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ANTsR: towards CRAN & standardization of development #8

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stnava opened this issue Jan 26, 2015 · 188 comments
Open

ANTsR: towards CRAN & standardization of development #8

stnava opened this issue Jan 26, 2015 · 188 comments

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@stnava
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@stnava stnava commented Jan 26, 2015

@ntustison , @bkandel , @dorianps, @jeffduda , @cookpa , @armaneshaghi, @muschellij2

hoping to work toward a CRAN submission for ANTsR - some updates on this topic:

i ran rd2roxygen and dealt with most of the issues. hopefully wont have

to do that again ... so, in the future, we should write documentation

using the roxygen2 style and just roxygenize() regularly.

a couple other changes

  • enabled plot( antsImage ) so we dont need to type plotANTsImage
  • added resampleImage
  • updated invariantImageSimilarity to use reflection as well as rotation, only tested in 2D so far
  • added CreateJacobianDeterminantImage
  • added a simple kmeansSegmentation filter ...
  • would like to start running R CMD CHECK and get failures to a minimum ...
  • need to write a quick vignette, possibly based on the README.md ...

@muschellij2 - would appreciate any advice / help on this ....

some advice from wickham: http://www.rstudio.com/products/rpackages/devtools/

it's a very good page with strategies that will help with most of the issues we've had in the past ...

any thoughts appreciated.

@bkandel
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@bkandel bkandel commented Jan 26, 2015

I thought the major issue with CRAN was the size of the package. Did you
find a way to work around that?

On 26 January 2015 at 10:32, stnava notifications@github.com wrote:

@ntustison https://github.com/ntustison , @bkandel
https://github.com/bkandel , @dorianps https://github.com/dorianps,
@jeffduda https://github.com/jeffduda , @cookpa
https://github.com/cookpa , @armaneshaghi
https://github.com/armaneshaghi, @muschellij2
https://github.com/muschellij2

hoping to work toward a CRAN submission for ANTsR - some updates on this
topic:

i ran rd2roxygen and dealt with most of the issues. hopefully wont have

to do that again ... so, in the future, we should write documentation

using the roxygen2 style and just roxygenize() regularly.

a couple other changes

enabled plot( antsImage ) so we dont need to type plotANTsImage

added resampleImage

updated invariantImageSimilarity to use reflection as well as
rotation, only tested in 2D so far

added CreateJacobianDeterminantImage

added a simple kmeansSegmentation filter ...

would like to start running R CMD CHECK and get failures to a minimum
...

need to write a quick vignette, possibly based on the README.md ...

@muschellij2 https://github.com/muschellij2 - would appreciated any
advice / help on this ....

some advice from wickham:
http://www.rstudio.com/products/rpackages/devtools/

it's a very good page with strategies that will help with most of the
issues we've had in the past ...

any thoughts appreciated.


Reply to this email directly or view it on GitHub
#8.

@armaneshaghi
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@armaneshaghi armaneshaghi commented Jan 26, 2015

Brian, this is an excellent idea, and really essential for the whole community. I know R and Cpp both very well, but I have been involved only in ANTs development, and not ANTsR and would appreciate if you could give me pointers where you need help.

@armaneshaghi
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@armaneshaghi armaneshaghi commented Jan 26, 2015

Perhaps by assigning something (more specifically)

@stnava
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@stnava stnava commented Jan 26, 2015

cran policies are here

100MB is the limit which ANTsR just sneaks under (last i checked) after R
CMD Build

the package must pass on 2 platforms ( e.g. linux , osx ) for CRAN
acceptance ...

compile time might be an issue but this can likely be resolved by making
a thin ANTs build that focuses on only the programs necessary for ANTsR
... this could be done within a new ANTs branch that gets updated as needed.

i still see install_github or R CMD INSTALL being the way we employ ANTsR
but, for broader use, CRAN would be great. so hopefully we would branch
to thin ANTs only occasionally ... primarily, it would be a change to one
or maybe two CMakeLists.txt files ...

ref issue thin ants

brian

On Mon, Jan 26, 2015 at 10:43 AM, bkandel notifications@github.com wrote:

I thought the major issue with CRAN was the size of the package. Did you
find a way to work around that?

On 26 January 2015 at 10:32, stnava notifications@github.com wrote:

@ntustison https://github.com/ntustison , @bkandel
https://github.com/bkandel , @dorianps https://github.com/dorianps,
@jeffduda https://github.com/jeffduda , @cookpa
https://github.com/cookpa , @armaneshaghi
https://github.com/armaneshaghi, @muschellij2
https://github.com/muschellij2

hoping to work toward a CRAN submission for ANTsR - some updates on this
topic:

i ran rd2roxygen and dealt with most of the issues. hopefully wont have

to do that again ... so, in the future, we should write documentation

using the roxygen2 style and just roxygenize() regularly.

a couple other changes

enabled plot( antsImage ) so we dont need to type plotANTsImage

added resampleImage

updated invariantImageSimilarity to use reflection as well as

rotation, only tested in 2D so far

added CreateJacobianDeterminantImage

added a simple kmeansSegmentation filter ...

would like to start running R CMD CHECK and get failures to a minimum

...

need to write a quick vignette, possibly based on the README.md ...

@muschellij2 https://github.com/muschellij2 - would appreciated any
advice / help on this ....

some advice from wickham:
http://www.rstudio.com/products/rpackages/devtools/

it's a very good page with strategies that will help with most of the
issues we've had in the past ...

any thoughts appreciated.


Reply to this email directly or view it on GitHub
#8.


Reply to this email directly or view it on GitHub
#8 (comment).

@stnava
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@stnava stnava commented Jan 26, 2015

oops - just checked latest R CMD Build & it's quite large ... easy to
resolve with some carefully crafted rm calls ... will assign myself to that.

#9

brian

On Mon, Jan 26, 2015 at 11:12 AM, brian avants stnava@gmail.com wrote:

cran policies are here

100MB is the limit which ANTsR just sneaks under (last i checked) after R
CMD Build

the package must pass on 2 platforms ( e.g. linux , osx ) for CRAN
acceptance ...

compile time might be an issue but this can likely be resolved by making
a thin ANTs build that focuses on only the programs necessary for ANTsR
... this could be done within a new ANTs branch that gets updated as needed.

i still see install_github or R CMD INSTALL being the way we employ ANTsR
but, for broader use, CRAN would be great. so hopefully we would branch
to thin ANTs only occasionally ... primarily, it would be a change to one
or maybe two CMakeLists.txt files ...

ref issue thin ants

brian

On Mon, Jan 26, 2015 at 10:43 AM, bkandel notifications@github.com
wrote:

I thought the major issue with CRAN was the size of the package. Did you
find a way to work around that?

On 26 January 2015 at 10:32, stnava notifications@github.com wrote:

@ntustison https://github.com/ntustison , @bkandel
https://github.com/bkandel , @dorianps https://github.com/dorianps,

@jeffduda https://github.com/jeffduda , @cookpa
https://github.com/cookpa , @armaneshaghi
https://github.com/armaneshaghi, @muschellij2
https://github.com/muschellij2

hoping to work toward a CRAN submission for ANTsR - some updates on
this
topic:

i ran rd2roxygen and dealt with most of the issues. hopefully wont have

to do that again ... so, in the future, we should write documentation

using the roxygen2 style and just roxygenize() regularly.

a couple other changes

enabled plot( antsImage ) so we dont need to type plotANTsImage

added resampleImage

updated invariantImageSimilarity to use reflection as well as

rotation, only tested in 2D so far

added CreateJacobianDeterminantImage

added a simple kmeansSegmentation filter ...

would like to start running R CMD CHECK and get failures to a minimum

...

need to write a quick vignette, possibly based on the README.md ...

@muschellij2 https://github.com/muschellij2 - would appreciated any
advice / help on this ....

some advice from wickham:
http://www.rstudio.com/products/rpackages/devtools/

it's a very good page with strategies that will help with most of the
issues we've had in the past ...

any thoughts appreciated.


Reply to this email directly or view it on GitHub
#8.


Reply to this email directly or view it on GitHub
#8 (comment).

@bkandel
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@bkandel bkandel commented Jan 26, 2015

100 MB sounds ambitious to me if we're going to include ITK build--in my
current ANTsR build, the ITKv4-build dir alone is 392MB. I imagine that
most of this can be deleted safely, though, once ANTs is installed.

On 26 January 2015 at 11:16, stnava notifications@github.com wrote:

oops - just checked latest R CMD Build & it's quite large ... easy to
resolve with some carefully crafted rm calls ... will assign myself to
that.

#9

brian

On Mon, Jan 26, 2015 at 11:12 AM, brian avants stnava@gmail.com wrote:

cran policies are here

100MB is the limit which ANTsR just sneaks under (last i checked) after
R
CMD Build

the package must pass on 2 platforms ( e.g. linux , osx ) for CRAN
acceptance ...

compile time might be an issue but this can likely be resolved by
making
a thin ANTs build that focuses on only the programs necessary for
ANTsR
... this could be done within a new ANTs branch that gets updated as
needed.

i still see install_github or R CMD INSTALL being the way we employ
ANTsR
but, for broader use, CRAN would be great. so hopefully we would branch
to thin ANTs only occasionally ... primarily, it would be a change to
one
or maybe two CMakeLists.txt files ...

ref issue thin ants

brian

On Mon, Jan 26, 2015 at 10:43 AM, bkandel notifications@github.com
wrote:

I thought the major issue with CRAN was the size of the package. Did
you
find a way to work around that?

On 26 January 2015 at 10:32, stnava notifications@github.com wrote:

@ntustison https://github.com/ntustison , @bkandel
https://github.com/bkandel , @dorianps https://github.com/dorianps,

@jeffduda https://github.com/jeffduda , @cookpa
https://github.com/cookpa , @armaneshaghi
https://github.com/armaneshaghi, @muschellij2
https://github.com/muschellij2

hoping to work toward a CRAN submission for ANTsR - some updates on
this
topic:

i ran rd2roxygen and dealt with most of the issues. hopefully wont
have

to do that again ... so, in the future, we should write documentation

using the roxygen2 style and just roxygenize() regularly.

a couple other changes

enabled plot( antsImage ) so we dont need to type plotANTsImage

added resampleImage

updated invariantImageSimilarity to use reflection as well as

rotation, only tested in 2D so far

added CreateJacobianDeterminantImage

added a simple kmeansSegmentation filter ...

would like to start running R CMD CHECK and get failures to a minimum

...

need to write a quick vignette, possibly based on the README.md ...

@muschellij2 https://github.com/muschellij2 - would appreciated
any
advice / help on this ....

some advice from wickham:
http://www.rstudio.com/products/rpackages/devtools/

it's a very good page with strategies that will help with most of the
issues we've had in the past ...

any thoughts appreciated.


Reply to this email directly or view it on GitHub
#8.


Reply to this email directly or view it on GitHub
#8 (comment).


Reply to this email directly or view it on GitHub
#8 (comment).

@stnava
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@stnava stnava commented Jan 26, 2015

ANTsR.so is the main indicator and it's currently around 77MB

brian

On Mon, Jan 26, 2015 at 11:24 AM, bkandel notifications@github.com wrote:

100 MB sounds ambitious to me if we're going to include ITK build--in my
current ANTsR build, the ITKv4-build dir alone is 392MB. I imagine that
most of this can be deleted safely, though, once ANTs is installed.

On 26 January 2015 at 11:16, stnava notifications@github.com wrote:

oops - just checked latest R CMD Build & it's quite large ... easy to
resolve with some carefully crafted rm calls ... will assign myself to
that.

#9

brian

On Mon, Jan 26, 2015 at 11:12 AM, brian avants stnava@gmail.com
wrote:

cran policies are here

100MB is the limit which ANTsR just sneaks under (last i checked)
after
R
CMD Build

the package must pass on 2 platforms ( e.g. linux , osx ) for CRAN
acceptance ...

compile time might be an issue but this can likely be resolved by
making
a thin ANTs build that focuses on only the programs necessary for
ANTsR
... this could be done within a new ANTs branch that gets updated as
needed.

i still see install_github or R CMD INSTALL being the way we employ
ANTsR
but, for broader use, CRAN would be great. so hopefully we would
branch
to thin ANTs only occasionally ... primarily, it would be a change to
one
or maybe two CMakeLists.txt files ...

ref issue thin ants

brian

On Mon, Jan 26, 2015 at 10:43 AM, bkandel notifications@github.com
wrote:

I thought the major issue with CRAN was the size of the package. Did
you
find a way to work around that?

On 26 January 2015 at 10:32, stnava notifications@github.com
wrote:

@ntustison https://github.com/ntustison , @bkandel
https://github.com/bkandel , @dorianps <
https://github.com/dorianps>,

@jeffduda https://github.com/jeffduda , @cookpa
https://github.com/cookpa , @armaneshaghi
https://github.com/armaneshaghi, @muschellij2
https://github.com/muschellij2

hoping to work toward a CRAN submission for ANTsR - some updates on
this
topic:

i ran rd2roxygen and dealt with most of the issues. hopefully wont
have

to do that again ... so, in the future, we should write
documentation

using the roxygen2 style and just roxygenize() regularly.

a couple other changes

enabled plot( antsImage ) so we dont need to type plotANTsImage

added resampleImage

updated invariantImageSimilarity to use reflection as well as

rotation, only tested in 2D so far

added CreateJacobianDeterminantImage

added a simple kmeansSegmentation filter ...

would like to start running R CMD CHECK and get failures to a
minimum

...

need to write a quick vignette, possibly based on the README.md ...

@muschellij2 https://github.com/muschellij2 - would appreciated
any
advice / help on this ....

some advice from wickham:
http://www.rstudio.com/products/rpackages/devtools/

it's a very good page with strategies that will help with most of
the
issues we've had in the past ...

any thoughts appreciated.


Reply to this email directly or view it on GitHub
#8.


Reply to this email directly or view it on GitHub
#8 (comment).


Reply to this email directly or view it on GitHub
#8 (comment).


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#8 (comment).

@stnava
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@stnava stnava commented Jan 26, 2015

http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Configure-and-cleanup

brian

On Mon, Jan 26, 2015 at 11:28 AM, brian avants stnava@gmail.com wrote:

ANTsR.so is the main indicator and it's currently around 77MB

brian

On Mon, Jan 26, 2015 at 11:24 AM, bkandel notifications@github.com
wrote:

100 MB sounds ambitious to me if we're going to include ITK build--in my
current ANTsR build, the ITKv4-build dir alone is 392MB. I imagine that
most of this can be deleted safely, though, once ANTs is installed.

On 26 January 2015 at 11:16, stnava notifications@github.com wrote:

oops - just checked latest R CMD Build & it's quite large ... easy to
resolve with some carefully crafted rm calls ... will assign myself to
that.

#9

brian

On Mon, Jan 26, 2015 at 11:12 AM, brian avants stnava@gmail.com
wrote:

cran policies are here

100MB is the limit which ANTsR just sneaks under (last i checked)
after
R
CMD Build

the package must pass on 2 platforms ( e.g. linux , osx ) for CRAN
acceptance ...

compile time might be an issue but this can likely be resolved by
making
a thin ANTs build that focuses on only the programs necessary for
ANTsR
... this could be done within a new ANTs branch that gets updated as
needed.

i still see install_github or R CMD INSTALL being the way we employ
ANTsR
but, for broader use, CRAN would be great. so hopefully we would
branch
to thin ANTs only occasionally ... primarily, it would be a change to
one
or maybe two CMakeLists.txt files ...

ref issue thin ants

brian

On Mon, Jan 26, 2015 at 10:43 AM, bkandel notifications@github.com
wrote:

I thought the major issue with CRAN was the size of the package. Did
you
find a way to work around that?

