ANTsR: towards CRAN & standardization of development

[stnava]

@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]

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 https://github.com/stnava/ANTsR/issues/8.

[armaneshaghi]

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]

Perhaps by assigning something (more specifically)

[stnava]

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 https://github.com/stnava/ANTsR/issues/8.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71480627.

[stnava]

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.

https://github.com/stnava/ANTsR/issues/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 https://github.com/stnava/ANTsR/issues/8.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71480627.

[bkandel]

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.

https://github.com/stnava/ANTsR/issues/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 https://github.com/stnava/ANTsR/issues/8.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71480627.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71486722.

[stnava]

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.

https://github.com/stnava/ANTsR/issues/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 https://github.com/stnava/ANTsR/issues/8.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71480627.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71486722.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71488096.

[stnava]

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.

https://github.com/stnava/ANTsR/issues/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 https://github.com/stnava/ANTsR/issues/8.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71480627.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71486722.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71488096.

[jefferis]

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.

https://github.com/stnava/ANTsR/issues/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 https://github.com/stnava/ANTsR/issues/8.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71480627.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71486722.

— Reply to this email directly or view it on GitHub.

[stnava]

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.

https://github.com/stnava/ANTsR/issues/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 https://github.com/stnava/ANTsR/issues/8.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71480627.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71486722.

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-71491377.

[stnava]

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]

@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]

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

[bkandel]

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 https://github.com/stnava/ANTsR/issues/8#issuecomment-72560264.

[jefferis]

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]

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 https://github.com/stnava/ANTsR/issues/8#issuecomment-72555963.

[stnava]

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'

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-72555963.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-72737203.

[stnava]

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'

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-72555963.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-72737203.

[stnava]

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]

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]

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]

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

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73075173.

[bkandel]

@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.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-72919042.

[dorianps]

@stnava Thanks, a clean install resolved the problem.

[jeffduda]

@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.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73094989.

[stnava]

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]

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]

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]

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 ...

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73277179.

[stnava]

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 ....

[jeffduda]

probably worth getting rid of antsMotionCorrStats.R for now and build a R-native version of something similar in the future.

On Fri, Feb 6, 2015 at 1:02 PM, stnava notifications@github.com wrote:

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 ....

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73283496.

[stnava]

as of commit: 2e32fb787bfbc9219f6f72ec39313ee22b8d97fe

we have 0 example errors ( though some are in dontrun ) and 0 documentation issues ...

@bkandel : i "hid" antsMotionCorrStats since it is only called as a helper function anyway

the current ants reference manual is here: http://we.tl/LI0tQSS7PE ( link active for 7 days )

[stnava]

hmm real cran check produces additional warnings:

1) not sure about this one

Undocumented S4 methods: generic '[' and siglist 'antsImage,NULL,NULL' generic '[' and siglist 'antsImage,NULL,numeric' generic '[' and siglist 'antsImage,numeric,NULL' generic '[' and siglist 'antsImage,numeric,numeric' generic '[<-' and siglist 'antsImage,NULL,ANY,ANY' generic '[<-' and siglist 'antsImage,NULL,NULL,numeric' generic '[<-' and siglist 'antsImage,NULL,antsRegion,ANY' generic '[<-' and siglist 'antsImage,NULL,numeric,numeric' generic '[<-' and siglist 'antsImage,array,ANY,ANY' generic '[<-' and siglist 'antsImage,array,antsRegion,ANY' generic '[<-' and siglist 'antsImage,list,ANY,ANY' generic '[<-' and siglist 'antsImage,logical,ANY,ANY' generic '[<-' and siglist 'antsImage,logical,antsRegion,ANY' generic '[<-' and siglist 'antsImage,matrix,ANY,ANY' generic '[<-' and siglist 'antsImage,matrix,antsRegion,ANY' generic '[<-' and siglist 'antsImage,numeric,NULL,numeric' generic '[<-' and siglist 'antsImage,numeric,numeric,numeric' generic 'as.list' and siglist 'antsImageList'

2) another oddball ... no cerr in that code ... must be in a linked library ...

