ANTsR
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ANTsX
ANTsR: towards CRAN & standardization of development
@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.
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 [email protected] 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.
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.
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 [email protected] 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 [email protected] 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.
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 [email protected] 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 [email protected] 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 [email protected] 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.
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 [email protected] 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 [email protected] 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 [email protected] 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 [email protected] 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.
ANTsR.so is the main indicator and it's currently around 77MB
brian
On Mon, Jan 26, 2015 at 11:24 AM, bkandel [email protected] 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 [email protected] 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 [email protected] 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 [email protected] 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 [email protected] 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.
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 [email protected] wrote:
ANTsR.so is the main indicator and it's currently around 77MB
brian
On Mon, Jan 26, 2015 at 11:24 AM, bkandel [email protected] 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 [email protected] 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 [email protected] 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 [email protected] 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 [email protected] 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.
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 [email protected] 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 [email protected] 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 [email protected] 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 [email protected] 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 [email protected] 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.
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 <[email protected]
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 [email protected] 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 [email protected] 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 [email protected] 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 [email protected]
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 [email protected] 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.
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 ....
@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'
for vignettes: will follow http://stackoverflow.com/questions/24861970/using-rmarkdown-as-a-vignette-engine
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 [email protected] 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.
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)
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 [email protected] 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.
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" [email protected] 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 [email protected] 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.
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" [email protected] 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" [email protected] 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 [email protected] 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.
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.
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=
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=
Undocumented arguments in documentation object 'frequencyFilterfMRI'
‘boldmat’ ‘tr’ ‘freqLo’ ‘freqHi’ ‘opt’
Documented arguments not in \usage in documentation object 'frequencyFilterfMRI':
‘tr=
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=
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.
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
Unrelated ... probably just need clean build. On Feb 5, 2015 11:21 AM, "dorianps" [email protected] 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.
@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 [email protected] 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.
@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 [email protected] 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.
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 [email protected]’ 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.
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.
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 ...
will work on adding in that documentation now.
On Fri, Feb 6, 2015 at 12:24 PM, stnava [email protected] 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.
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 ....