On 26 January 2015 at 10:32, stnava notifications@github.com
wrote:

@ntustison https://github.com/ntustison , @bkandel
https://github.com/bkandel , @dorianps <
https://github.com/dorianps>,

@jeffduda https://github.com/jeffduda , @cookpa
https://github.com/cookpa , @armaneshaghi
https://github.com/armaneshaghi, @muschellij2
https://github.com/muschellij2

hoping to work toward a CRAN submission for ANTsR - some updates
on
this
topic:

i ran rd2roxygen and dealt with most of the issues. hopefully wont
have

to do that again ... so, in the future, we should write
documentation

using the roxygen2 style and just roxygenize() regularly.

a couple other changes

enabled plot( antsImage ) so we dont need to type plotANTsImage

added resampleImage

updated invariantImageSimilarity to use reflection as well as

rotation, only tested in 2D so far

added CreateJacobianDeterminantImage

added a simple kmeansSegmentation filter ...

would like to start running R CMD CHECK and get failures to a
minimum

...

need to write a quick vignette, possibly based on the README.md
...

@muschellij2 https://github.com/muschellij2 - would appreciated
any
advice / help on this ....

some advice from wickham:
http://www.rstudio.com/products/rpackages/devtools/

it's a very good page with strategies that will help with most of
the
issues we've had in the past ...

any thoughts appreciated.


Reply to this email directly or view it on GitHub
#8.


Reply to this email directly or view it on GitHub
#8 (comment).


Reply to this email directly or view it on GitHub
#8 (comment).


Reply to this email directly or view it on GitHub
#8 (comment).

@jefferis
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@jefferis jefferis commented Jan 26, 2015

Would be happy to see this on CRAN. Would there be any sense in producing an ITK only package. Could be useful for others and could help re space. Of course you could rely on system ITK but that would somewhat defeat the ease of use advantage of a CRAN package (on OS X one can have binary installs, which is convenient for many). Best,

Gregory Jefferis

On 26 Jan 2015, at 08:24, bkandel notifications@github.com wrote:

100 MB sounds ambitious to me if we're going to include ITK build--in my
current ANTsR build, the ITKv4-build dir alone is 392MB. I imagine that
most of this can be deleted safely, though, once ANTs is installed.

On 26 January 2015 at 11:16, stnava notifications@github.com wrote:

oops - just checked latest R CMD Build & it's quite large ... easy to
resolve with some carefully crafted rm calls ... will assign myself to
that.

#9

brian

On Mon, Jan 26, 2015 at 11:12 AM, brian avants stnava@gmail.com wrote:

cran policies are here

100MB is the limit which ANTsR just sneaks under (last i checked) after
R
CMD Build

the package must pass on 2 platforms ( e.g. linux , osx ) for CRAN
acceptance ...

compile time might be an issue but this can likely be resolved by
making
a thin ANTs build that focuses on only the programs necessary for
ANTsR
... this could be done within a new ANTs branch that gets updated as
needed.

i still see install_github or R CMD INSTALL being the way we employ
ANTsR
but, for broader use, CRAN would be great. so hopefully we would branch
to thin ANTs only occasionally ... primarily, it would be a change to
one
or maybe two CMakeLists.txt files ...

ref issue thin ants

brian

On Mon, Jan 26, 2015 at 10:43 AM, bkandel notifications@github.com
wrote:

I thought the major issue with CRAN was the size of the package. Did
you
find a way to work around that?

On 26 January 2015 at 10:32, stnava notifications@github.com wrote:

@ntustison https://github.com/ntustison , @bkandel
https://github.com/bkandel , @dorianps https://github.com/dorianps,

@jeffduda https://github.com/jeffduda , @cookpa
https://github.com/cookpa , @armaneshaghi
https://github.com/armaneshaghi, @muschellij2
https://github.com/muschellij2

hoping to work toward a CRAN submission for ANTsR - some updates on
this
topic:

i ran rd2roxygen and dealt with most of the issues. hopefully wont
have

to do that again ... so, in the future, we should write documentation

using the roxygen2 style and just roxygenize() regularly.

a couple other changes

enabled plot( antsImage ) so we dont need to type plotANTsImage

added resampleImage

updated invariantImageSimilarity to use reflection as well as

rotation, only tested in 2D so far

added CreateJacobianDeterminantImage

added a simple kmeansSegmentation filter ...

would like to start running R CMD CHECK and get failures to a minimum

...

need to write a quick vignette, possibly based on the README.md ...

@muschellij2 https://github.com/muschellij2 - would appreciated
any
advice / help on this ....

some advice from wickham:
http://www.rstudio.com/products/rpackages/devtools/

it's a very good page with strategies that will help with most of the
issues we've had in the past ...

any thoughts appreciated.


Reply to this email directly or view it on GitHub
#8.


Reply to this email directly or view it on GitHub
#8 (comment).


Reply to this email directly or view it on GitHub
#8 (comment).


Reply to this email directly or view it on GitHub.

@stnava
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@stnava stnava commented Jan 26, 2015

yes - we have talked about that ... i do believe the right way to do this
is to have a CRAN RcppITK package (or whatever it is called) that might be
similar to Rcpp, RcppArmadillo, RcppEigen etc. its primary purpose would
be to make ITK libraries available s.t. projects like ANTsR might use them.

the primary obstacle is not so much technical but more so the burden of
maintaining two separate packages, test suites, documentation "parties",
etc ... however, with ants releases becoming more standardized, we might
hope to deal w/this in more streamlined fashion.

i cannot volunteer to make such a package but would be happy to assist /
build against such a package if it were created.

brian

On Mon, Jan 26, 2015 at 11:41 AM, Gregory Jefferis <notifications@github.com

wrote:

Would be happy to see this on CRAN. Would there be any sense in producing
an ITK only package. Could be useful for others and could help re space. Of
course you could rely on system ITK but that would somewhat defeat the ease
of use advantage of a CRAN package (on OS X one can have binary installs,
which is convenient for many). Best,

Gregory Jefferis

On 26 Jan 2015, at 08:24, bkandel notifications@github.com wrote:

100 MB sounds ambitious to me if we're going to include ITK build--in my
current ANTsR build, the ITKv4-build dir alone is 392MB. I imagine that
most of this can be deleted safely, though, once ANTs is installed.

On 26 January 2015 at 11:16, stnava notifications@github.com wrote:

oops - just checked latest R CMD Build & it's quite large ... easy to
resolve with some carefully crafted rm calls ... will assign myself to
that.

#9

brian

On Mon, Jan 26, 2015 at 11:12 AM, brian avants stnava@gmail.com
wrote:

cran policies are here

100MB is the limit which ANTsR just sneaks under (last i checked)
after
R
CMD Build

the package must pass on 2 platforms ( e.g. linux , osx ) for CRAN
acceptance ...

compile time might be an issue but this can likely be resolved by
making
a thin ANTs build that focuses on only the programs necessary for
ANTsR
... this could be done within a new ANTs branch that gets updated as
needed.

i still see install_github or R CMD INSTALL being the way we employ
ANTsR
but, for broader use, CRAN would be great. so hopefully we would
branch
to thin ANTs only occasionally ... primarily, it would be a change
to
one
or maybe two CMakeLists.txt files ...

ref issue thin ants

brian

On Mon, Jan 26, 2015 at 10:43 AM, bkandel notifications@github.com

wrote:

I thought the major issue with CRAN was the size of the package.
Did
you
find a way to work around that?

On 26 January 2015 at 10:32, stnava notifications@github.com
wrote:

@ntustison https://github.com/ntustison , @bkandel
https://github.com/bkandel , @dorianps <
https://github.com/dorianps>,

@jeffduda https://github.com/jeffduda , @cookpa
https://github.com/cookpa , @armaneshaghi
https://github.com/armaneshaghi, @muschellij2
https://github.com/muschellij2

hoping to work toward a CRAN submission for ANTsR - some updates
on
this
topic:

i ran rd2roxygen and dealt with most of the issues. hopefully
wont
have

to do that again ... so, in the future, we should write
documentation

using the roxygen2 style and just roxygenize() regularly.

a couple other changes

enabled plot( antsImage ) so we dont need to type plotANTsImage

added resampleImage

updated invariantImageSimilarity to use reflection as well as

rotation, only tested in 2D so far

added CreateJacobianDeterminantImage

added a simple kmeansSegmentation filter ...

would like to start running R CMD CHECK and get failures to a
minimum

...

need to write a quick vignette, possibly based on the README.md
...

@muschellij2 https://github.com/muschellij2 - would
appreciated
any
advice / help on this ....

some advice from wickham:
http://www.rstudio.com/products/rpackages/devtools/

it's a very good page with strategies that will help with most of
the
issues we've had in the past ...

any thoughts appreciated.


Reply to this email directly or view it on GitHub
#8.


Reply to this email directly or view it on GitHub
#8 (comment).


Reply to this email directly or view it on GitHub
#8 (comment).


Reply to this email directly or view it on GitHub.


Reply to this email directly or view it on GitHub
#8 (comment).

@stnava
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@stnava stnava commented Feb 2, 2015

am working on R cmd check ... here is the procedure that i am using (likely to be refined in the future)

  • R CMD INSTALL ANTsR # to a custom library location
  • R CMD build ANTsR
  • R CMD check ANTsR_1.0.tar.gz --library=~/code/RLibs/ --no-install

after this passes (does not yet) will try vanilla and as-cran flags

this procedure lets you build the c++ once and then check the documentation / R examples - several issues arise at this stage which need to be dealt with manually. here you iterate this procedure:

  • make manual changes
  • R CMD INSTALL ANTsR # to custom location
  • R CMD check ANTsR_1.0.tar.gz --library=~/code/RLibs/ --no-install

until R CMD check issues are eliminated ....

one way to speed up checking examples is to directly run .R file called ANTsR-Ex.R that is generated by R cmd check ....

@stnava
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@stnava stnava commented Feb 2, 2015

@ntustison , @bkandel , @dorianps, @jeffduda , @cookpa

substantial progress towards passing R cmd check ... it's not there yet but i eliminated several "mysterious" warnings, notes and the like and fixed many documentation issues. also removed what i thought was dead code. in the future, it would be very helpful if we could adhere to documenting everything that goes into the main branch of antsr. if you want to do some test development, please do so on a repository branch. by doing this, we can avoid getting into the current situation described below.

the current R cmd check produces 2 warnings. one is for undocumented functions (mostly helper functions and dead code) and one for inconsistent documentation (should be resolvable with roxygen2's help but must be done manually). the list of issues is below - i will whittle away at these and would appreciate if you would help with any of these as you get time:

undocumented functions - will remove these when possible

‘ExtractDenseNetwork’ ‘LabelClustersUniquely’ ‘LabelGeometryMeasures’
‘LabelImageCentroids’ ‘N4BiasFieldCorrection’ ‘SummarizeClusters’
‘TileImages’ ‘antsAffineInitializer’ ‘antsBOLDNetworkAnalysis’
‘antsCopyImageInfo’ ‘antsGetDirection’ ‘antsGetOrigin’
‘antsGetPixels’ ‘antsGetSpacing’ ‘antsImagePair’
‘antsMotionCorrStats’ ‘antsSetDirection’ ‘antsSetOrigin’
‘antsSetPixels’ ‘antsSetSpacing’ ‘antsTransformIndexToPhysicalPoint’
‘antsTransformPhysicalPointToIndex’ ‘ants_brain_extraction’
‘ants_motion_estimation’ ‘ants_to_template’ ‘antsrGetPointerName’
‘antsrParseListToString’ ‘antsrParseListToString2’
‘antsr_frequency_filter’ ‘antsr_resting_state_corr_eigenanat’
‘antsrmakeRandomString’ ‘arCorrection’ ‘as.data.frame.antsMatrix’
‘as.list.antsMatrix’ ‘binarizeSNPs’ ‘computeDVARS’ ‘conjGradS’
‘cosineDist’ ‘diffmat’ ‘eanatcolMaxs’ ‘eanatsparsify’
‘eanatsparsifyv’ ‘filterPASLforNetworkAnalysis’ ‘getANTsRData’
‘getNetwork’ ‘getValueAtPoint’ ‘get_perfusion_predictors’
‘getvertices’ ‘int_antsProcessArguments’ ‘labels2matrix’
‘labels2vector’ ‘largeScaleCommunity’ ‘lowrank’ ‘lowrankRowMatrix’
‘makeDiffGraph’ ‘makefacet’ ‘makestl’ ‘matrix2timeseries’ ‘matrixSeg’
‘mergeLabels’ ‘motion_correction’ ‘networkCorrelation’
‘networkCovariance’ ‘networkOverlap’ ‘plot.antsImage’ ‘plotNetwork’
‘quantifySNPs’ ‘reduceNetwork’ ‘sliceTimingCorrection’ ‘snapColors’

undocumented arguments - will also remove these when possible or fix by hand

00check.log:Undocumented arguments in documentation object 'Atropos'
00check.log:Undocumented arguments in documentation object 'CreateJacobianDeterminantImage'
00check.log:Undocumented arguments in documentation object 'ImageMath'
00check.log:Undocumented arguments in documentation object 'KellyKapowski'
00check.log:Undocumented arguments in documentation object 'MeasureMinMaxMean'
00check.log:Undocumented arguments in documentation object 'N3BiasFieldCorrection'
00check.log:Undocumented arguments in documentation object 'SmoothImage'
00check.log:Undocumented arguments in documentation object 'ThresholdImage'
00check.log:Undocumented arguments in documentation object 'abpBrainExtraction'
00check.log:Undocumented arguments in documentation object 'abpN4'
00check.log:Undocumented arguments in documentation object 'antsApplyTransforms'
00check.log:Undocumented arguments in documentation object 'antsGetNeighborhood'
00check.log:Undocumented arguments in documentation object 'antsImageMutualInformation'
00check.log:Undocumented arguments in documentation object 'antsMotionCorr'
00check.log:Undocumented arguments in documentation object 'antsPreprocessfMRI'
00check.log:Undocumented arguments in documentation object 'antsRegistration'
00check.log:Undocumented arguments in documentation object 'aslDenoiseR'
00check.log:Undocumented arguments in documentation object 'aslPerfusion'
00check.log:Undocumented arguments in documentation object 'bayesianCBF'
00check.log:Undocumented arguments in documentation object 'bayesianlm'
00check.log:Undocumented arguments in documentation object 'clusterTimeSeries'
00check.log:Undocumented arguments in documentation object 'compcor'
00check.log:Undocumented arguments in documentation object 'corw'
00check.log:Undocumented arguments in documentation object 'eigSeg'
00check.log:Undocumented arguments in documentation object 'fastwhiten'
00check.log:Undocumented arguments in documentation object 'filterfMRIforNetworkAnalysis'
00check.log:Undocumented arguments in documentation object 'frequencyFilterfMRI'
00check.log:Undocumented arguments in documentation object 'getAverageOfTimeSeries'
00check.log:Undocumented arguments in documentation object 'getCentroids'
00check.log:Undocumented arguments in documentation object 'getMultivariateTemplateCoordinates'
00check.log:Undocumented arguments in documentation object 'getROIValues'
00check.log:Undocumented arguments in documentation object 'getTemplateCoordinates'
00check.log:Undocumented arguments in documentation object 'getfMRInuisanceVariables'
00check.log:Undocumented arguments in documentation object 'icawhiten'
00check.log:Undocumented arguments in documentation object 'image2ClusterImages'
00check.log:Undocumented arguments in documentation object 'imageFileNames2ImageList'
00check.log:Undocumented arguments in documentation object 'initializeEigenanatomy'
00check.log:Undocumented arguments in documentation object 'inspectImageData3D'
00check.log:Undocumented arguments in documentation object 'interleaveMatrixWithItself'
00check.log:Undocumented arguments in documentation object 'invariantImageSimilarity'
00check.log:Undocumented arguments in documentation object 'joinEigenanatomy'
00check.log:Undocumented arguments in documentation object 'kmeansSegmentation'
00check.log:Undocumented arguments in documentation object 'labelClusters'
00check.log:Undocumented arguments in documentation object 'lappend'
00check.log:Undocumented arguments in documentation object 'makeGraph'
00check.log:Undocumented arguments in documentation object 'makeImage'
00check.log:Undocumented arguments in documentation object 'mni2tal'
00check.log:Undocumented arguments in documentation object 'networkEiganat'
00check.log:Undocumented arguments in documentation object 'pairwiseImageDistanceMatrix'
00check.log:Undocumented arguments in documentation object 'partialVolumeCorrection'
00check.log:Undocumented arguments in documentation object 'perfusionregression'
00check.log:Undocumented arguments in documentation object 'plotANTsImage'
00check.log:Undocumented arguments in documentation object 'plotBasicNetwork'
00check.log:Undocumented arguments in documentation object 'plotPrettyGraph'
00check.log:Undocumented arguments in documentation object 'projectImageAlongAxis'
00check.log:Undocumented arguments in documentation object 'quantifyCBF'
00check.log:Undocumented arguments in documentation object 'regressionNetworkViz'
00check.log:Undocumented arguments in documentation object 'renderImageLabels'
00check.log:Undocumented arguments in documentation object 'renderNetwork'
00check.log:Undocumented arguments in documentation object 'renderSurfaceFunction'
00check.log:Undocumented arguments in documentation object 'reorientImage'
00check.log:Undocumented arguments in documentation object 'rfSegmentation'
00check.log:Undocumented arguments in documentation object 'rfSegmentationPredict'
00check.log:Undocumented arguments in documentation object 'rsfDenoise'
00check.log:Undocumented arguments in documentation object 'sccan'
00check.log:Undocumented arguments in documentation object 'sparseDecom'
00check.log:Undocumented arguments in documentation object 'sparseDecom2'
00check.log:Undocumented arguments in documentation object 'sparseDecom2boot'
00check.log:Undocumented arguments in documentation object 'sparseDecomboot'
00check.log:Undocumented arguments in documentation object 'subgradientL1Regression'
00check.log:Undocumented arguments in documentation object 'taskFMRI'
00check.log:Undocumented arguments in documentation object 'temporalwhiten'
00check.log:Undocumented arguments in documentation object 'timeseriesN3'
00check.log:Undocumented arguments in documentation object 'usePkg'
00check.log:Undocumented arguments in documentation object 'whiten'

