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List: insight-users
Subject: Re: [Insight-users] Wrapping R with SimpleITK
From: Brandon Whitcher <bwhitcher () gmail ! com>
Date: 2011-12-31 19:07:15
Message-ID: CAJZBSfFhOajXo2w=-=bNPGENV7BzXyNOnuCehskiY4uz4VNsnA () mail ! gmail ! com
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Brad,
Ah, the source directory... and not the binary directory. Thanks!
A major hurdle to overcome with the installation is the fact that R (I am
using R 2.14.1) now requires complete man pages with all information filled
in! Given the number of files in the man/ directory
ls SimpleITK/man/ | wc
3169 3169 118025
an automated method must be implemented in order to install SimpleITK as an
R package.
Also, the manual copying of "libSimpleITK.so" is slightly non-standard. I
know that a customized installation process is allowed, but I don't know
how it would be applied to SimpleITK.
I would recommend engaging the R-developer mailing list to get some advice
on brining together SimpleITK (the ITK version) and SimpleITK (the R
package... maybe RITK or rITK?).
I'll keep trying as a dynamic library instead of a full-on package.
Happy New Year!
Brandon
On 31 December 2011 18:11, Bradley Lowekamp <blowekamp@mail.nih.gov> wrote:
> Hello Brandon,
>
> The particular files you looking for are in the SimpleITK source directory
> not the build. You will need both the DESCRIPTION and the zzz.R files from
> the {SIMPLEITK_SOURCE}/Wrapping/R_Package directory.
>
> We have been calling R a Tier 2 or Tier 3 language in SimpleITK because is
> not as well supported as the other wrapped languages such as Python, Java,
> CSharp or even Ruby, or TCL. The primary reason for this is that we have
> not gotten the automatic testing working for R, so that it will show up on
> the nightly dashboard. Additionally, we also are hoping for contribution
> from the community to get the R language specific features polished and up
> to the expected R standard conventions.
>
> I hope this helps you with getting SimpleITK working R,
>
> Brad
>
> ========================================================
>
> Bradley Lowekamp
>
> Medical Science and Computing for
>
> Office of High Performance Computing and Communications
>
> National Library of Medicine
>
> blowekamp@mail.nih.gov
>
> On Dec 31, 2011, at 9:28 AM, Brandon Whitcher wrote:
>
> Dear ITK/SimpleITK experts,
>
> I have installed SimpleITK by turning off all wrapping facilities except
> WRAP_R. I am now following the instructions in
>
> http://www.itk.org/SimpleITKDoxygen/html/Wrapping.html
>
> Specifically,
>
>
> - 6) Copy the file
>
> SimpleITK/Wrapping/R_Package/DESCRIPTION
>
> into the current
>
> SimpleITK/DESCRIPTION
>
> ...but I cannot find the file Wrapping/R_package/DESCRIPTION in my
> SimpleITK-binary installation. Where is this file?
