On Nov 7, 2017, at 12:58 PM, Marta Moreno <[log in to unmask]> wrote:

I was able to install required versions with install.packages. Since they are current versions it seams you do not need to specify version to get them. 

I left the hcp_fix script running, will confirm later today if everything is ok.

You helped a lot, much appreciation.

On Nov 7, 2017, at 12:33 PM, Niels Bergsland <[log in to unmask]> wrote:

I guess you would have to try running it and seeing for yourself, but you should be able to find the correct versions. I'm not sure why they aren't showing up in that mirror, but here is the ROCR version 1.0.7 tgz, for example:

https://cran.r-project.org/src/contrib/ROCR_1.0-7.tar.gz

You might be able to find the other ones there too.

On Tue, Nov 7, 2017 at 6:17 PM, Marta Moreno <[log in to unmask]> wrote:

Thank you.

That link helped. I installed dev_tools and following packages on R version 4.3.2. But the packages highlighted in red were not available so I installed the closest. Is that a problem?

 The versions required/suggested are not available in http://cran.us.r-project.org.

> packageVersion('kernlab')

[1] ‘0.9.24’

> packageVersion('ROCR')

[1] ‘1.0.6’

> packageVersion('class')

[1] ‘7.3.13’

> packageVersion('party')

[1] ‘1.0.25’

> packageVersion('e1071')

[1] ‘1.6.7’

> packageVersion('randomForest')

[1] ‘4.6.10’

On Nov 7, 2017, at 10:39 AM, Niels Bergsland <[log in to unmask]> wrote:

Okay, it looks like you will need to follow the instructions here:

http://thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/

(The link has mavericks in the name, but a quick read shows that it's still relevant for Sierra)

On Tue, Nov 7, 2017 at 4:33 PM, Marta Moreno <[log in to unmask]> wrote:

Thanks.

I am using Mac Pro (Late 2013) and macOS Sierra version 10.12.15

Trying packageurl..., see below:

"(..) with some warnings, and then:

clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o kernlab.so brweight.o ctable.o cweight.o dbreakpt.o dcauchy.o dgpnrm.o dgpstep.o dprecond.o dprsrch.o dspcg.o dtron.o dtrpcg.o dtrqsol.o esa.o expdecayweight.o inductionsort.o kspectrumweight.o lcp.o misc.o msufsort.o solvebqp.o stringk.o stringkernel.o svm.o wkasailcp.o wmsufsort.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'

ld: library not found for -lquadmath

clang: error: linker command failed with exit code 1 (use -v to see invocation)

make: *** [kernlab.so] Error 1

ERROR: compilation failed for package ‘kernlab’

* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/kernlab’

* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/kernlab’

Warning message:

In install.packages(packageurl, repos = NULL, type = "source") :

  installation of package ‘/tmp/Rtmpz5x6QK/downloaded_packages/kernlab_0.9-24.tar.gz’ had non-zero exit status"

On Nov 7, 2017, at 10:29 AM, Niels Bergsland <[log in to unmask]> wrote:

Hmm, that's not something that I've run into myself. What kind of system are you running on?

What happens if you try installing it this way:

packageurl <- "https://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_0.9-24.tar.gz"
install.packages(packageurl, repos=NULL, type="source")

On Tue, Nov 7, 2017 at 4:21 PM, Marta Moreno <[log in to unmask]> wrote:

Thanks again.

I am getting an error with the installation, please advice. See below:

> install_version("kernlab", version = "0.9-24", repos = "http://cran.us.r-project.org")

Downloading package from url: http://cran.us.r-project.org/src/contrib/Archive/kernlab/kernlab_0.9-24.tar.gz

Installing kernlab

Installation failed: run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout),      stderr_line_callback = real_callback(stderr), stdout_callback = real_block_callback,      stderr_callback = real_block_callback, echo_cmd = echo, echo = show,      spinner = spinner, error_on_status = fail_on_status, timeout = timeout) : System command error

nstallation failed: run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout),      stderr_line_callback = real_callback(stderr), stdout_callback = real_block_callback,      stderr_callback = real_block_callback, echo_cmd = echo, echo = show,      spinner = spinner, error_on_status = fail_on_status, timeout = timeout) : System command error

On Nov 7, 2017, at 10:12 AM, Niels Bergsland <[log in to unmask]> wrote:

Sorry, I had a typo there, you need to specify the version the same way that it's listed in the archive link.