@stnava
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@stnava stnava commented Feb 2, 2015

@bkandel
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@bkandel bkandel commented Feb 3, 2015

I'll try to cover most or all of the ASL-related functions.

One note on style: It looks like a lot of the undocumented functions were
intended to be subroutines in documented functions but were put outside the
brackets. R does support subroutines that don't pollute the global
namespace.

I know that naming is a big mess now, but maybe we can decide on a system
going forward. Are we prefacing everything with ants (e.g.
antsBlahBlahBlah)? I would prefer not to, and just use ANTsR:: as a
preface if necessary, while avoiding conflicts with core packages. Should
we decide on lower-case camelCase? It seems to me to be trending as the
preferred naming style for functions.

Ben

On 2 February 2015 at 18:20, stnava notifications@github.com wrote:

for vignettes: will follow
http://stackoverflow.com/questions/24861970/using-rmarkdown-as-a-vignette-engine


Reply to this email directly or view it on GitHub
#8 (comment).

@jefferis
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@jefferis jefferis commented Feb 3, 2015

One note on style: It looks like a lot of the undocumented functions were
intended to be subroutines in documented functions but were put outside the
brackets. R does support subroutines that don't pollute the global
namespace.

I would recommend allowing roxygen2 to generate your NAMESPACE file (a build option in rstudio if you are using that). The normal approach would be to have a file ANTsR-package.R looking something like this:

#' Access to ANTs routines in R
#' 
#' R package \bold{ANTsR} provides functions to do ...
#' 
#' @name ANTsR-package
#' @aliases ANTsR
#' @useDynLib ANTsR
#' @import Rcpp methods
#' @references some ref
#' @seealso \code{\link{useful_func1}}, \code{\link{useful_func2}}
NULL

Then you would tag all functions that you want exported with @export tags in their doc sections. The use of

exportPattern("^[^.]")

in NAMESPACE is generally not recommended (see http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Specifying-imports-and-exports), but you can prefix all private functions with a period as an alternative to using the approach mentioned above.

I know that naming is a big mess now, but maybe we can decide on a system
going forward. Are we prefacing everything with ants (e.g.
antsBlahBlahBlah)? I would prefer not to, and just use ANTsR:: as a
preface if necessary, while avoiding conflicts with core packages.

That seems reasonable to me, although you may want to keep an eye out for functions from popular extension packages (e.g. the hadleyverse)

@bkandel
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@bkandel bkandel commented Feb 3, 2015

I assume this is related: I'm now getting errors building ANTsR because I'm
missing packages 'irlba' and 'png'. These aren't in the dependency list,
but they must have crept in somewhere.

On 2 February 2015 at 17:51, stnava notifications@github.com wrote:

@ntustison https://github.com/ntustison , @bkandel
https://github.com/bkandel , @dorianps https://github.com/dorianps,
@jeffduda https://github.com/jeffduda , @cookpa
https://github.com/cookpa

substantial progress towards passing R cmd check ... it's not there yet
but i eliminated several "mysterious" warnings, notes and the like and
fixed many documentation issues. also removed what i thought was dead code.
in the future, it would be very helpful if we could adhere to documenting
everything that goes into the main branch of antsr. if you want to do
some test development, please do so on a repository branch. by doing this,
we can avoid getting into the current situation described below.

the current R cmd check produces 2 warnings. one is for undocumented
functions (mostly helper functions and dead code) and one for inconsistent
documentation (should be resolvable with roxygen2's help but must be done
manually). the list of issues is below - i will whittle away at these and
would appreciate if you would help with any of these as you get time:
undocumented functions - will remove these when possible

‘ExtractDenseNetwork’ ‘LabelClustersUniquely’ ‘LabelGeometryMeasures’
‘LabelImageCentroids’ ‘N4BiasFieldCorrection’ ‘SummarizeClusters’
‘TileImages’ ‘antsAffineInitializer’ ‘antsBOLDNetworkAnalysis’
‘antsCopyImageInfo’ ‘antsGetDirection’ ‘antsGetOrigin’
‘antsGetPixels’ ‘antsGetSpacing’ ‘antsImagePair’
‘antsMotionCorrStats’ ‘antsSetDirection’ ‘antsSetOrigin’
‘antsSetPixels’ ‘antsSetSpacing’ ‘antsTransformIndexToPhysicalPoint’
‘antsTransformPhysicalPointToIndex’ ‘ants_brain_extraction’
‘ants_motion_estimation’ ‘ants_to_template’ ‘antsrGetPointerName’
‘antsrParseListToString’ ‘antsrParseListToString2’
‘antsr_frequency_filter’ ‘antsr_resting_state_corr_eigenanat’
‘antsrmakeRandomString’ ‘arCorrection’ ‘as.data.frame.antsMatrix’
‘as.list.antsMatrix’ ‘binarizeSNPs’ ‘computeDVARS’ ‘conjGradS’
‘cosineDist’ ‘diffmat’ ‘eanatcolMaxs’ ‘eanatsparsify’
‘eanatsparsifyv’ ‘filterPASLforNetworkAnalysis’ ‘getANTsRData’
‘getNetwork’ ‘getValueAtPoint’ ‘get_perfusion_predictors’
‘getvertices’ ‘int_antsProcessArguments’ ‘labels2matrix’
‘labels2vector’ ‘largeScaleCommunity’ ‘lowrank’ ‘lowrankRowMatrix’
‘makeDiffGraph’ ‘makefacet’ ‘makestl’ ‘matrix2timeseries’ ‘matrixSeg’
‘mergeLabels’ ‘motion_correction’ ‘networkCorrelation’
‘networkCovariance’ ‘networkOverlap’ ‘plot.antsImage’ ‘plotNetwork’
‘quantifySNPs’ ‘reduceNetwork’ ‘sliceTimingCorrection’ ‘snapColors’
undocumented arguments - will also remove these when possible or fix by
hand

00check.log:Undocumented arguments in documentation object 'Atropos'
00check.log:Undocumented arguments in documentation object
'CreateJacobianDeterminantImage'
00check.log:Undocumented arguments in documentation object 'ImageMath'
00check.log:Undocumented arguments in documentation object 'KellyKapowski'
00check.log:Undocumented arguments in documentation object
'MeasureMinMaxMean'
00check.log:Undocumented arguments in documentation object
'N3BiasFieldCorrection'
00check.log:Undocumented arguments in documentation object 'SmoothImage'
00check.log:Undocumented arguments in documentation object 'ThresholdImage'
00check.log:Undocumented arguments in documentation object
'abpBrainExtraction'
00check.log:Undocumented arguments in documentation object 'abpN4'
00check.log:Undocumented arguments in documentation object
'antsApplyTransforms'
00check.log:Undocumented arguments in documentation object
'antsGetNeighborhood'
00check.log:Undocumented arguments in documentation object
'antsImageMutualInformation'
00check.log:Undocumented arguments in documentation object 'antsMotionCorr'
00check.log:Undocumented arguments in documentation object
'antsPreprocessfMRI'
00check.log:Undocumented arguments in documentation object
'antsRegistration'
00check.log:Undocumented arguments in documentation object 'aslDenoiseR'
00check.log:Undocumented arguments in documentation object 'aslPerfusion'
00check.log:Undocumented arguments in documentation object 'bayesianCBF'
00check.log:Undocumented arguments in documentation object 'bayesianlm'
00check.log:Undocumented arguments in documentation object
'clusterTimeSeries'
00check.log:Undocumented arguments in documentation object 'compcor'
00check.log:Undocumented arguments in documentation object 'corw'
00check.log:Undocumented arguments in documentation object 'eigSeg'
00check.log:Undocumented arguments in documentation object 'fastwhiten'
00check.log:Undocumented arguments in documentation object
'filterfMRIforNetworkAnalysis'
00check.log:Undocumented arguments in documentation object
'frequencyFilterfMRI'
00check.log:Undocumented arguments in documentation object
'getAverageOfTimeSeries'
00check.log:Undocumented arguments in documentation object 'getCentroids'
00check.log:Undocumented arguments in documentation object
'getMultivariateTemplateCoordinates'
00check.log:Undocumented arguments in documentation object 'getROIValues'
00check.log:Undocumented arguments in documentation object
'getTemplateCoordinates'
00check.log:Undocumented arguments in documentation object
'getfMRInuisanceVariables'
00check.log:Undocumented arguments in documentation object 'icawhiten'
00check.log:Undocumented arguments in documentation object
'image2ClusterImages'
00check.log:Undocumented arguments in documentation object
'imageFileNames2ImageList'
00check.log:Undocumented arguments in documentation object
'initializeEigenanatomy'
00check.log:Undocumented arguments in documentation object
'inspectImageData3D'
00check.log:Undocumented arguments in documentation object
'interleaveMatrixWithItself'
00check.log:Undocumented arguments in documentation object
'invariantImageSimilarity'
00check.log:Undocumented arguments in documentation object
'joinEigenanatomy'
00check.log:Undocumented arguments in documentation object
'kmeansSegmentation'
00check.log:Undocumented arguments in documentation object 'labelClusters'
00check.log:Undocumented arguments in documentation object 'lappend'
00check.log:Undocumented arguments in documentation object 'makeGraph'
00check.log:Undocumented arguments in documentation object 'makeImage'
00check.log:Undocumented arguments in documentation object 'mni2tal'
00check.log:Undocumented arguments in documentation object 'networkEiganat'
00check.log:Undocumented arguments in documentation object
'pairwiseImageDistanceMatrix'
00check.log:Undocumented arguments in documentation object
'partialVolumeCorrection'
00check.log:Undocumented arguments in documentation object
'perfusionregression'
00check.log:Undocumented arguments in documentation object 'plotANTsImage'
00check.log:Undocumented arguments in documentation object
'plotBasicNetwork'
00check.log:Undocumented arguments in documentation object
'plotPrettyGraph'
00check.log:Undocumented arguments in documentation object
'projectImageAlongAxis'
00check.log:Undocumented arguments in documentation object 'quantifyCBF'
00check.log:Undocumented arguments in documentation object
'regressionNetworkViz'
00check.log:Undocumented arguments in documentation object
'renderImageLabels'
00check.log:Undocumented arguments in documentation object 'renderNetwork'
00check.log:Undocumented arguments in documentation object
'renderSurfaceFunction'
00check.log:Undocumented arguments in documentation object 'reorientImage'
00check.log:Undocumented arguments in documentation object 'rfSegmentation'
00check.log:Undocumented arguments in documentation object
'rfSegmentationPredict'
00check.log:Undocumented arguments in documentation object 'rsfDenoise'
00check.log:Undocumented arguments in documentation object 'sccan'
00check.log:Undocumented arguments in documentation object 'sparseDecom'
00check.log:Undocumented arguments in documentation object 'sparseDecom2'
00check.log:Undocumented arguments in documentation object
'sparseDecom2boot'
00check.log:Undocumented arguments in documentation object
'sparseDecomboot'
00check.log:Undocumented arguments in documentation object
'subgradientL1Regression'
00check.log:Undocumented arguments in documentation object 'taskFMRI'
00check.log:Undocumented arguments in documentation object 'temporalwhiten'
00check.log:Undocumented arguments in documentation object 'timeseriesN3'
00check.log:Undocumented arguments in documentation object 'usePkg'
00check.log:Undocumented arguments in documentation object 'whiten'


Reply to this email directly or view it on GitHub
#8 (comment).

@stnava
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@stnava stnava commented Feb 3, 2015

Yes. For cran check, we must list all dependencies ... we know how to
reduce these for future work but for now , need to be explicit. Can relax
in the future.
On Feb 3, 2015 4:20 PM, "bkandel" notifications@github.com wrote:

I assume this is related: I'm now getting errors building ANTsR because
I'm
missing packages 'irlba' and 'png'. These aren't in the dependency list,
but they must have crept in somewhere.

