
>>>>>> running MELODIC
>>>>>> running FIX
>>>>>> FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica
>>>>>> create edge masks
>>>>>> run FAST
>>>>>> registration of standard space masks
>>>>>> extract features
>>>>>> FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica
>>>>>> using training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData
>>>>>> and threshold 10
>>>>>> FIX Applying cleanup using cleanup file:
>>>>>> RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup
>>>>>> set to 1
>>>>>> sh: line 1: 10513 Killed: 9
>>>>>> /Applications/MATLAB_R2017b.app/bin/matlab -nojvm -nodisplay -nodesktop
>>>>>> -nosplash -r "addpath('/usr/local/fix1.065');
>>>>>> addpath('/usr/local/fsl/etc/matlab'); fix_3_clean('.fix',0,1,2000)" >>
>>>>>> .fix.log 2>&1
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> -L
>>>>>>
>>>>>> _______________________________________________
>>>>>> HCP-Users mailing list
>>>>>> [email protected] <mailto:[email protected]>
>>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
>>>>> _______________________________________________
>>>>> HCP-Users mailing list
>>>>> [email protected] <mailto:[email protected]>
>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
>>>> _______________________________________________
>>>> HCP-Users mailing list
>>>> [email protected] <mailto:[email protected]>
>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
>>>
>>> ---------------------------------------------------------------------------
>>> Stephen M. Smith, Professor of Biomedical Engineering
>>> Head of Analysis, Oxford University FMRIB Centre
>>>
>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>> +44 (0) 1865 222726 (fax 222717)
>>> [email protected] <mailto:[email protected]>
>>> http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve>
>>> ---------------------------------------------------------------------------
>>>
>>> Stop the cultural destruction of Tibet <http://smithinks.net/>
>>>
>>>
>>>
>>>
>>>
>>
>
>
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