Dear Tim,
How did you install randomForest' version 4.6.12? I am getting the following
error (see below). Do I need R-devel as well to install randomForest? Please
advice this should be the last step before having hcp_fix running properly.
install_version("randomForest", version = "4.6-12", repos =
"http://cran.us.r-project.org <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 a lot!
-L
*******************************************
Leah Moreno, PhD
Associate Research Scientist
Division of Experimental Therapeutics
Department of Psychiatry
Columbia University Medical Center
1051 Riverside Drive, Unit 21
New York, NY 10032
phone: (914) 218-7311
email: [email protected]
email: [email protected]
> On May 27, 2018, at 11:20 PM, Marta Moreno <[email protected]> wrote:
>
> 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 <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]
>> <mailto:[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
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>>>>>> 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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