On 2 February 2015 at 17:51, stnava notifications@github.com wrote:

@ntustison https://github.com/ntustison , @bkandel
https://github.com/bkandel , @dorianps https://github.com/dorianps,
@jeffduda https://github.com/jeffduda , @cookpa
https://github.com/cookpa

substantial progress towards passing R cmd check ... it's not there yet
but i eliminated several "mysterious" warnings, notes and the like and
fixed many documentation issues. also removed what i thought was dead
code.
in the future, it would be very helpful if we could adhere to
documenting
everything that goes into the main branch of antsr. if you want to do
some test development, please do so on a repository branch. by doing
this,
we can avoid getting into the current situation described below.

the current R cmd check produces 2 warnings. one is for undocumented
functions (mostly helper functions and dead code) and one for
inconsistent
documentation (should be resolvable with roxygen2's help but must be
done
manually). the list of issues is below - i will whittle away at these
and
would appreciate if you would help with any of these as you get time:
undocumented functions - will remove these when possible

‘ExtractDenseNetwork’ ‘LabelClustersUniquely’ ‘LabelGeometryMeasures’
‘LabelImageCentroids’ ‘N4BiasFieldCorrection’ ‘SummarizeClusters’
‘TileImages’ ‘antsAffineInitializer’ ‘antsBOLDNetworkAnalysis’
‘antsCopyImageInfo’ ‘antsGetDirection’ ‘antsGetOrigin’
‘antsGetPixels’ ‘antsGetSpacing’ ‘antsImagePair’
‘antsMotionCorrStats’ ‘antsSetDirection’ ‘antsSetOrigin’
‘antsSetPixels’ ‘antsSetSpacing’ ‘antsTransformIndexToPhysicalPoint’
‘antsTransformPhysicalPointToIndex’ ‘ants_brain_extraction’
‘ants_motion_estimation’ ‘ants_to_template’ ‘antsrGetPointerName’
‘antsrParseListToString’ ‘antsrParseListToString2’
‘antsr_frequency_filter’ ‘antsr_resting_state_corr_eigenanat’
‘antsrmakeRandomString’ ‘arCorrection’ ‘as.data.frame.antsMatrix’
‘as.list.antsMatrix’ ‘binarizeSNPs’ ‘computeDVARS’ ‘conjGradS’
‘cosineDist’ ‘diffmat’ ‘eanatcolMaxs’ ‘eanatsparsify’
‘eanatsparsifyv’ ‘filterPASLforNetworkAnalysis’ ‘getANTsRData’
‘getNetwork’ ‘getValueAtPoint’ ‘get_perfusion_predictors’
‘getvertices’ ‘int_antsProcessArguments’ ‘labels2matrix’
‘labels2vector’ ‘largeScaleCommunity’ ‘lowrank’ ‘lowrankRowMatrix’
‘makeDiffGraph’ ‘makefacet’ ‘makestl’ ‘matrix2timeseries’ ‘matrixSeg’
‘mergeLabels’ ‘motion_correction’ ‘networkCorrelation’
‘networkCovariance’ ‘networkOverlap’ ‘plot.antsImage’ ‘plotNetwork’
‘quantifySNPs’ ‘reduceNetwork’ ‘sliceTimingCorrection’ ‘snapColors’
undocumented arguments - will also remove these when possible or fix by
hand

00check.log:Undocumented arguments in documentation object 'Atropos'
00check.log:Undocumented arguments in documentation object
'CreateJacobianDeterminantImage'
00check.log:Undocumented arguments in documentation object 'ImageMath'
00check.log:Undocumented arguments in documentation object
'KellyKapowski'
00check.log:Undocumented arguments in documentation object
'MeasureMinMaxMean'
00check.log:Undocumented arguments in documentation object
'N3BiasFieldCorrection'
00check.log:Undocumented arguments in documentation object 'SmoothImage'
00check.log:Undocumented arguments in documentation object
'ThresholdImage'
00check.log:Undocumented arguments in documentation object
'abpBrainExtraction'
00check.log:Undocumented arguments in documentation object 'abpN4'
00check.log:Undocumented arguments in documentation object
'antsApplyTransforms'
00check.log:Undocumented arguments in documentation object
'antsGetNeighborhood'
00check.log:Undocumented arguments in documentation object
'antsImageMutualInformation'
00check.log:Undocumented arguments in documentation object
'antsMotionCorr'
00check.log:Undocumented arguments in documentation object
'antsPreprocessfMRI'
00check.log:Undocumented arguments in documentation object
'antsRegistration'
00check.log:Undocumented arguments in documentation object 'aslDenoiseR'
00check.log:Undocumented arguments in documentation object
'aslPerfusion'
00check.log:Undocumented arguments in documentation object 'bayesianCBF'
00check.log:Undocumented arguments in documentation object 'bayesianlm'
00check.log:Undocumented arguments in documentation object
'clusterTimeSeries'
00check.log:Undocumented arguments in documentation object 'compcor'
00check.log:Undocumented arguments in documentation object 'corw'
00check.log:Undocumented arguments in documentation object 'eigSeg'
00check.log:Undocumented arguments in documentation object 'fastwhiten'
00check.log:Undocumented arguments in documentation object
'filterfMRIforNetworkAnalysis'
00check.log:Undocumented arguments in documentation object
'frequencyFilterfMRI'
00check.log:Undocumented arguments in documentation object
'getAverageOfTimeSeries'
00check.log:Undocumented arguments in documentation object
'getCentroids'
00check.log:Undocumented arguments in documentation object
'getMultivariateTemplateCoordinates'
00check.log:Undocumented arguments in documentation object
'getROIValues'
00check.log:Undocumented arguments in documentation object
'getTemplateCoordinates'
00check.log:Undocumented arguments in documentation object
'getfMRInuisanceVariables'
00check.log:Undocumented arguments in documentation object 'icawhiten'
00check.log:Undocumented arguments in documentation object
'image2ClusterImages'
00check.log:Undocumented arguments in documentation object
'imageFileNames2ImageList'
00check.log:Undocumented arguments in documentation object
'initializeEigenanatomy'
00check.log:Undocumented arguments in documentation object
'inspectImageData3D'
00check.log:Undocumented arguments in documentation object
'interleaveMatrixWithItself'
00check.log:Undocumented arguments in documentation object
'invariantImageSimilarity'
00check.log:Undocumented arguments in documentation object
'joinEigenanatomy'
00check.log:Undocumented arguments in documentation object
'kmeansSegmentation'
00check.log:Undocumented arguments in documentation object
'labelClusters'
00check.log:Undocumented arguments in documentation object 'lappend'
00check.log:Undocumented arguments in documentation object 'makeGraph'
00check.log:Undocumented arguments in documentation object 'makeImage'
00check.log:Undocumented arguments in documentation object 'mni2tal'
00check.log:Undocumented arguments in documentation object
'networkEiganat'
00check.log:Undocumented arguments in documentation object
'pairwiseImageDistanceMatrix'
00check.log:Undocumented arguments in documentation object
'partialVolumeCorrection'
00check.log:Undocumented arguments in documentation object
'perfusionregression'
00check.log:Undocumented arguments in documentation object
'plotANTsImage'
00check.log:Undocumented arguments in documentation object
'plotBasicNetwork'
00check.log:Undocumented arguments in documentation object
'plotPrettyGraph'
00check.log:Undocumented arguments in documentation object
'projectImageAlongAxis'
00check.log:Undocumented arguments in documentation object 'quantifyCBF'
00check.log:Undocumented arguments in documentation object
'regressionNetworkViz'
00check.log:Undocumented arguments in documentation object
'renderImageLabels'
00check.log:Undocumented arguments in documentation object
'renderNetwork'
00check.log:Undocumented arguments in documentation object
'renderSurfaceFunction'
00check.log:Undocumented arguments in documentation object
'reorientImage'
00check.log:Undocumented arguments in documentation object
'rfSegmentation'
00check.log:Undocumented arguments in documentation object
'rfSegmentationPredict'
00check.log:Undocumented arguments in documentation object 'rsfDenoise'
00check.log:Undocumented arguments in documentation object 'sccan'
00check.log:Undocumented arguments in documentation object 'sparseDecom'
00check.log:Undocumented arguments in documentation object
'sparseDecom2'
00check.log:Undocumented arguments in documentation object
'sparseDecom2boot'
00check.log:Undocumented arguments in documentation object
'sparseDecomboot'
00check.log:Undocumented arguments in documentation object
'subgradientL1Regression'
00check.log:Undocumented arguments in documentation object 'taskFMRI'
00check.log:Undocumented arguments in documentation object
'temporalwhiten'
00check.log:Undocumented arguments in documentation object
'timeseriesN3'
00check.log:Undocumented arguments in documentation object 'usePkg'
00check.log:Undocumented arguments in documentation object 'whiten'


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#8 (comment).


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#8 (comment).

@stnava
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@stnava stnava commented Feb 4, 2015

Another useful resource: http://r-pkgs.had.co.nz/description.html

Regarding suggests, imports, etc ... we could do a better job of these ...
am working on it.
On Feb 3, 2015 6:48 PM, "brian avants" stnava@gmail.com wrote:

Yes. For cran check, we must list all dependencies ... we know how to
reduce these for future work but for now , need to be explicit. Can relax
in the future.
On Feb 3, 2015 4:20 PM, "bkandel" notifications@github.com wrote:

I assume this is related: I'm now getting errors building ANTsR because
I'm
missing packages 'irlba' and 'png'. These aren't in the dependency list,
but they must have crept in somewhere.

On 2 February 2015 at 17:51, stnava notifications@github.com wrote:

@ntustison https://github.com/ntustison , @bkandel
https://github.com/bkandel , @dorianps https://github.com/dorianps,

@jeffduda https://github.com/jeffduda , @cookpa
https://github.com/cookpa

substantial progress towards passing R cmd check ... it's not there yet
but i eliminated several "mysterious" warnings, notes and the like and
fixed many documentation issues. also removed what i thought was dead
code.
in the future, it would be very helpful if we could adhere to
documenting
everything that goes into the main branch of antsr. if you want to do
some test development, please do so on a repository branch. by doing
this,
we can avoid getting into the current situation described below.

the current R cmd check produces 2 warnings. one is for undocumented
functions (mostly helper functions and dead code) and one for
inconsistent
documentation (should be resolvable with roxygen2's help but must be
done
manually). the list of issues is below - i will whittle away at these
and
would appreciate if you would help with any of these as you get time:
undocumented functions - will remove these when possible

‘ExtractDenseNetwork’ ‘LabelClustersUniquely’ ‘LabelGeometryMeasures’
‘LabelImageCentroids’ ‘N4BiasFieldCorrection’ ‘SummarizeClusters’
‘TileImages’ ‘antsAffineInitializer’ ‘antsBOLDNetworkAnalysis’
‘antsCopyImageInfo’ ‘antsGetDirection’ ‘antsGetOrigin’
‘antsGetPixels’ ‘antsGetSpacing’ ‘antsImagePair’
‘antsMotionCorrStats’ ‘antsSetDirection’ ‘antsSetOrigin’
‘antsSetPixels’ ‘antsSetSpacing’ ‘antsTransformIndexToPhysicalPoint’
‘antsTransformPhysicalPointToIndex’ ‘ants_brain_extraction’
‘ants_motion_estimation’ ‘ants_to_template’ ‘antsrGetPointerName’
‘antsrParseListToString’ ‘antsrParseListToString2’
‘antsr_frequency_filter’ ‘antsr_resting_state_corr_eigenanat’
‘antsrmakeRandomString’ ‘arCorrection’ ‘as.data.frame.antsMatrix’
‘as.list.antsMatrix’ ‘binarizeSNPs’ ‘computeDVARS’ ‘conjGradS’
‘cosineDist’ ‘diffmat’ ‘eanatcolMaxs’ ‘eanatsparsify’
‘eanatsparsifyv’ ‘filterPASLforNetworkAnalysis’ ‘getANTsRData’
‘getNetwork’ ‘getValueAtPoint’ ‘get_perfusion_predictors’
‘getvertices’ ‘int_antsProcessArguments’ ‘labels2matrix’
‘labels2vector’ ‘largeScaleCommunity’ ‘lowrank’ ‘lowrankRowMatrix’
‘makeDiffGraph’ ‘makefacet’ ‘makestl’ ‘matrix2timeseries’ ‘matrixSeg’
‘mergeLabels’ ‘motion_correction’ ‘networkCorrelation’
‘networkCovariance’ ‘networkOverlap’ ‘plot.antsImage’ ‘plotNetwork’
‘quantifySNPs’ ‘reduceNetwork’ ‘sliceTimingCorrection’ ‘snapColors’
undocumented arguments - will also remove these when possible or fix by
hand

00check.log:Undocumented arguments in documentation object 'Atropos'
00check.log:Undocumented arguments in documentation object
'CreateJacobianDeterminantImage'
00check.log:Undocumented arguments in documentation object 'ImageMath'
00check.log:Undocumented arguments in documentation object
'KellyKapowski'
00check.log:Undocumented arguments in documentation object
'MeasureMinMaxMean'
00check.log:Undocumented arguments in documentation object
'N3BiasFieldCorrection'
00check.log:Undocumented arguments in documentation object
'SmoothImage'
00check.log:Undocumented arguments in documentation object
'ThresholdImage'
00check.log:Undocumented arguments in documentation object
'abpBrainExtraction'
00check.log:Undocumented arguments in documentation object 'abpN4'
00check.log:Undocumented arguments in documentation object
'antsApplyTransforms'
00check.log:Undocumented arguments in documentation object
'antsGetNeighborhood'
00check.log:Undocumented arguments in documentation object
'antsImageMutualInformation'
00check.log:Undocumented arguments in documentation object
'antsMotionCorr'
00check.log:Undocumented arguments in documentation object
'antsPreprocessfMRI'
00check.log:Undocumented arguments in documentation object
'antsRegistration'
00check.log:Undocumented arguments in documentation object
'aslDenoiseR'
00check.log:Undocumented arguments in documentation object
'aslPerfusion'
00check.log:Undocumented arguments in documentation object
'bayesianCBF'
00check.log:Undocumented arguments in documentation object 'bayesianlm'
00check.log:Undocumented arguments in documentation object
'clusterTimeSeries'
00check.log:Undocumented arguments in documentation object 'compcor'
00check.log:Undocumented arguments in documentation object 'corw'
00check.log:Undocumented arguments in documentation object 'eigSeg'
00check.log:Undocumented arguments in documentation object 'fastwhiten'
00check.log:Undocumented arguments in documentation object
'filterfMRIforNetworkAnalysis'
00check.log:Undocumented arguments in documentation object
'frequencyFilterfMRI'
00check.log:Undocumented arguments in documentation object
'getAverageOfTimeSeries'
00check.log:Undocumented arguments in documentation object
'getCentroids'
00check.log:Undocumented arguments in documentation object
'getMultivariateTemplateCoordinates'
00check.log:Undocumented arguments in documentation object
'getROIValues'
00check.log:Undocumented arguments in documentation object
'getTemplateCoordinates'
00check.log:Undocumented arguments in documentation object
'getfMRInuisanceVariables'
00check.log:Undocumented arguments in documentation object 'icawhiten'
00check.log:Undocumented arguments in documentation object
'image2ClusterImages'
00check.log:Undocumented arguments in documentation object
'imageFileNames2ImageList'
00check.log:Undocumented arguments in documentation object
'initializeEigenanatomy'
00check.log:Undocumented arguments in documentation object
'inspectImageData3D'
00check.log:Undocumented arguments in documentation object
'interleaveMatrixWithItself'
00check.log:Undocumented arguments in documentation object
'invariantImageSimilarity'
00check.log:Undocumented arguments in documentation object
'joinEigenanatomy'
00check.log:Undocumented arguments in documentation object
'kmeansSegmentation'
00check.log:Undocumented arguments in documentation object
'labelClusters'
00check.log:Undocumented arguments in documentation object 'lappend'
00check.log:Undocumented arguments in documentation object 'makeGraph'
00check.log:Undocumented arguments in documentation object 'makeImage'
00check.log:Undocumented arguments in documentation object 'mni2tal'
00check.log:Undocumented arguments in documentation object
'networkEiganat'
00check.log:Undocumented arguments in documentation object
'pairwiseImageDistanceMatrix'
00check.log:Undocumented arguments in documentation object
'partialVolumeCorrection'
00check.log:Undocumented arguments in documentation object
'perfusionregression'
00check.log:Undocumented arguments in documentation object
'plotANTsImage'
00check.log:Undocumented arguments in documentation object
'plotBasicNetwork'
00check.log:Undocumented arguments in documentation object
'plotPrettyGraph'
00check.log:Undocumented arguments in documentation object
'projectImageAlongAxis'
00check.log:Undocumented arguments in documentation object
'quantifyCBF'
00check.log:Undocumented arguments in documentation object
'regressionNetworkViz'
00check.log:Undocumented arguments in documentation object
'renderImageLabels'
00check.log:Undocumented arguments in documentation object
'renderNetwork'
00check.log:Undocumented arguments in documentation object
'renderSurfaceFunction'
00check.log:Undocumented arguments in documentation object
'reorientImage'
00check.log:Undocumented arguments in documentation object
'rfSegmentation'
00check.log:Undocumented arguments in documentation object
'rfSegmentationPredict'
00check.log:Undocumented arguments in documentation object 'rsfDenoise'
00check.log:Undocumented arguments in documentation object 'sccan'
00check.log:Undocumented arguments in documentation object
'sparseDecom'
00check.log:Undocumented arguments in documentation object
'sparseDecom2'
00check.log:Undocumented arguments in documentation object
'sparseDecom2boot'
00check.log:Undocumented arguments in documentation object
'sparseDecomboot'
00check.log:Undocumented arguments in documentation object
'subgradientL1Regression'
00check.log:Undocumented arguments in documentation object 'taskFMRI'
00check.log:Undocumented arguments in documentation object
'temporalwhiten'
00check.log:Undocumented arguments in documentation object
'timeseriesN3'
00check.log:Undocumented arguments in documentation object 'usePkg'
00check.log:Undocumented arguments in documentation object 'whiten'


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@stnava stnava commented Feb 4, 2015

Explanation of current dev/check system:

  • hide utility functions by using .functionName

  • these are still accessible via ANTsR:::.functionName in the R user (scripting) space

  • these can be called internally w/in ANTsR as .functionName

  • these functions do not need documentation

  • document all other functions with roxygen2

  • make sure usage variable names and roxygen2 variable names are consistent

  • NAMESPACE: put packages that we minimally rely on in Suggests

    • call haverobust<-usePkg("robust") to use this package internally - never use require or library
    • if ( ! haverobust ) { do something useful like print message and return Null } e.g.

    if ( !usePkg("fpc") ) { print("Need fpc package"); return(NULL) }

    • another example
  if ( predalgorithm == 'svm' )
    {
    havesvm<-usePkg("e1071")
    if ( !havesvm ) predalgorithm<-"lm"
    }
  • Regularly build and check the package .... My current approach is to build two versions of ANTsR
    • one with only the Depends packages
    • another that includes the Suggests packages

then call

R CMD build ANTsR

on a clean version of ANTsR - e.g. a fresh clone or git pull w/o any extra files related to installation ... this creates ANTsR_1.0.tar.gz

then point R CMD check to a library version of ANTsR

R CMD check ANTsR_1.0.tar.gz --library=${R_LIBS} --no-install --as-cran --no-examples

will check that code and not run examples

R CMD check ANTsR_1.0.tar.gz --library=${R_LIBS} --no-install --as-cran

will check the code and run examples

R CMD check ANTsR_1.0.tar.gz --library=${R_LIBS} --no-install --as-cran

will install, check the code and run examples

this last call is the one that we must ultimately pass.