• checking compiled code ... NOTE File ‘ANTsR/libs/ANTsR.so’: Found ‘ZNSt314cerrE’, possibly from ‘std::cerr’ (C++) Object: ‘invariantImageSimilarity.o’

3) presumably can clean up this one via cleanup

• checking package subdirectories ... WARNING Found the following directories with names of version control directories: ./src/ANTS/ANTS-build/ITKv4/.git ./src/ANTS/ANTS-build/ITKv4/Modules/Remote/MGHIO/.git ./src/ANTS/ANTS-src/.git

[muschellij2]

So I've been following this thread closely and I didn't give a lot of feedback because you guys are doing fantastic.

I'm sure it was a hurdle getting R CMD check to work but I'm very excited for this package to be on CRAN! On Feb 6, 2015 2:59 PM, "stnava" notifications@github.com wrote:

as of commit: 2e32fb7 https://github.com/stnava/ANTsR/commit/2e32fb787bfbc9219f6f72ec39313ee22b8d97fe

we have 0 example errors ( though some are in dontrun ) and 0 documentation issues ...

@bkandel https://github.com/bkandel : i "hid" antsMotionCorrStats since it is only called as a helper function anyway

the current ants reference manual is here: http://we.tl/LI0tQSS7PE ( link active for 7 days )

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73302362.

[bkandel]

I don't think we really need ThresholdImage now that we can just do img[img<thresh] <- 0 or whatever. It was more useful when everything was a command-line binary.

I would also move for throwing out ImageMath and only keep imageMath (with R style) -- having two nearly identical commands that do different things is bound to be a source of confusion.

On 6 February 2015 at 16:34, John Muschelli notifications@github.com wrote:

So I've been following this thread closely and I didn't give a lot of feedback because you guys are doing fantastic.

I'm sure it was a hurdle getting R CMD check to work but I'm very excited for this package to be on CRAN! On Feb 6, 2015 2:59 PM, "stnava" notifications@github.com wrote:

as of commit: 2e32fb7 < https://github.com/stnava/ANTsR/commit/2e32fb787bfbc9219f6f72ec39313ee22b8d97fe

we have 0 example errors ( though some are in dontrun ) and 0 documentation issues ...

@bkandel https://github.com/bkandel : i "hid" antsMotionCorrStats since it is only called as a helper function anyway

the current ants reference manual is here: http://we.tl/LI0tQSS7PE ( link active for 7 days )

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73302362.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73316653.

[stnava]

understood - but one reason to keep the older version is it's still useful for some functions that dont actually match the R variant syntax. probably best dealt with by recommending ( via link in ImageMath documentation ) that people use iMath ...

ThresholdImage is now thresholdImage so it'll stick around mainly b/c it's used in several places and is much faster ( i think ) than the equivalent R operation ...

am now working on getting this https://travis-ci.org/stnava/ANTsR right

it's pretty close, i think ....

brian

On Fri, Feb 6, 2015 at 4:50 PM, bkandel notifications@github.com wrote:

I don't think we really need ThresholdImage now that we can just do img[img<thresh] <- 0 or whatever. It was more useful when everything was a command-line binary.

I would also move for throwing out ImageMath and only keep imageMath (with R style) -- having two nearly identical commands that do different things is bound to be a source of confusion.

On 6 February 2015 at 16:34, John Muschelli notifications@github.com wrote:

So I've been following this thread closely and I didn't give a lot of feedback because you guys are doing fantastic.

I'm sure it was a hurdle getting R CMD check to work but I'm very excited for this package to be on CRAN! On Feb 6, 2015 2:59 PM, "stnava" notifications@github.com wrote:

as of commit: 2e32fb7 <

https://github.com/stnava/ANTsR/commit/2e32fb787bfbc9219f6f72ec39313ee22b8d97fe

we have 0 example errors ( though some are in dontrun ) and 0 documentation issues ...

@bkandel https://github.com/bkandel : i "hid" antsMotionCorrStats since it is only called as a helper function anyway

the current ants reference manual is here: http://we.tl/LI0tQSS7PE ( link active for 7 days )

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73302362.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73316653.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73319128.