>
> thank-you,
>
> Brandon
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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>
>
>
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Brad,<br><br>Ah, the source directory... and not the binary directory. \
Thanks!<br><br>A major hurdle to overcome with the installation is the fact that R (I \
am using R 2.14.1) now requires complete man pages with all information filled in! \
Given the number of files in the man/ directory <br> <br><span \
style="font-family:courier new,monospace">ls SimpleITK/man/ | wc</span><br \
style="font-family:courier new,monospace"><span style="font-family:courier \
new,monospace"> 3169 3169 118025</span><br><br>an automated method must be \
implemented in order to install SimpleITK as an R package. <br> <br>Also, the manual \
copying of "libSimpleITK.so" is slightly non-standard. I know that a \
customized installation process is allowed, but I don't know how it would be \
applied to SimpleITK. <br><br>I would recommend engaging the R-developer mailing \
list to get some advice on brining together SimpleITK (the ITK version) and SimpleITK \
(the R package... maybe RITK or rITK?). <br> <br>I'll keep trying as a dynamic \
library instead of a full-on package.<br><br>Happy New \
Year!<br><br>Brandon<br><br><div class="gmail_quote">On 31 December 2011 18:11, \
Bradley Lowekamp <span dir="ltr"><<a \
href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>></span> wrote:<br> \
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc \
solid;padding-left:1ex"><div style="word-wrap:break-word">Hello \
Brandon,<div><br></div><div>The particular files you looking for are in the SimpleITK \
source directory not the build. You will need both the DESCRIPTION and the zzz.R \
files from the {SIMPLEITK_SOURCE}/Wrapping/R_Package directory.</div> \
<div><br></div><div>We have been calling R a Tier 2 or Tier 3 language in SimpleITK \
because is not as well supported as the other wrapped languages such as Python, Java, \
CSharp or even Ruby, or TCL. The primary reason for this is that we have not gotten \
the automatic testing working for R, so that it will show up on the nightly \
dashboard. Additionally, we also are hoping for contribution from the community to \
get the R language specific features polished and up to the expected R standard \
conventions.</div> <div><br></div><div>I hope this helps you with getting SimpleITK \
working R,</div><div><br></div><div>Brad</div><div><br><div> <span \
style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:norm \
al;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;tex \
t-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium"><span \
style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-size:12px; \
font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-he \
ight:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div \
style="word-wrap:break-word"> <div><p \
style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font \
style="font:normal normal normal 12px/normal Helvetica" face="Helvetica" \
size="3">========================================================</font></p> <p \
style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font \
style="font:normal normal normal 12px/normal Helvetica" face="Helvetica" \
size="3">Bradley Lowekamp<span> </span><span> </span></font></p><p \
style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"> <font \
style="font:normal normal normal 12px/normal Helvetica" face="Helvetica" \
size="3">Medical Science and Computing for</font></p><p \
style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font \
style="font:normal normal normal 12px/normal Helvetica" face="Helvetica" \
size="3">Office of High Performance Computing and Communications</font></p> <p \
style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font \
style="font:normal normal normal 12px/normal Helvetica" face="Helvetica" \
size="3">National Library of Medicine<span> </span></font></p><p \
style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"> <font \
style="font:normal normal normal 12px/normal Helvetica" face="Helvetica" size="3"><a \
href="mailto:blowekamp@mail.nih.gov" \
target="_blank">blowekamp@mail.nih.gov</a></font></p></div></div></span></span> \
</div> <br><div><div><div class="h5"><div>On Dec 31, 2011, at 9:28 AM, Brandon \
Whitcher wrote:</div><br></div></div><blockquote type="cite"><div><div \
class="h5">Dear ITK/SimpleITK experts,<br><br>I have installed SimpleITK by turning \
off all wrapping facilities except WRAP_R. I am now following the instructions \
in<br> <br><div style="margin-left:40px"><a \
href="http://www.itk.org/SimpleITKDoxygen/html/Wrapping.html" \
target="_blank">http://www.itk.org/SimpleITKDoxygen/html/Wrapping.html</a><br> \
</div><br>Specifically, <br><br><ul><li>6) Copy the file</li></ul> <div><pre> \
SimpleITK/Wrapping/R_Package/DESCRIPTION </pre></div><p> into the current</p>
<div><pre> SimpleITK/DESCRIPTION
</pre></div>...but I cannot find the file Wrapping/R_package/DESCRIPTION in my \
SimpleITK-binary installation. Where is this \
file?<br><br>thank-you,<br><br>Brandon<br><br></div></div> \
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offers ITK Training Courses, for more information visit:<br><a \
href="http://www.kitware.com/products/protraining.html" \
target="_blank">http://www.kitware.com/products/protraining.html</a><br><br>Please \
keep messages on-topic and check the ITK FAQ at:<br> <a \
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</blockquote></div><br></div></div></blockquote></div><br>
_____________________________________
Powered by www.kitware.com
Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html
Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ
Follow this link to subscribe/unsubscribe:
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