@stnava
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@stnava stnava commented Feb 4, 2015

Currently, there are a few undocumented code bits that @jeffduda will contribute. There are many more inconsistent documentation and usage functions. This is where the most help is currently needed in order to get over the first major barrier to submitting to CRAN. They are here ( note: i reduced this list by a third with about 2 hours' work it's still over 300 lines)

  • checking Rd \usage sections ... WARNING
    Undocumented arguments in documentation object 'ThresholdImage'
    ‘...’
    Documented arguments not in \usage in documentation object 'ThresholdImage':
    ‘imageDimension2|3’ ‘thresh-low’ ‘thresh-high’ ‘inside-value’
    ‘outside-value’ ‘number-of-thresholds’ ‘inputImage’ ‘outputImage’

Undocumented arguments in documentation object 'antsApplyTransforms'
‘moving’ ‘whichtoinvert’ ‘...’
Documented arguments not in \usage in documentation object 'antsApplyTransforms':
‘movingImage’

Undocumented arguments in documentation object 'antsGetNeighborhood'
‘x’
Documented arguments not in \usage in documentation object 'antsGetNeighborhood':
‘image’

Undocumented arguments in documentation object 'antsImage-class'
‘.Object’ ‘pixeltype’ ‘dimension’ ‘x’ ‘mask’ ‘region’ ‘i’ ‘j’ ‘e1’
‘e2’

Undocumented arguments in documentation object 'antsMatrix-class'
‘.Object’ ‘elementtype’ ‘x’

Undocumented arguments in documentation object 'antsMotionCorr'
‘...’
Documented arguments not in \usage in documentation object 'antsMotionCorr':
‘d-or-dimensionality=’

Undocumented arguments in documentation object 'antsPreprocessfMRI'
‘maskingMeanRatioThreshold’ ‘residualizeMatrix’
Documented arguments not in \usage in documentation object 'antsPreprocessfMRI':
‘maskingThreshold’

Undocumented arguments in documentation object 'antsRegistration'
‘...’

Undocumented arguments in documentation object 'as.antsImage'
‘pixeltype’ ‘spacing’ ‘origin’
Documented arguments not in \usage in documentation object 'as.antsImage':
‘data’ ‘Fun’

Undocumented arguments in documentation object 'as.antsMatrix'
‘elementtype’
Documented arguments not in \usage in documentation object 'as.antsMatrix':
‘Fun’

Undocumented arguments in documentation object 'aslDenoiseR'
‘boldmatrix’ ‘targety’ ‘motionparams’ ‘selectionthresh’
‘maxnoisepreds’ ‘debug’ ‘polydegree’ ‘crossvalidationgroups’
‘scalemat’ ‘noisepoolfun’ ‘usecompcor’
Documented arguments not in \usage in documentation object 'aslDenoiseR':
‘mat’

Undocumented arguments in documentation object 'aslPerfusion'
‘asl’ ‘maskThresh’ ‘moreaccurate’ ‘dorobust’ ‘m0’ ‘skip’ ‘mask’
‘interpolation’ ‘checkmeansignal’ ‘moco_results’ ‘regweights’
‘useDenoiser’ ‘useBayesian’ ‘verbose’ ‘ncompcor’ ‘N3’
Documented arguments not in \usage in documentation object 'aslPerfusion':
‘maskThresh=’ ‘dorobust=’
‘asl_antsr_image_or_filename’

Undocumented arguments in documentation object 'eigSeg'
‘imgList’
Documented arguments not in \usage in documentation object 'eigSeg':
‘imageList’

Undocumented arguments in documentation object 'fastwhiten'
‘x’ ‘mynu’
Documented arguments not in \usage in documentation object 'fastwhiten':
‘mat’

Undocumented arguments in documentation object 'filterfMRIforNetworkAnalysis'
‘aslmat’ ‘tr’ ‘freqLo’ ‘freqHi’ ‘cbfnetwork’ ‘mask’ ‘labels’
‘graphdensity’ ‘seg’ ‘useglasso’ ‘nuisancein’ ‘usesvd’ ‘robustcorr’
Documented arguments not in \usage in documentation object 'filterfMRIforNetworkAnalysis':
‘tr=’ ‘freqLo=’ ‘freqHi=’ ‘cbfnetwork="ASLCBF"’
‘maskThresh=’ ‘smoother=’ ‘outputprefix=’
‘asl_antsr_image_or_filename’

Undocumented arguments in documentation object 'frequencyFilterfMRI'
‘boldmat’ ‘tr’ ‘freqLo’ ‘freqHi’ ‘opt’
Documented arguments not in \usage in documentation object 'frequencyFilterfMRI':
‘tr=’ ‘freqLo=’ ‘freqHi=’ ‘opt=c('trig'’
‘'butt'’ ‘'stl')’ ‘boldMatrix’

Undocumented arguments in documentation object 'getAverageOfTimeSeries'
‘timeseriesimage’
Documented arguments not in \usage in documentation object 'getAverageOfTimeSeries':
‘img’

Undocumented arguments in documentation object 'getCentroids'
‘outprefix’

Undocumented arguments in documentation object 'getMultivariateTemplateCoordinates'
‘templateWithLabels’ ‘labelnames’ ‘outprefix’ ‘convertToTal’
‘threshparam’ ‘clustparam’ ‘identifier’

Undocumented arguments in documentation object 'getROIValues'
‘maskImage’
Duplicated \argument entries in documentation object 'getROIValues':
‘valueImage’

Undocumented arguments in documentation object 'getTemplateCoordinates'
‘imagePairToBeLabeled’ ‘templatePairWithLabels’ ‘labelnames’
‘outprefix’ ‘convertToTal’
Documented arguments not in \usage in documentation object 'getTemplateCoordinates':
‘x’

Undocumented arguments in documentation object 'getfMRInuisanceVariables'
‘fmri’ ‘moreaccurate’
Documented arguments not in \usage in documentation object 'getfMRInuisanceVariables':
‘boldImageOrFileName’

Undocumented arguments in documentation object 'icawhiten'
‘Xin’ ‘verbose’
Documented arguments not in \usage in documentation object 'icawhiten':
‘mat’

Undocumented arguments in documentation object 'image2ClusterImages'
‘x’ ‘minClusterSize’ ‘minThresh’ ‘maxThresh’
Documented arguments not in \usage in documentation object 'image2ClusterImages':
‘img’

Undocumented arguments in documentation object 'imageFileNames2ImageList'
‘dim’

Undocumented arguments in documentation object 'initializeEigenanatomy'
‘initmat’
Documented arguments not in \usage in documentation object 'initializeEigenanatomy':
‘mat’

Undocumented arguments in documentation object 'interleaveMatrixWithItself'
‘x’ ‘n’
Documented arguments not in \usage in documentation object 'interleaveMatrixWithItself':
‘mat’

Undocumented arguments in documentation object 'invariantImageSimilarity'
‘in_image1’ ‘in_image2’ ‘txfn’
Documented arguments not in \usage in documentation object 'invariantImageSimilarity':
‘fixedImg’ ‘movingImg’ ‘txFilename’

Undocumented arguments in documentation object 'kmeansSegmentation'
‘img’ ‘kmask’ ‘mrf’

Undocumented arguments in documentation object 'labelClusters'
‘imagein’ ‘minClusterSize’ ‘minThresh’ ‘maxThresh’
Documented arguments not in \usage in documentation object 'labelClusters':
‘img’

Undocumented arguments in documentation object 'lappend'
‘lst’ ‘obj’
Documented arguments not in \usage in documentation object 'lappend':
‘inlist’ ‘myitem’

Undocumented arguments in documentation object 'makeImage'
‘imagesize’ ‘voxval’
Documented arguments not in \usage in documentation object 'makeImage':
‘mat’ ‘val’

Documented arguments not in \usage in documentation object 'matrixToImages':
‘outputRoot’

Undocumented arguments in documentation object 'mni2tal'
‘xin’
Documented arguments not in \usage in documentation object 'mni2tal':
‘x’

Undocumented arguments in documentation object 'networkEiganat'
‘Xin’ ‘sparseness’ ‘nvecs’ ‘its’ ‘gradparam’ ‘mask’ ‘v’ ‘prior’
‘pgradparam’ ‘clustval’ ‘downsample’ ‘doscale’ ‘domin’ ‘verbose’
‘dowhite’ ‘timeme’ ‘addb’ ‘useregression’
Documented arguments not in \usage in documentation object 'networkEiganat':
‘inmatrix’ ‘inmask’ ‘otherparams’

Undocumented arguments in documentation object 'pairwiseImageDistanceMatrix'
‘metrictype’ ‘nclusters’

Undocumented arguments in documentation object 'perfusionregression'
‘skip’ ‘selectionValsForRegweights’ ‘useBayesian’
Documented arguments not in \usage in documentation object 'perfusionregression':
‘m0’

Undocumented arguments in documentation object 'plot.antsImage'
‘color’ ‘axis’ ‘slices’ ‘threshold’ ‘quality’ ‘outname’ ‘alpha’ ‘...’
Documented arguments not in \usage in documentation object 'plot.antsImage':
‘color=’ ‘axis=’ ‘slices=’
‘threshold=’ ‘quality=’ ‘outname='figx.jpg'’

Undocumented arguments in documentation object 'plotBasicNetwork'
‘weights’ ‘edgecolors’ ‘nodecolors’ ‘nodetype’ ‘scaling’ ‘lwd’
‘radius’ ‘showOnlyConnectedNodes’

Undocumented arguments in documentation object 'plotPrettyGraph'
‘functionToPlot’ ‘hueval’
Documented arguments not in \usage in documentation object 'plotPrettyGraph':
‘graphMetricValue’

Undocumented arguments in documentation object 'projectImageAlongAxis'
‘imageND’ ‘referenceImageNDminus1’
Documented arguments not in \usage in documentation object 'projectImageAlongAxis':
‘img4d’ ‘refimg3d’

Undocumented arguments in documentation object 'quantifyCBF'
‘perfusion’ ‘mask’ ‘M0val’ ‘outlierValue’
Documented arguments not in \usage in documentation object 'quantifyCBF':
‘aslmat’ ‘aslmask’

Undocumented arguments in documentation object 'regressionNetworkViz'
‘mylm’
Documented arguments not in \usage in documentation object 'regressionNetworkViz':
‘myLM’

Undocumented arguments in documentation object 'renderImageLabels'
‘blobrender’ ‘alphafunc’ ‘outdir’ ‘outfn’ ‘labels’

Undocumented arguments in documentation object 'renderNetwork'
‘nodecolors’

Undocumented arguments in documentation object 'renderSurfaceFunction'
‘smoothsval’ ‘smoothfval’ ‘alphasurf’ ‘alphafunc’ ‘outdir’ ‘outfn’
‘mycol’ ‘physical’

Undocumented arguments in documentation object 'reorientImage'
‘axis1’ ‘doscale’
Documented arguments not in \usage in documentation object 'reorientImage':
‘axis’

Undocumented arguments in documentation object 'rfSegmentation'
‘labelimg’ ‘ntrees’ ‘verbose’
Documented arguments not in \usage in documentation object 'rfSegmentation':
‘labelimage’

Undocumented arguments in documentation object 'rsfDenoise'
‘boldmatrix’ ‘targety’ ‘motionparams’ ‘selectionthresh’
‘maxnoisepreds’ ‘debug’ ‘polydegree’ ‘crossvalidationgroups’ ‘tr’
‘scalemat’ ‘noisepoolfun’
Documented arguments not in \usage in documentation object 'rsfDenoise':
‘mat’

Undocumented arguments in documentation object 'sparseDecom2'
‘sparseness’ ‘nvecs’ ‘its’ ‘cthresh’ ‘statdir’ ‘perms’ ‘uselong’ ‘z’
‘smooth’ ‘robust’ ‘mycoption’ ‘initializationList’
‘initializationList2’ ‘ell1’
Documented arguments not in \usage in documentation object 'sparseDecom2':
‘otherparams’

Undocumented arguments in documentation object 'sparseDecom2boot'
‘sparseness’ ‘nvecs’ ‘its’ ‘cthresh’ ‘statdir’ ‘perms’ ‘uselong’ ‘z’
‘smooth’ ‘robust’ ‘mycoption’ ‘initializationList’
‘initializationList2’ ‘ell1’ ‘doseg’
Documented arguments not in \usage in documentation object 'sparseDecom2boot':
‘otherparams’

Undocumented arguments in documentation object 'subgradientL1Regression'
‘s’ ‘percentvals’ ‘nits’ ‘betas’ ‘sparval’

Undocumented arguments in documentation object 'taskFMRI'
‘mat’ ‘hrf’ ‘myvars’ ‘correctautocorr’ ‘residualizedesignmatrix’
‘myformula’
Documented arguments not in \usage in documentation object 'taskFMRI':
‘fmriMatrix’ ‘blockDesign’

Undocumented arguments in documentation object 'timeseriesN3'
‘boldimg’
Documented arguments not in \usage in documentation object 'timeseriesN3':
‘mat’

Bad \usage lines found in documentation object 'combineNuisancePredictors':
combineNuisancePredictors <- function(inmat, target,
globalpredictors=NA, localpredictors=NA, maxpreds=4, k=5)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

@dorianps
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@dorianps dorianps commented Feb 5, 2015

I am having trouble with updating ANTsR in cluster. This is what happens when loading the package:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsR/libs/ANTsR.so':
/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsR/libs/ANTsR.so: undefined symbol: _ZN3itk24ImageToImageFilterCommon34GetGlobalDefaultDirectionToleranceEv

Is this related to the problems described above? Do you advise to start over with a clean build?

Dorian

@stnava
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@stnava stnava commented Feb 5, 2015

Unrelated ... probably just need clean build.
On Feb 5, 2015 11:21 AM, "dorianps" notifications@github.com wrote:

I am having trouble with updating ANTsR in cluster. This is what happens
when loading the package:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsR/libs/ANTsR.so':
/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsR/libs/ANTsR.so:
undefined symbol:
_ZN3itk24ImageToImageFilterCommon34GetGlobalDefaultDirectionToleranceEv

Is this related to the problems described above? Do you advise to start
over with a clean build?