So it would be something like:

install_version("kernlab", version = "0.9-24", repos = "http://cran.us.r-project.org")

which will result in it pulling the following:

http://cran.us.r-project.org/src/contrib/Archive/kernlab/kernlab_0.9-24.tar.gz


On Tue, Nov 7, 2017 at 4:03 PM, Marta Moreno <[log in to unmask]> wrote:
>
> Thanks.
>
> I have installed dev_tools, and then type what was suggested for specific version but I am getting the following error
>
> > require(devtools)
> Loading required package: devtools
> > install_version("kernlab", version = "0.9.24", repos = "http://cran.us.r-project.org")
> Error in install_version("kernlab", version = "0.9.24", repos = "http://cran.us.r-project.org") :
>   version '0.9.24' is invalid for package ‘kernlab’
>
>
> On Nov 7, 2017, at 8:02 AM, Niels Bergsland <[log in to unmask]> wrote:
>
> You can't install specific versions that way. You can either install the package dev_tools so that you can do something like:
>
> install_version("kernlab", version = "0.9.24", repos = "http://cran.us.r-project.org")
>
> Otherwise you can something like:
>
> packageurl <- "https://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_0.9-24.tar.gz"
> install.packages(packageurl, repos=NULL, type="source")
>
>
>
> On Tue, Nov 7, 2017 at 1:46 PM, Marta Moreno <[log in to unmask]> wrote:
> >
> > Thanks.
> >
> > I am using R version 3.3.2 now but still I am getting same message of package not available, see below:
> > "install.packages("kernlab0.9.24", dependencies=TRUE)
> > package ‘kernlab_0.9.24’ is not available (for R version 3.3.2)"
> >
> > On Nov 7, 2017, at 7:37 AM, Niels Bergsland <[log in to unmask]> wrote:
> >
> > The list of packages is correct but it doesn't specify a specific version(s) of R itself to be used. Might be helpful for others to add when you get a chance.
> >
> > On Tue, Nov 7, 2017 at 1:28 PM, Stephen Smith <[log in to unmask]> wrote:
> >>
> >> hi - AFAIK the list at
> >> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide
> >> is up to date - but it's really hard to keep the R versions/package version numbering up to date because the R community keeps breaking compatibility with different versions......!
> >>
> >> Cheers.
> >>
> >>
> >>
> >> On 7 Nov 2017, at 12:20, Marta Moreno <[log in to unmask]> wrote:
> >>
> >> Thanks.
> >> What is the R version required to have these packageVersions installed? I am downgrading R and still package ‘kernlab_0.9.24’ is not available for the R version.
> >>
> >>
> >> On Nov 7, 2017, at 12:32 AM, Niels Bergsland <[log in to unmask]> wrote:
> >>
> >> Hi,
> >> If you install these specific versions, it should work as expected:
> >>
> >> > packageVersion('kernlab')
> >> [1] ‘0.9.24’
> >> > packageVersion('ROCR')
> >> [1] ‘1.0.7’
> >> > packageVersion('class')
> >> [1] ‘7.3.14’
> >> > packageVersion('party')
> >> [1] ‘1.0.25’
> >> > packageVersion('e1071')
> >> [1] ‘1.6.7’
> >> > packageVersion('randomForest')
> >> [1] ‘4.6.12’
> >>
> >>
> >> On Tue, Nov 7, 2017 at 04:54 Marta Moreno <[log in to unmask]> wrote:
> >>>
> >>> Dear experts,
> >>>
> >>> I am running hcp_fix and getting the following error:
> >>> "FIX Classifying components in Melodic directory: RS_fMRI_2_hp2000.ica using training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and threshold 10
> >>> No valid labelling file specified”
> >>>
> >>> In the log file: .fix_2b_predict.log, I found the following error message:
> >>> "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 -> .Call
> >>> Execution halted”
> >>>
> >>> I am running R 4.3.2 and packageVersion("party”) is 1.2.3. Fix version is 1.065. Please advice.
> >>>
> >>> Thank you,
> >>>
> >>> -L
> >>>
> >> --
> >> Niels Bergsland
> >> Integration Director / Research Assistant Professor of Neurology
> >> Buffalo Neuroimaging Analysis Center / University at Buffalo
> >> 100 High St. Buffalo NY 14203
> >> [log in to unmask]
> >>
> >>
> >>
> >>
> >> ---------------------------------------------------------------------------
> >> 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)
> >> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> >> ---------------------------------------------------------------------------
> >>
> >> Stop the cultural destruction of Tibet
> >>
> >>
> >>
> >>
> >>
> >
> >
> >
> > --
> > Niels Bergsland
> > Integration Director / Research Assistant Professor of Neurology
> > Buffalo Neuroimaging Analysis Center / University at Buffalo
> > 100 High St. Buffalo NY 14203
> > [log in to unmask]
> >
> >
>
>
>
> --
> Niels Bergsland
> Integration Director / Research Assistant Professor of Neurology
> Buffalo Neuroimaging Analysis Center / University at Buffalo
> 100 High St. Buffalo NY 14203
> [log in to unmask]
>
>



--
Niels Bergsland
Integration Director / Research Assistant Professor of Neurology
Buffalo Neuroimaging Analysis Center / University at Buffalo
100 High St. Buffalo NY 14203
[log in to unmask]

--

Niels Bergsland
Integration Director / Research Assistant Professor of Neurology
Buffalo Neuroimaging Analysis Center / University at Buffalo
100 High St. Buffalo NY 14203
[log in to unmask]

--

Niels Bergsland
Integration Director / Research Assistant Professor of Neurology
Buffalo Neuroimaging Analysis Center / University at Buffalo
100 High St. Buffalo NY 14203
[log in to unmask]

--

Niels Bergsland
Integration Director / Research Assistant Professor of Neurology
Buffalo Neuroimaging Analysis Center / University at Buffalo
100 High St. Buffalo NY 14203
[log in to unmask]