[stnava]

OK - this is finally set up (more or less) correctly for antsr

https://travis-ci.org/stnava/ANTsR

so we can see whether builds (on linux and osx in the future http://docs.travis-ci.com/user/multi-os/ ) are passing, which includes a coarse R CMD check call ...

the results are displayed in the red/green badge on http://stnava.github.io/ANTsR/ or on the github page

these builds also trigger an email to whoever wants one ( currently only me ) which indicate pass / failure and show the build log ...

this was already set up on ants thanks to @armaneshaghi and i built from his work ... there remain some issues wrt which specific compile configuration is most stable for travis but i'll keep testing til it's settled.

[armaneshaghi]

We could also add automatic coverage testing similar to dplyr , but I need Brian to activate coverall for ANTsR here if everyone agrees. I will then start writing test codes.

CRAN requires each package to have the following structure, and we are still missing tests

• A file named DESCRIPTION with descriptions of the package, author, and license conditions in a structured text format that is readable by computers and by people. • A man/ subdirectory of documentation files. • An R/ subdirectory of R code. • A data/ subdirectory of datasets. Less commonly it contains • A src/ subdirectory of C, Fortran or C++ source. • tests/ for validation tests. • exec/ for other executables (eg Perl or Java). • inst/ for miscellaneous other stuff. The contents of this directory are completely copied to the installed version of a package. • A configure script to check for other required software or handle differences between sys- tems.

[armaneshaghi]

also we need a license file that CRAN understands, I recommend creative commons, but you have other options

EDIT: sorry, found the license in DESCRIPTION file

[stnava]

we have GPL >= 2 - following https://github.com/RcppCore/Rcpp

brian

On Mon, Feb 9, 2015 at 6:17 AM, Arman Eshaghi notifications@github.com wrote:

also we need a license file that CRAN understands, I recommend creative commons, but you have other options https://svn.r-project.org/R/trunk/share/licenses/license.db

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73492939.

[stnava]

happy to try this ... will activate momentarily

brian

On Mon, Feb 9, 2015 at 6:17 AM, Arman Eshaghi notifications@github.com wrote:

also we need a license file that CRAN understands, I recommend creative commons, but you have other options https://svn.r-project.org/R/trunk/share/licenses/license.db

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73492939.

[stnava]

The saga continues though we are very close to having a clean and efficient ANTsR build.

This "pure" CRAN check:

R CMD INSTALL ANTsR R CMD build ANTsR R CMD check ANTsR_1.0.tar.gz --as-cran

produces several issues:

1. it uncovered some actual bugs which i fixed ( not pushed yet )
2. it uncovers namespace issues e.g. functions that you call but which are not resolved ... our "usePkg" trick can't get past this afaik. two options
   • we add all actual dependencies as defined by cran - this is a long list ... i will update antsr with the full list in a little bit ... ultimately, we can "back out" these changes once we get the CRAN check to pass which will get us back to a "quick loading" antsr ( agree this is very desirable ) ... furthermore, for development, we can always go back to a simplified DESCRIPTION/NAMESPACE and change to the CRAN ready DESCRIPTION/NAMESPACE as needed
   • we make a different (R code only) project ANTsRMas which has (1) extra test data (2) houses functions that cause lots (unwanted) dependencies to increase ... e.g. rapidlyInspectImageData, plotPrettyGraph, frequencyFilterfMRI, antsSpatialICAfMRI.R .... i already have an "extra" package that could be repurposed for this and which has some useful stuff in it anyway : RKRNS ... we could add (more) data and these extra functions ... this would clean up ANTsR a bit ... but then we'd have to get 2 repos on CRAN to enable full functionality .... or just accept this 2nd one would be an install_github which would be easy b/c it would be fast.
3. a long list of this generic '[' and siglist 'antsImage,NULL,ANY,ANY' ... and ... generic '[<-' and siglist 'antsImage,NULL,ANY,ANY' ...

related to our versions of: http://stackoverflow.com/questions/10961842/how-to-define-the-subset-operators-for-a-s4-class this last one is tricky b/c it take a long time to test at least i havent figured out a way to get the check for this w/o a full install from scratch ...