Dorian


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#8 (comment).

@bkandel
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@bkandel bkandel commented Feb 5, 2015

@jeffduda Not sure what the status of the undocumented get/set antsImage
methods is. It looks like the best way to go about this would be to have
one common 'get-set' methods man file, like what R has for ?Normal. It
appears that it is possible to do this with Roxygen:
http://r-pkgs.had.co.nz/man.html#dry2
http://stackoverflow.com/questions/15932585/roxygen-two-functions-in-one-rd-file
If you haven't done this yet, I'll take a stab at it, but I don't want to
replicate your work if you've already done some of it.

On 4 February 2015 at 14:16, stnava notifications@github.com wrote:

Currently, there are a few undocumented code bits that @jeffduda
https://github.com/jeffduda will contribute. There are _many more
_inconsistent* documentation and usage functions. This is where the most
help is currently needed in order to get over the first major barrier to
submitting to CRAN. They are here:

  • checking Rd \usage sections ... WARNING Undocumented arguments in
    documentation object 'Atropos' ‘d’ ‘a’ ‘x’ ‘i’ ‘m’ ‘c’ ‘priorweight’ ‘...’
    Duplicated \argument entries in documentation object 'Atropos': ‘list()’
    ‘list()’ ‘’ ‘list()’ ‘’ ‘list(list()’ ‘list()’ ‘’ ‘’ ‘’ ‘)')’ ‘list()’ ‘’
    ‘’ ‘’ ‘list(list()’ ‘list()’ ‘list()’ ‘list()’ ‘list()’ ‘list(list()’
    ‘list()’ ‘list(list()’ ‘list()’ ‘To’ Documented arguments not in \usage in
    documentation object 'Atropos': ‘d-or-'image-dimensionality'=’
    ‘a-or-'intensity-image'=c(’ ‘’ ‘etc)’ ‘b-or-bspline=list(’ ‘’ ‘)’
    ‘i-or-initialization=’ ‘list(list()’ ‘list('list(name='Random'’ ‘)')’
    ‘list()’ ‘list('list(name='Otsu'’ ‘)')’ ‘list('list(name='KMeans'’ ‘’
    ‘)')’ ‘list('list(name='PriorProbabilityImages'’ ‘’ ‘’ ‘)')’
    ‘list('list(name='PriorLabelImage'’ ‘’ ‘)')’
    ‘s-or-'partial-volume-label-set'=’ ‘'use-partial-volume-likelihoods'=’
    ‘p-or-'posterior-formulation'=’ ‘list('list(name='Socrates'’ ‘’ ‘’ ‘’
    ‘)')’ ‘list('list(name='Plato'’ ‘list('list(name='Aristotle'’ ‘)'))’
    ‘x-or-'mask-image'=’ ‘c-or-convergence=list(’ ‘)’
    ‘k-or-'likelihood-model'=’ ‘list(''Gaussian'')’
    ‘list('list(name='HistogramParzenWindows'’ ‘’ ‘)')’
    ‘list('list(name='ManifoldParzenWindows'’ ‘’ ‘’ ‘’ ‘)')’
    ‘list('list(name='JointShapeAndOrientationProbability'’ ‘’ ‘’ ‘’ ‘)')’
    ‘list(''LogEuclideanGaussian'')’ ‘m-or-mrf=’ ‘list('list(’ ‘)')’
    ‘list('list(’ ‘)'))’ ‘g-or-icm=list(’ ‘’ ‘)’ ‘o-or-output=list(’ ‘)’
    ‘u-or-'minimize-memory-usage'=’ ‘w-or-'winsorize-outliers'=’
    ‘list('list(name=BoxPlot’ ‘’ ‘’ ‘)')’ ‘list('list(name=GrubbsRosner’ ‘’
    ‘)'))’ ‘e-or-'use-euclidean-distance'=’
    ‘l-or-'label-propagation'=list(name=whichLabel’ ‘’ ‘)’ ‘To’ ‘Different’
    ‘Both’ ‘Markov’

Undocumented arguments in documentation object 'ImageMath'
‘...’
Documented arguments not in \usage in documentation object 'ImageMath':
‘imageDimension2|3’ ‘outputImage’ ‘operator’ ‘inputImage’
‘otherParams’

Undocumented arguments in documentation object 'KellyKapowski'
‘d’ ‘outimg’ ‘...’
Documented arguments not in \usage in documentation object 'KellyKapowski':
‘imageDimension2|3|4’ ‘inputImage’

Undocumented arguments in documentation object 'MeasureMinMaxMean'
‘mask’

Undocumented arguments in documentation object 'N3BiasFieldCorrection'
‘...’
Documented arguments not in \usage in documentation object
'N3BiasFieldCorrection':
‘imageDimension2|3’ ‘inputImage’ ‘outputImage’ ‘shrikFactor’
‘maskImage’ ‘numberofIterations’ ‘numberofFittingLevels’
‘outputBiasField’

Undocumented arguments in documentation object 'SmoothImage'
‘...’
Documented arguments not in \usage in documentation object 'SmoothImage':
‘imageDimension2|3|4’ ‘inputImage’ ‘Sigma’ ‘outputImage’

Undocumented arguments in documentation object 'ThresholdImage'
‘...’
Documented arguments not in \usage in documentation object
'ThresholdImage':
‘imageDimension2|3’ ‘thresh-low’ ‘thresh-high’ ‘inside-value’
‘outside-value’ ‘number-of-thresholds’ ‘inputImage’ ‘outputImage’

Undocumented arguments in documentation object 'abpBrainExtraction'
‘temmask’ ‘tempriors’ ‘tdir’
Documented arguments not in \usage in documentation object
'abpBrainExtraction':
‘tempriors=c(img1’ ‘imgN)’ ‘tmask’ ‘img2’

Undocumented arguments in documentation object 'abpN4'
‘img’ ‘weightimg’
Documented arguments not in \usage in documentation object 'abpN4':
‘image’ ‘weightimage’

Undocumented arguments in documentation object 'antsApplyTransforms'
‘moving’ ‘whichtoinvert’ ‘...’
Documented arguments not in \usage in documentation object
'antsApplyTransforms':
‘movingImage’

Undocumented arguments in documentation object 'antsGetNeighborhood'
‘x’
Documented arguments not in \usage in documentation object
'antsGetNeighborhood':
‘image’

Undocumented arguments in documentation object 'antsImage-class'
‘.Object’ ‘pixeltype’ ‘dimension’ ‘x’ ‘mask’ ‘region’ ‘i’ ‘j’ ‘e1’
‘e2’

Undocumented arguments in documentation object 'antsMatrix-class'
‘.Object’ ‘elementtype’ ‘x’

Undocumented arguments in documentation object 'antsMotionCorr'
‘...’
Documented arguments not in \usage in documentation object
'antsMotionCorr':
‘d-or-dimensionality=’

Undocumented arguments in documentation object 'antsPreprocessfMRI'
‘maskingMeanRatioThreshold’ ‘residualizeMatrix’
Documented arguments not in \usage in documentation object
'antsPreprocessfMRI':
‘maskingThreshold’

Undocumented arguments in documentation object 'antsRegistration'
‘moving’ ‘...’
Documented arguments not in \usage in documentation object
'antsRegistration':
‘movingImage’

Undocumented arguments in documentation object 'as.antsImage'
‘pixeltype’ ‘spacing’ ‘origin’
Documented arguments not in \usage in documentation object 'as.antsImage':
‘data’ ‘Fun’

Undocumented arguments in documentation object 'as.antsMatrix'
‘elementtype’
Documented arguments not in \usage in documentation object 'as.antsMatrix':
‘Fun’

Undocumented arguments in documentation object 'aslDenoiseR'
‘boldmatrix’ ‘targety’ ‘motionparams’ ‘selectionthresh’
‘maxnoisepreds’ ‘debug’ ‘polydegree’ ‘crossvalidationgroups’
‘scalemat’ ‘noisepoolfun’ ‘usecompcor’
Documented arguments not in \usage in documentation object 'aslDenoiseR':
‘mat’

Undocumented arguments in documentation object 'aslPerfusion'
‘asl’ ‘maskThresh’ ‘moreaccurate’ ‘dorobust’ ‘m0’ ‘skip’ ‘mask’
‘interpolation’ ‘checkmeansignal’ ‘moco_results’ ‘regweights’
‘useDenoiser’ ‘useBayesian’ ‘verbose’ ‘ncompcor’ ‘N3’
Documented arguments not in \usage in documentation object 'aslPerfusion':
‘maskThresh=’ ‘dorobust=’
‘asl_antsr_image_or_filename’

Documented arguments not in \usage in documentation object 'basicInpaint':
‘speedimage’ ‘its’ ‘gparam’
Assignments in \usage in documentation object 'basicInpaint':
approximg <- basicInpaint(img, paintMask)

Undocumented arguments in documentation object 'bayesianCBF'
‘seg’
Documented arguments not in \usage in documentation object 'bayesianCBF':
‘segmentation’

Undocumented arguments in documentation object 'bayesianlm'
‘priorPrecision’ ‘priorIntercept’ ‘regweights’
Documented arguments not in \usage in documentation object 'bayesianlm':
‘precisionMatrix’

Undocumented arguments in documentation object 'clusterTimeSeries'
‘mat’ ‘nsvddims’ ‘criterion’
Documented arguments not in \usage in documentation object
'clusterTimeSeries':
‘img’ ‘mask’

Undocumented arguments in documentation object 'compcor'
‘fmri’ ‘ncompcor’ ‘variance_extreme’ ‘mask’ ‘fastsvd’ ‘useimagemath’
‘randomSamples’ ‘returnhighvarmatinds’ ‘highvarmatinds’
Documented arguments not in \usage in documentation object 'compcor':
‘mat’ ‘returnhighvarmat’

Undocumented arguments in documentation object 'corw'
‘weights’

Undocumented arguments in documentation object 'eigSeg'
‘imgList’
Documented arguments not in \usage in documentation object 'eigSeg':
‘imageList’

Undocumented arguments in documentation object 'fastwhiten'
‘x’ ‘mynu’
Documented arguments not in \usage in documentation object 'fastwhiten':
‘mat’

Undocumented arguments in documentation object
'filterfMRIforNetworkAnalysis'
‘aslmat’ ‘tr’ ‘freqLo’ ‘freqHi’ ‘cbfnetwork’ ‘mask’ ‘labels’
‘graphdensity’ ‘seg’ ‘useglasso’ ‘nuisancein’ ‘usesvd’ ‘robustcorr’
Documented arguments not in \usage in documentation object
'filterfMRIforNetworkAnalysis':
‘tr=’ ‘freqLo=’ ‘freqHi=’ ‘cbfnetwork="ASLCBF"’
‘maskThresh=’ ‘smoother=’ ‘outputprefix=’
‘asl_antsr_image_or_filename’

Undocumented arguments in documentation object 'frequencyFilterfMRI'
‘boldmat’ ‘tr’ ‘freqLo’ ‘freqHi’ ‘opt’
Documented arguments not in \usage in documentation object
'frequencyFilterfMRI':
‘tr=’ ‘freqLo=’ ‘freqHi=’ ‘opt=c('trig'’
‘'butt'’ ‘'stl')’ ‘boldMatrix’

Undocumented arguments in documentation object 'getAverageOfTimeSeries'
‘timeseriesimage’
Documented arguments not in \usage in documentation object
'getAverageOfTimeSeries':
‘img’

Undocumented arguments in documentation object 'getCentroids'
‘outprefix’

Undocumented arguments in documentation object
'getMultivariateTemplateCoordinates'
‘templateWithLabels’ ‘labelnames’ ‘outprefix’ ‘convertToTal’
‘threshparam’ ‘clustparam’ ‘identifier’

Undocumented arguments in documentation object 'getROIValues'
‘maskImage’
Duplicated \argument entries in documentation object 'getROIValues':
‘valueImage’

Undocumented arguments in documentation object 'getTemplateCoordinates'
‘imagePairToBeLabeled’ ‘templatePairWithLabels’ ‘labelnames’
‘outprefix’ ‘convertToTal’
Documented arguments not in \usage in documentation object
'getTemplateCoordinates':
‘x’

Undocumented arguments in documentation object 'getfMRInuisanceVariables'
‘fmri’ ‘moreaccurate’
Documented arguments not in \usage in documentation object
'getfMRInuisanceVariables':
‘boldImageOrFileName’

Undocumented arguments in documentation object 'icawhiten'
‘Xin’ ‘verbose’
Documented arguments not in \usage in documentation object 'icawhiten':
‘mat’

Undocumented arguments in documentation object 'image2ClusterImages'
‘x’ ‘minClusterSize’ ‘minThresh’ ‘maxThresh’
Documented arguments not in \usage in documentation object
'image2ClusterImages':
‘img’

Undocumented arguments in documentation object 'imageFileNames2ImageList'
‘dim’

Undocumented arguments in documentation object 'initializeEigenanatomy'
‘initmat’
Documented arguments not in \usage in documentation object
'initializeEigenanatomy':
‘mat’

Undocumented arguments in documentation object 'inspectImageData3D'
‘myfiles’
Documented arguments not in \usage in documentation object
'inspectImageData3D':
‘fn’

Undocumented arguments in documentation object 'interleaveMatrixWithItself'
‘x’ ‘n’
Documented arguments not in \usage in documentation object
'interleaveMatrixWithItself':
‘mat’

Undocumented arguments in documentation object 'invariantImageSimilarity'
‘in_image1’ ‘in_image2’ ‘txfn’
Documented arguments not in \usage in documentation object
'invariantImageSimilarity':
‘fixedImg’ ‘movingImg’ ‘txFilename’

Undocumented arguments in documentation object 'joinEigenanatomy'
‘list_of_eanat_images’ ‘verbose’
Documented arguments not in \usage in documentation object
'joinEigenanatomy':
‘listEanatImages’

Undocumented arguments in documentation object 'kmeansSegmentation'
‘img’ ‘kmask’ ‘mrf’

Undocumented arguments in documentation object 'labelClusters'
‘imagein’ ‘minClusterSize’ ‘minThresh’ ‘maxThresh’
Documented arguments not in \usage in documentation object 'labelClusters':
‘img’

Undocumented arguments in documentation object 'lappend'
‘lst’ ‘obj’
Documented arguments not in \usage in documentation object 'lappend':
‘inlist’ ‘myitem’

Undocumented arguments in documentation object 'makeGraph'
‘myrsfnetworkcorrsin’ ‘getEfficiency’
Documented arguments not in \usage in documentation object 'makeGraph':
‘mat’

Undocumented arguments in documentation object 'makeImage'
‘imagesize’ ‘voxval’
Documented arguments not in \usage in documentation object 'makeImage':
‘mat’ ‘val’

Documented arguments not in \usage in documentation object
'matrixToImages':
‘outputRoot’

Undocumented arguments in documentation object 'mni2tal'
‘xin’
Documented arguments not in \usage in documentation object 'mni2tal':
‘x’

Undocumented arguments in documentation object 'networkEiganat'
‘Xin’ ‘sparseness’ ‘nvecs’ ‘its’ ‘gradparam’ ‘mask’ ‘v’ ‘prior’
‘pgradparam’ ‘clustval’ ‘downsample’ ‘doscale’ ‘domin’ ‘verbose’
‘dowhite’ ‘timeme’ ‘addb’ ‘useregression’
Documented arguments not in \usage in documentation object
'networkEiganat':
‘inmatrix’ ‘inmask’ ‘otherparams’

Undocumented arguments in documentation object
'pairwiseImageDistanceMatrix'
‘metrictype’ ‘nclusters’

Undocumented arguments in documentation object 'partialVolumeCorrection'
‘img’ ‘img.gm’ ‘img.wm’
Documented arguments not in \usage in documentation object
'partialVolumeCorrection':
‘image’ ‘image.gm’ ‘image.wm’

Undocumented arguments in documentation object 'perfusionregression'
‘skip’ ‘selectionValsForRegweights’ ‘useBayesian’
Documented arguments not in \usage in documentation object
'perfusionregression':
‘m0’

Undocumented arguments in documentation object 'plot.antsImage'
‘color’ ‘axis’ ‘slices’ ‘threshold’ ‘quality’ ‘outname’ ‘alpha’ ‘...’
Documented arguments not in \usage in documentation object
'plot.antsImage':
‘color=’ ‘axis=’ ‘slices=’
‘threshold=’ ‘quality=’ ‘outname='figx.jpg'’

Undocumented arguments in documentation object 'plotBasicNetwork'
‘weights’ ‘edgecolors’ ‘nodecolors’ ‘nodetype’ ‘scaling’ ‘lwd’
‘radius’ ‘showOnlyConnectedNodes’

Undocumented arguments in documentation object 'plotPrettyGraph'
‘functionToPlot’ ‘hueval’
Documented arguments not in \usage in documentation object
'plotPrettyGraph':
‘graphMetricValue’

Undocumented arguments in documentation object 'projectImageAlongAxis'
‘imageND’ ‘referenceImageNDminus1’
Documented arguments not in \usage in documentation object
'projectImageAlongAxis':
‘img4d’ ‘refimg3d’

Undocumented arguments in documentation object 'quantifyCBF'
‘perfusion’ ‘mask’ ‘M0val’ ‘outlierValue’
Documented arguments not in \usage in documentation object 'quantifyCBF':
‘aslmat’ ‘aslmask’

Undocumented arguments in documentation object 'regressionNetworkViz'
‘mylm’ ‘sigthresh’ ‘whichviz’ ‘outfile’ ‘mygroup’ ‘logvals’ ‘verbose’
‘correlateMyOutcomes’ ‘corthresh’ ‘zoom’ ‘doFDR’
Documented arguments not in \usage in documentation object
'regressionNetworkViz':
‘myLM’

Undocumented arguments in documentation object 'renderImageLabels'
‘blobrender’ ‘alphafunc’ ‘outdir’ ‘outfn’ ‘labels’

Undocumented arguments in documentation object 'renderNetwork'
‘nodecolors’

Undocumented arguments in documentation object 'renderSurfaceFunction'
‘smoothsval’ ‘smoothfval’ ‘alphasurf’ ‘alphafunc’ ‘outdir’ ‘outfn’
‘mycol’ ‘physical’

Undocumented arguments in documentation object 'reorientImage'
‘axis1’ ‘doscale’
Documented arguments not in \usage in documentation object 'reorientImage':
‘axis’

Undocumented arguments in documentation object 'rfSegmentation'
‘labelimg’ ‘ntrees’ ‘verbose’
Documented arguments not in \usage in documentation object
'rfSegmentation':
‘labelimage’

Undocumented arguments in documentation object 'rfSegmentationPredict'
‘rfSegmentationModel’ ‘mask’ ‘verbose’
Documented arguments not in \usage in documentation object
'rfSegmentationPredict':
‘model’

Undocumented arguments in documentation object 'rsfDenoise'
‘boldmatrix’ ‘targety’ ‘motionparams’ ‘selectionthresh’
‘maxnoisepreds’ ‘debug’ ‘polydegree’ ‘crossvalidationgroups’ ‘tr’
‘scalemat’ ‘noisepoolfun’
Documented arguments not in \usage in documentation object 'rsfDenoise':
‘mat’

Undocumented arguments in documentation object 'sparseDecom'
‘sparseness’ ‘nvecs’ ‘its’ ‘cthresh’ ‘statdir’ ‘z’ ‘smooth’
‘initializationList’ ‘mycoption’ ‘robust’ ‘ell1’
Documented arguments not in \usage in documentation object 'sparseDecom':
‘otherparams’

Undocumented arguments in documentation object 'sparseDecom2'
‘sparseness’ ‘nvecs’ ‘its’ ‘cthresh’ ‘statdir’ ‘perms’ ‘uselong’ ‘z’
‘smooth’ ‘robust’ ‘mycoption’ ‘initializationList’
‘initializationList2’ ‘ell1’
Documented arguments not in \usage in documentation object 'sparseDecom2':
‘otherparams’

Undocumented arguments in documentation object 'sparseDecom2boot'
‘sparseness’ ‘nvecs’ ‘its’ ‘cthresh’ ‘statdir’ ‘perms’ ‘uselong’ ‘z’
‘smooth’ ‘robust’ ‘mycoption’ ‘initializationList’
‘initializationList2’ ‘ell1’ ‘doseg’
Documented arguments not in \usage in documentation object
'sparseDecom2boot':
‘otherparams’

Undocumented arguments in documentation object 'sparseDecomboot'
‘sparseness’ ‘nvecs’ ‘its’ ‘cthresh’ ‘statdir’ ‘z’ ‘smooth’
‘initializationList’ ‘mycoption’ ‘robust’ ‘doseg’
Documented arguments not in \usage in documentation object
'sparseDecomboot':
‘otherparams’

Undocumented arguments in documentation object 'subgradientL1Regression'
‘s’ ‘percentvals’ ‘nits’ ‘betas’ ‘sparval’

Undocumented arguments in documentation object 'taskFMRI'
‘mat’ ‘hrf’ ‘myvars’ ‘correctautocorr’ ‘residualizedesignmatrix’
‘myformula’
Documented arguments not in \usage in documentation object 'taskFMRI':
‘fmriMatrix’ ‘blockDesign’

Undocumented arguments in documentation object 'temporalwhiten'
‘myord’

Undocumented arguments in documentation object 'timeseriesN3'
‘boldimg’
Documented arguments not in \usage in documentation object 'timeseriesN3':
‘mat’

Bad \usage lines found in documentation object 'combineNuisancePredictors':
combineNuisancePredictors <- function(inmat, target,
globalpredictors=NA, localpredictors=NA, maxpreds=4, k=5)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.


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#8 (comment).

@dorianps
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@dorianps dorianps commented Feb 5, 2015

@stnava Thanks, a clean install resolved the problem.

@jeffduda
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@jeffduda jeffduda commented Feb 5, 2015

@bkandel https://github.com/bkandel, I haven't had a chance to work on
that yet, but I agree that a common man file would be best if possible.

On Thu, Feb 5, 2015 at 1:04 PM, dorianps notifications@github.com wrote:

@stnava https://github.com/stnava Thanks, a clean install resolved the
problem.


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#8 (comment).

@stnava
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@stnava stnava commented Feb 5, 2015

We crushed it over the last few days. Here is the new R CMD check result:

  • using log directory ‘/Users/stnava/Downloads/temp/ANTsR.Rcheck’
  • using R version 3.1.2 (2014-10-31)
  • using platform: x86_64-apple-darwin13.4.0 (64-bit)
  • using session charset: UTF-8
  • using options ‘--no-install --no-examples’
  • checking for file ‘ANTsR/DESCRIPTION’ ... OK
  • checking extension type ... Package
  • this is package ‘ANTsR’ version ‘1.0’
  • checking CRAN incoming feasibility ... NOTE
    Maintainer: ‘Brian B. Avants stnava@gmail.com
    New submission
  • checking if this is a source package ... OK
  • checking if there is a namespace ... OK
  • checking for executable files ... OK
  • checking for hidden files and directories ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking package directory ... OK
  • checking DESCRIPTION meta-information ... OK
  • checking top-level files ... OK
  • checking for left-over files ... OK
  • checking index information ... OK
  • checking package subdirectories ... OK
  • checking R files for non-ASCII characters ... OK
  • checking R files for syntax errors ... OK
  • checking dependencies in R code ... OK
  • checking S3 generic/method consistency ... OK
  • checking replacement functions ... OK
  • checking foreign function calls ... OK
  • checking R code for possible problems ... OK
  • checking Rd files ... OK
  • checking Rd metadata ... OK
  • checking Rd line widths ... OK
  • checking Rd cross-references ... OK
  • checking for missing documentation entries ... WARNING
    Undocumented code objects:
    ‘antsCopyImageInfo’ ‘antsGetPixels’ ‘antsMotionCorrStats’
    ‘antsSetPixels’ ‘antsTransformIndexToPhysicalPoint’
    ‘antsTransformPhysicalPointToIndex’ ‘as.data.frame.antsMatrix’
    All user-level objects in a package should have documentation entries.
    See the chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
  • checking for code/documentation mismatches ... OK
  • checking Rd \usage sections ... WARNING
    Undocumented arguments in documentation object 'antsImage-class'
    ‘.Object’ ‘pixeltype’ ‘dimension’ ‘x’ ‘mask’ ‘region’ ‘i’ ‘j’ ‘e1’
    ‘e2’

Undocumented arguments in documentation object 'antsMatrix-class'
‘.Object’ ‘elementtype’ ‘x’

Undocumented arguments in documentation object 'as.antsImage'
‘pixeltype’ ‘spacing’ ‘origin’
Documented arguments not in \usage in documentation object 'as.antsImage':
‘data’ ‘Fun’

Undocumented arguments in documentation object 'as.antsMatrix'
‘elementtype’
Documented arguments not in \usage in documentation object 'as.antsMatrix':
‘Fun’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

  • checking Rd contents ... OK
  • checking contents of ‘data’ directory ... OK
  • checking data for non-ASCII characters ... OK
  • checking data for ASCII and uncompressed saves ... OK
  • checking line endings in C/C++/Fortran sources/headers ... OK
  • checking line endings in Makefiles ... OK
  • checking compilation flags in Makevars ... OK
  • checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
  • checking examples ... SKIPPED
  • checking PDF version of manual ... OK
  • DONE
    WARNING: There were 2 warnings.
    NOTE: There was 1 note.
@stnava
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@stnava stnava commented Feb 6, 2015

Current state on OSX Yosemite:

  • all examples run well with dependencies installed (and likely even without, though i've not tested this recently)
  • almost all code is documented ( except above ) hopefully can figure out above soon
  • compile time remains an issue that will bother cran - may be helped by "thin ants"
  • example run time remains an issue that will bother cran but this can be fixed w/just a little effort
  • checking examples ... OK
    Examples with CPU or elapsed time > 5s
    user system elapsed
    combineNuisancePredictors 135.926 9.865 90.198
    getASLNoisePredictors 87.043 5.630 37.793
    antsMotionCalculation 84.499 5.454 35.636
    antsGetNeighborhoodMatrix 11.707 0.930 12.812
  • much of the time cost in some examples is in downloading data
  • package footprint may be an issue but seems to be under official 100MB limit --- need to check this again .... the result of R cmd build is under 500k ....
  • will be some small issues with MAKEFILE and git calls but @jeffduda is working on this

that's all i can think of at the moment re:cran... other design issues include

  • quality of documentation is inconsistent
  • should have rimageMath to complement ImageMath with the former following R style and the latter ANTs style
  • similar for other functions ...
  • need a vignette ...

am ultimately hopeful these issues may be overcome .... but if not, perhaps install_github isnt so bad .... esp if we have well-documented code with use-cases etc readily available.

@stnava
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@stnava stnava commented Feb 6, 2015

ok - major progress: no documentation inconsistencies for the first time ... but still some undocumented code:

Undocumented code objects:
‘antsCopyImageInfo’ ‘antsGetPixels’ ‘antsMotionCorrStats’
‘antsSetPixels’ ‘antsTransformIndexToPhysicalPoint’
‘antsTransformPhysicalPointToIndex’

am reading through the antsr manual and correcting typos etc though this will probably take several iterations to get right.

  • inconsistent use of quotations is a major annoyance
  • need to use double quotes "r16" to keep the quotations in the final documentation pdf

so we are down to 1 warning ...

@jeffduda
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@jeffduda jeffduda commented Feb 6, 2015

will work on adding in that documentation now.

On Fri, Feb 6, 2015 at 12:24 PM, stnava notifications@github.com wrote:

ok - major progress: no documentation inconsistencies for the first
time ... but still some undocumented code:

Undocumented code objects:
‘antsCopyImageInfo’ ‘antsGetPixels’ ‘antsMotionCorrStats’
‘antsSetPixels’ ‘antsTransformIndexToPhysicalPoint’
‘antsTransformPhysicalPointToIndex’

am reading through the antsr manual and correcting typos etc though this
will probably take several iterations to get right.

inconsistent use of quotations is a major annoyance

need to use double quotes "r16" to keep the quotations in the final
documentation pdf

so we are down to 1 warning ...


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#8 (comment).

@stnava
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@stnava stnava commented Feb 6, 2015

re STYLE: have mostly eliminated calls of the form FunctionName(dim, img, ... ) and replaced with functionName( img , ... ) stragglers include:

  • ThresholdImage
  • ImageMath

for the latter, i will implement antsImageMath with usage similar to:

output<-iMath( img,"operationName", ... )

and (maybe) where you will be able to do

ops<-iMath("GetOperations")

to see its possible uses ...

will keep ImageMath(...) around but replace with iMath in documentation examples ....

any suggestions welcome before i start this ....

@bkandel
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@bkandel bkandel commented Mar 23, 2015

Another representation of current feeling re: cran:
http://blog.ironholds.org/dont-use-the-mailing-lists-a-love-letter-to-the-r-community/

2015-03-23 13:10 GMT-04:00 stnava notifications@github.com:

@bkandel https://github.com/bkandel , @armaneshaghi
https://github.com/armaneshaghi , @dorianps
https://github.com/dorianps - very good points ... in terms of time
invested / payoff, certainly the way to go, at least for the moment. in
addition, releasing binary versions of the packages, cmaker, ITKR, and
ANTsR. we can also make homepages mimic CRAN package homepages in some
respects.

as alluded to above, i would like to separate ITKR and ANTsR within the
main development branch because of consistent time to install savings. that
would also let us work out ITKR on windows and follow that with ANTsR (if
possible).


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#8 (comment).

@stnava
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@stnava stnava commented Mar 23, 2015

yes - lots of people thinking about ideas like @muschellij2 mentioned - ie ways to workaround the mercurial CRAN gatekeeper. the comments on that blog post are interesting.

updated ANTsR to expect ITKR. this will probably cause some pain, at first, but should ease maintenance and development, longer term. +lets us consider how to build ITKR on windows. if we get that working, might submit ITKR to cran again, just for "fun" and to see if i get another brian ripley "No further submissions will be considered."

@bkandel
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@bkandel bkandel commented Mar 24, 2015

Continuing conversation I started with Brian here to get broader feedback:
The one thing that CRAN does nicely is dependency checks. As far as I
know, there is no elegant, automated way of getting dependency checks when
not using CRAN. devtools points us in the right direction, but does not
quite get there: install_github's install_deps only works for CRAN
packages, for example, and Hadley has said a few times that he doesn't see
devtools as a full replacement for CRAN. install_github does, however,
allow for installation of specific git tags or releases, which is a huge
step in the right direction.

One critical point for us is to make sure that we can link ITKR and ANTsR
versions: If updated ANTsR requires a new version of ITKR, then ITKR
should be reinstalled. We could hack a solution for ITKR alone, or try to
see if we can find a generic (non-CRAN) solution. The closest thing I've
seen is the collection of repos from Gabor Csardi (who is also clearly very
frustrated with CRAN culture and procedures), linked to at the bottom of
that blog post. I'll explore this a bit more and see if I can find
anything reasonable.

2015-03-23 14:50 GMT-04:00 stnava notifications@github.com:

yes - lots of people thinking about ideas like @muschellij2
https://github.com/muschellij2 mentioned - ie ways to workaround the
mercurial CRAN gatekeeper. the comments on that blog post are interesting.

updated ANTsR to expect ITKR. this will probably cause some pain, at
first, but should ease maintenance and development, longer term. +lets us
consider how to build ITKR on windows. if we get that working, might submit
ITKR to cran again, just for "fun" and to see if i get another brian ripley
"No further submissions will be considered."