[armaneshaghi]

I'm stuck here for travis after R CMD build ANTsR:

Error: processing vignette 'ANTsR.Rmd' failed with diagnostics: 'html_vignette' is not an exported object from 'namespace:rmarkdown'

First it was a problem with pandoc version, but now seems to be something else

[bkandel]

Why can't we use Suggests for all of the extra packages that are only occasionally needed? That shouldn't affect installation or loading speed, and we'd be able to keep all the functions in ANTsR.

In any case, I think we should have some centralized list of all packages needed at one time or another in ANTsR.

It may not be a bad idea to have a "core" ANTsR and a "bells and whistles" version that would do more, but I'm not sure it's really worth it. I think having a decent set of vignettes would go a long way to making the basic functions not get lost in all the more specialized stuff.

On 9 February 2015 at 11:36, stnava notifications@github.com wrote:

The saga continues though we are very close to having a clean and efficient ANTsR build.

This "pure" CRAN check:

R CMD INSTALL ANTsR R CMD build ANTsR R CMD check ANTsR_1.0.tar.gz --as-cran

produces several issues:

1.

it uncovered some actual bugs which i fixed ( not pushed yet ) 2.

it uncovers namespace issues e.g. functions that you call but which are not resolved ... our "usePkg" trick can't get past this afaik. two options

  we add all actual dependencies as defined by cran - this is a long
  list ... i will update antsr with the full list in a little bit ...
  ultimately, we can "back out" these changes once we get the CRAN check to
  pass which will get us back to a "quick loading" antsr ( agree this is very
  desirable ) ... furthermore, for development, we can always go back to a
  simplified DESCRIPTION/NAMESPACE and change to the CRAN ready
  DESCRIPTION/NAMESPACE as needed
  -

  we make a different (R code only) project ANTsRMas which has (1)
  extra test data (2) houses functions that cause lots (unwanted)
  dependencies to increase ... e.g. rapidlyInspectImageData, plotPrettyGraph,
  frequencyFilterfMRI, antsSpatialICAfMRI.R .... i already have an "extra"
  package that could be repurposed for this and which has some useful stuff
  in it anyway : RKRNS ... we could add (more) data and these extra functions
  ... this would clean up ANTsR a bit ... but then we'd have to get 2 repos
  on CRAN to enable full functionality .... or just accept this 2nd one would
  be an install_github which would be easy b/c it would be fast.
   3.

a long list of this generic '[' and siglist 'antsImage,NULL,ANY,ANY' ... and ... generic '[<-' and siglist 'antsImage,NULL,ANY,ANY' ...

this last one is tricky b/c it take a long time to test at least i havent figured out a way to get the check for this w/o a full install from scratch ...

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73540765.

[stnava]

"Suggests" contributes to the problem - names of functions dont get imported thus triggering several different types of check failures. Importing is what's time consuming on startup.

[bkandel]

Would using "suggests" also trigger failures if all the functions were accessed via '::' calls?

On 9 February 2015 at 12:05, stnava notifications@github.com wrote:

"Suggests" contributes to the problem - names of functions dont get imported thus triggering several different types of check failures. Importing is what's time consuming on startup.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73546722.

[stnava]

yes - those are prohibited

brian

On Mon, Feb 9, 2015 at 12:14 PM, bkandel notifications@github.com wrote:

Would using "suggests" also trigger failures if all the functions were accessed via '::' calls?

On 9 February 2015 at 12:05, stnava notifications@github.com wrote:

"Suggests" contributes to the problem - names of functions dont get imported thus triggering several different types of check failures. Importing is what's time consuming on startup.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73546722.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73548262.

[bkandel]

The R extension manual ( http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies) says: R code in the package should call library or require only exceptionally. Such calls are never needed for packages listed in ‘Depends’ as they will already be on the search path. It used to be common practice to use require calls for packages listed in ‘suggests’ in functions which used their functionality, but nowadays it is better to access such functionality via :: calls.