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#8 (comment).

@stnava
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@stnava stnava commented Mar 24, 2015

​it's true that the only solution i know is a manual one ... or we
reinstate the old build style: distribute ( or git clone ) both ITK and
ANTS.​

brian

On Tue, Mar 24, 2015 at 9:56 AM, bkandel notifications@github.com wrote:

Continuing conversation I started with Brian here to get broader feedback:
The one thing that CRAN does nicely is dependency checks. As far as I
know, there is no elegant, automated way of getting dependency checks when
not using CRAN. devtools points us in the right direction, but does not
quite get there: install_github's install_deps only works for CRAN
packages, for example, and Hadley has said a few times that he doesn't see
devtools as a full replacement for CRAN. install_github does, however,
allow for installation of specific git tags or releases, which is a huge
step in the right direction.

One critical point for us is to make sure that we can link ITKR and ANTsR
versions: If updated ANTsR requires a new version of ITKR, then ITKR
should be reinstalled. We could hack a solution for ITKR alone, or try to
see if we can find a generic (non-CRAN) solution. The closest thing I've
seen is the collection of repos from Gabor Csardi (who is also clearly very
frustrated with CRAN culture and procedures), linked to at the bottom of
that blog post. I'll explore this a bit more and see if I can find
anything reasonable.

2015-03-23 14:50 GMT-04:00 stnava notifications@github.com:

yes - lots of people thinking about ideas like @muschellij2
https://github.com/muschellij2 mentioned - ie ways to workaround the
mercurial CRAN gatekeeper. the comments on that blog post are
interesting.

updated ANTsR to expect ITKR. this will probably cause some pain, at
first, but should ease maintenance and development, longer term. +lets us
consider how to build ITKR on windows. if we get that working, might
submit
ITKR to cran again, just for "fun" and to see if i get another brian
ripley
"No further submissions will be considered."


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#8 (comment).

@stnava
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@stnava stnava commented Mar 25, 2015

The travis build is now running R CMD check.

We should be better off from here on out wrt detecting documentation or example code issues.

@stnava
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@stnava stnava commented Mar 25, 2015

updated the website http://stnava.github.io/ANTsR/ with CRAN like links / structure

@zarquon42b
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@zarquon42b zarquon42b commented Apr 17, 2015

First of all, thumbs up for all your efforts and that great software (and especially bringing ANTs to R).
The submission to CRAN, is a pain in the a**, which keeps me from pushing some packages to CRAN (I had to argue about a failing build on Solaris).
Have you looked at Dirk Edelbuettels's new drat package? It seems that you can use that to create your custom CRAN like repositiories on gh-pages.

Here is some further info: http://dirk.eddelbuettel.com/blog/2015/03/13/

@bkandel
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@bkandel bkandel commented Apr 17, 2015

Yes, CRAN is very frustrating. We tried drat, but couldn't get it to
work. It didn't appear to deal with dependencies correctly. Even though I
registered the "stnava" repo, it didn't properly process the CMakeR and
ITKR dependencies. The drat model of forking the drat parent repo does not
really lend itself to easy deployment.

If you have gotten drat to work successfully on your projects, I'd be very
interested in hearing more details.

2015-04-17 15:48 GMT-04:00 Stefan Schlager notifications@github.com:

First of all, thumbs up for all your efforts and that great software (and
especially bringing ANTs to R).
The submission to CRAN, is a pain in the a**, which keeps me from pushing
some packages to CRAN (I had to argue about a failing build on Solaris).
Have you looked at Dirk Edelbuettels's new drat
http://cran.rstudio.com/web/packages/drat/index.html package? It seems
that you can use that to create your custom CRAN like repositiories on
gh-pages.

Here is some further info: http://dirk.eddelbuettel.com/blog/2015/03/13/


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@zarquon42b
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@zarquon42b zarquon42b commented Apr 17, 2015

No, I only read the posts about drat, but thought of playing with it, if I find the time. Maybe I can have a look at it next week and report back if I succeeded (or not).

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@zarquon42b zarquon42b commented Apr 17, 2015

OK, I just set up a quick and dirty repo for ANTsR and it seems to work (though I had to set the -fpermissive flag again in ~/R/Makevar - see here )
please try (after installing drat):

drat::addRepo("zarquon42b")
install.packages("ANTsR")

You do not need to fork the drat repo, simply a gh-pages branch (https://github.com/zarquon42b/drat/tree/gh-pages/src/contrib) with a similar folder layout and register the new tarballs with drat::insertPackage locally in your local github repo and then push it.

EDIT: renamed repo drattest to drat as it actually worked now and simplified the addRepo step.

@jefferis
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@jefferis jefferis commented Apr 17, 2015

On 17 Apr 2015, at 21:44, Stefan Schlager notifications@github.com wrote:

OK, I just set up a quick and dirty repo for ANTsR and it seems to work (though I had to set the -fpermissive flag again in ~/R/Makevar - see here )
please try (after installing drat):

drat::addRepo("zarquon42b",alturl = "http://zarquon42b.github.io/drattest")
install.packages("ANTsR")
You do not need to fork the drat repo, simply a gh-pages branch with a similar folder layout and register the new tarballs with drat::insertPackage locally in your local github repo and then push it.

Good stuff @zarquon42b. I did a bit more mucking around here if it’s of interest:

https://jefferis.github.io/drattest/

Best, Greg.

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@zarquon42b zarquon42b commented Apr 17, 2015

looks excellent @jefferis .
As you can see from my edit above, I renamed the repo, which makes the addRepo command even shorter (drat::addRepo("zarquon42b")) because addRepo assumes a repo named drat inf no alturl is specified.

Best
Stefan

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@bkandel bkandel commented Apr 17, 2015

Great! Thanks for doing this. I'll check it out--this would be a huge
help in keeping ITKR and ANTsR synced.

2015-04-17 17:54 GMT-04:00 Stefan Schlager notifications@github.com:

looks excellent @jefferis https://github.com/jefferis .
As you can see from my edit above, I renamed the repo, which makes the
addRepo command even shorter (drat::addRepo("zarquon42b")) because addRepo
assumes a repo named drat inf no alturl is specified.

Best
Stefan


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@zarquon42b
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@zarquon42b zarquon42b commented Apr 18, 2015

Maybe it would be useful to create a github organization called "ANTsR" with a repo named drats, where you put the tarballs.
The command to add the would be drat::addRepo("ANTsR") which is quite easy to remember.

Best
Stefan

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@zarquon42b zarquon42b commented Apr 19, 2015

Hi everybody,

I initialized a drat repo at https://github.com/ANTs-R/drat and added the latest snapshots of ANTsR, ITKR and cmaker (to be found in the gh-pages branch. To install ANTsR simply do:

drat::addRepo("ANTs-R")
install.packages("ANTsR")

I also wrote a (still somewhat messy) bash script to bump package version and options to build and add tarballs to a drat repo (you simply have to commit the changes and push them afterwards).

Best
Stefan

@stnava
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@stnava stnava commented Apr 20, 2015

@zarquon42b - i made a note of drat installation instructions in README/homepage. thank you for this.

@zarquon42b
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@zarquon42b zarquon42b commented Apr 20, 2015

@stnava - You are very welcome.
BTW: I pimped the script and added options for automatic commiting and/or pushing after version bump.

@bkandel
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@bkandel bkandel commented Apr 20, 2015

Just tested this out using packrat--works great! Easiest way I've seen to
manage dependencies. Thanks a lot for setting this up.

2015-04-20 11:04 GMT-04:00 Stefan Schlager notifications@github.com:

@stnava https://github.com/stnava - You are very welcome.
BTW: I pimped the script
https://github.com/zarquon42b/misc/blob/master/packageVersion.sh and
added options for automatic commiting and/or pushing after version bump.


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@stnava stnava commented May 7, 2015

Preparing to increment version here:

f9616a9

also added release notes

@bkandel , @jeffduda - do you have anything in the pipeline (imath, vignettes, multichannel) that would be ready relatively soon?

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@jeffduda jeffduda commented May 7, 2015

i could probably finish up the iMath revision by the end of next week

On Thu, May 7, 2015 at 5:32 PM, stnava notifications@github.com wrote:

Preparing to increment version here:

f9616a9
f9616a9

also added release notes

@bkandel https://github.com/bkandel , @jeffduda
https://github.com/jeffduda - do you have anything in the pipeline
(imath, vignettes, multichannel) that would be ready relatively soon?


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@bkandel bkandel commented May 7, 2015

All the ASL processing functions are already implemented. Although I don't
have an exhaustive vignette, I do have a working skeleton of
antsASLProcessing.R (not full interface to everything, but the basic
functionality is there) that I'm in the process of applying to several
datasets.

2015-05-07 17:34 GMT-04:00 Jeffrey Duda notifications@github.com:

i could probably finish up the iMath revision by the end of next week

On Thu, May 7, 2015 at 5:32 PM, stnava notifications@github.com wrote:

Preparing to increment version here:

f9616a9
<
f9616a9

also added release notes

@bkandel https://github.com/bkandel , @jeffduda
https://github.com/jeffduda - do you have anything in the pipeline
(imath, vignettes, multichannel) that would be ready relatively soon?


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#8 (comment).

@zarquon42b
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@zarquon42b zarquon42b commented May 8, 2015

If you want me to update the drat repo, please nudge me (BTW: I put some occasional"nightly builds" of ANTsR in my own drat repo at https://github.com/zarquon42b/drat/tree/gh-pages/src/contrib)

@stnava
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@stnava stnava commented Jan 7, 2016

@jeffduda i am trying to update the ANTsR manual online and found that it failed to build ... there could be a few possibilities but it would be great if you could address these first issues:

Undocumented code objects:
  ‘antsTransformFromDisplacementField’ ‘antsTransformInverse’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'as.antsImage' but not in code:
  as.antsImage

Functions or methods with usage in documentation object 'as.antsMatrix' but not in code:
  as.antsMatrix

Functions or methods with usage in documentation object '%>%' but not in code:
  %>%

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'antsApplyTransformToImage'
  ‘transform’ ‘reference’ ‘interpolation’
Documented arguments not in \usage in documentation object 'antsApplyTransformToImage':
  ‘tx’ ‘ref’

Undocumented arguments in documentation object 'antsApplyTransformToPoint'
  ‘point’

Undocumented arguments in documentation object 'antsTransformRead'
  ‘dimension’ ‘precision’

Documented arguments not in \usage in documentation object 'as.antsImage':
  ‘pixeltype’ ‘spacing’ ‘origin’ ‘direction’ ‘components’ ‘reference’

Documented arguments not in \usage in documentation object 'as.antsMatrix':
  ‘elementtype’

Duplicated \argument entries in documentation object 'computeDVARS':
  ‘boldMatrix’

Undocumented arguments in documentation object 'preprocessRestingBOLD'
  ‘denseFramewise’ ‘motionCorrectionIterations’

Undocumented arguments in documentation object '[,antsImage,NULL,ANY-method'
  ‘...’
Documented arguments not in \usage in documentation object '[,antsImage,NULL,ANY-method':
  ‘k’ ‘l’ ‘value’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

i found this simply via:

R CMD build --no-build-vignettes ANTsR
R CMD check  --no-build-vignettes  --no-install ANTsR_0.3.2.tar.gz 

which is fairly fast to run ... you might also (temporarily) edit the ANTsR/src/Makevars from this:

tlibs: ; cd ${PWD}/antb 

libs: ; cd ${PWD}/antb && $(MAKE) -j 2

to this:

libs: ; cd ${PWD}/antb 

tlibs: ; cd ${PWD}/antb && $(MAKE) -j 2

to avoid any wasted time recompiling c++.

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@jeffduda jeffduda commented Jan 7, 2016

Thanks for the tip on avoid the recompiling. That makes doing the check
much more convenient.

On Thu, Jan 7, 2016 at 11:04 AM, stnava notifications@github.com wrote:

@jeffduda https://github.com/jeffduda i am trying to update the ANTsR
manual online and found that it failed to build ... there could be a few
possibilities but it would be great if you could address these first issues:

Undocumented code objects:
‘antsTransformFromDisplacementField’ ‘antsTransformInverse’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

  • checking for code/documentation mismatches ... WARNING
    Functions or methods with usage in documentation object 'as.antsImage' but not in code:
    as.antsImage

Functions or methods with usage in documentation object 'as.antsMatrix' but not in code:
as.antsMatrix

Functions or methods with usage in documentation object '%>%' but not in code:
%>%

  • checking Rd \usage sections ... WARNING
    Undocumented arguments in documentation object 'antsApplyTransformToImage'
    ‘transform’ ‘reference’ ‘interpolation’
    Documented arguments not in \usage in documentation object 'antsApplyTransformToImage':
    ‘tx’ ‘ref’

Undocumented arguments in documentation object 'antsApplyTransformToPoint'
‘point’

Undocumented arguments in documentation object 'antsTransformRead'
‘dimension’ ‘precision’

Documented arguments not in \usage in documentation object 'as.antsImage':
‘pixeltype’ ‘spacing’ ‘origin’ ‘direction’ ‘components’ ‘reference’

Documented arguments not in \usage in documentation object 'as.antsMatrix':
‘elementtype’

Duplicated \argument entries in documentation object 'computeDVARS':
‘boldMatrix’

Undocumented arguments in documentation object 'preprocessRestingBOLD'
‘denseFramewise’ ‘motionCorrectionIterations’

Undocumented arguments in documentation object '[,antsImage,NULL,ANY-method'
‘...’
Documented arguments not in \usage in documentation object '[,antsImage,NULL,ANY-method':
‘k’ ‘l’ ‘value’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

i found this simply via:

R CMD build --no-build-vignettes ANTsR
R CMD check --no-build-vignettes --no-install ANTsR_0.3.2.tar.gz

which is fairly fast to run ... you might also (temporarily) edit the
ANTsR/src/Makevars from this:

tlibs: ; cd ${PWD}/antb

libs: ; cd ${PWD}/antb && $(MAKE) -j 2

to this:

libs: ; cd ${PWD}/antb

tlibs: ; cd ${PWD}/antb && $(MAKE) -j 2

to avoid any wasted time recompiling c++.


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@jefferis
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@jefferis jefferis commented Jan 7, 2016

Can I also suggest devtools::check_doc for rapid documentation checks. Best, Greg.

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@stnava stnava commented Jan 7, 2016

yes! just tried and works beautifully.

some prior version choked on antsr but this is now the clearly better
option!

brian

On Thu, Jan 7, 2016 at 3:37 PM, Gregory Jefferis notifications@github.com
wrote:

Can I also suggest devtools::check_doc for rapid documentation checks.
Best, Greg.


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@stnava
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@stnava stnava commented Jan 8, 2016

just found this nifty trick on stackoverflow to build the pdf manual for a package from inside R:

path <- find.package("ANTsR")
system(paste(shQuote(file.path(R.home("bin"), "R")),
    "CMD", "Rd2pdf", shQuote(path)))

more discussion here

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@muschellij2 muschellij2 commented Aug 11, 2016

Relevant discussion about CMake that happened today: https://stat.ethz.ch/pipermail/r-package-devel/2016q3/001036.html, seems like Uwes says it'd be fine in SystemRequirements: https://stat.ethz.ch/pipermail/r-package-devel/2016q2/000903.html.

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@stnava stnava commented Aug 11, 2016

that's fantastic. would make the cmaker package much easier to get in
cran, i guess, but may also make it irrelevant.

brian

On Thu, Aug 11, 2016 at 2:04 PM, John Muschelli notifications@github.com
wrote:

Relevant discussion about CMake that happened today: https://stat.ethz.ch/
pipermail/r-package-devel/2016q3/001036.html, seems like Uwes says it'd
be fine in SystemRequirements: https://stat.ethz.ch/
pipermail/r-package-devel/2016q2/000903.html.


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