Doesn't this imply that Suggests + :: calls are acceptable? (Or, 'exceptionally', to use require, but in any case Suggests + using external packages should be allowed.)

On 9 February 2015 at 12:20, stnava notifications@github.com wrote:

yes - those are prohibited

brian

On Mon, Feb 9, 2015 at 12:14 PM, bkandel notifications@github.com wrote:

Would using "suggests" also trigger failures if all the functions were accessed via '::' calls?

On 9 February 2015 at 12:05, stnava notifications@github.com wrote:

"Suggests" contributes to the problem - names of functions dont get imported thus triggering several different types of check failures. Importing is what's time consuming on startup.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73546722.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73548262.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73549557.

[stnava]

yes - maybe you are right .... definitely ::: is prohibited ...

if you want to pursue this, then you can try the following:

(1) change imports to suggests

(2) using NAMESPACE as a guide, identify all the functions that need :: and then fix them ...

(3) test with

R CMD INSTALL ANTsR R CMD build ANTsR R CMD check ANTsR_1.0.tar.gz --as-cran

i am making progress with the operators but not there yet ...

brian

On Mon, Feb 9, 2015 at 12:39 PM, bkandel notifications@github.com wrote:

The R extension manual (

http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies ) says: R code in the package should call library or require only exceptionally. Such calls are never needed for packages listed in ‘Depends’ as they will already be on the search path. It used to be common practice to use require calls for packages listed in ‘suggests’ in functions which used their functionality, but nowadays it is better to access such functionality via :: calls.

Doesn't this imply that Suggests + :: calls are acceptable? (Or, 'exceptionally', to use require, but in any case Suggests + using external packages should be allowed.)

On 9 February 2015 at 12:20, stnava notifications@github.com wrote:

yes - those are prohibited

brian

On Mon, Feb 9, 2015 at 12:14 PM, bkandel notifications@github.com wrote:

Would using "suggests" also trigger failures if all the functions were accessed via '::' calls?

On 9 February 2015 at 12:05, stnava notifications@github.com wrote:

"Suggests" contributes to the problem - names of functions dont get imported thus triggering several different types of check failures. Importing is what's time consuming on startup.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73546722.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73548262.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73549557.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73553075.

[bkandel]

OK, I'll try that.

On 9 February 2015 at 12:43, stnava notifications@github.com wrote:

yes - maybe you are right .... definitely ::: is prohibited ...

if you want to pursue this, then you can try the following:

(1) change imports to suggests

(2) using NAMESPACE as a guide, identify all the functions that need :: and then fix them ...

(3) test with

R CMD INSTALL ANTsR R CMD build ANTsR R CMD check ANTsR_1.0.tar.gz --as-cran

i am making progress with the operators but not there yet ...

brian

On Mon, Feb 9, 2015 at 12:39 PM, bkandel notifications@github.com wrote:

The R extension manual (

http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies ) says: R code in the package should call library or require only exceptionally. Such calls are never needed for packages listed in ‘Depends’ as they will already be on the search path. It used to be common practice to use require calls for packages listed in ‘suggests’ in functions which used their functionality, but nowadays it is better to access such functionality via :: calls.

Doesn't this imply that Suggests + :: calls are acceptable? (Or, 'exceptionally', to use require, but in any case Suggests + using external packages should be allowed.)

On 9 February 2015 at 12:20, stnava notifications@github.com wrote:

yes - those are prohibited

brian

On Mon, Feb 9, 2015 at 12:14 PM, bkandel notifications@github.com wrote:

Would using "suggests" also trigger failures if all the functions were accessed via '::' calls?

On 9 February 2015 at 12:05, stnava notifications@github.com wrote:

"Suggests" contributes to the problem - names of functions dont get imported thus triggering several different types of check failures. Importing is what's time consuming on startup.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73546722.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73548262.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73549557.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73553075.

— Reply to this email directly or view it on GitHub https://github.com/stnava/ANTsR/issues/8#issuecomment-73553932.