Re: [GRASS-user] Running r-grass examples when building a R package
Bernardo Santos via grass-stats <[email protected]> Tue, 30 Aug 2022 11:18:44 +0000 (UTC)
| Newsgroups | gmane.comp.gis.grass.stats,gmane.comp.gis.grass.user |
|---|---|
| Message-ID | <[email protected]> |
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Hi Stefan,(and thanks Roger and Floris for replying as well)
Your solution worked perfectly, Stefan. Thanks a lot!In the case of continu=
ous integration within Github as it is the case, it seems we must ask GRASS=
to be installed in the virtual machine.
This could be done with Stefan's suggestion, adding these lines to the yaml=
file within .github/workflows:
- name: Install GRASS GIS and other dependencies=C2=A0 =C2=A0 =C2=A0 =C2=A0=
run: |=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 sudo apt-get update -qq=C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 sudo apt-get install -y -qq grass grass-dev grass-=
doc wget
You can also see it here:=C2=A0Install GRASS for CI by ninsbl =C2=B7 Pull R=
equest #11 =C2=B7 NINAnor/oneimpact (github.com)
I guess this could be documented for GRASS/R users somewhere? Maybe in some=
wiki?Any suggestion on where to add this?
BestBernardo
Em sexta-feira, 26 de agosto de 2022 13:27:46 GMT+2, Stefan Blumentrath=
<[email protected]> escreveu: =20
=20
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Hi Bernardo,
=20
=C2=A0
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Seems like GRASS GIS isn`t installed on the CI VM.
=20
=C2=A0
=20
Please see:
=20
https://github.com/NINAnor/oneimpact/pulls
=20
=C2=A0
=20
You may add UbuntuGIS PPAs if you want other versions than shipped by plain=
Ubuntu.
=20
=C2=A0
=20
Cheers
=20
Stefan
=20
=C2=A0
=20
From: grass-user <[email protected]>On Behalf Of Bernardo =
Santos via grass-user
Sent: fredag 26. august 2022 12:56
To: [email protected]; GRASS User List <[email protected]=
g>
Subject: [GRASS-user] Running r-grass examples when building a R package
=20
=C2=A0
=20
Dear all,
=20
=C2=A0
=20
I am building a R package and some of the functions use rgrass to connect t=
o a GRASS project and run thingfs within GRASS.
=20
I have now set up a webpage for the package using pkgdown in integrated to =
Github actions. This means when I push new commits all the examples of R fu=
nctions are run again and the webpage is updated with the results of the ex=
amples. Here is the webpage:=C2=A0https://ninanor.github.io/oneimpact/
=20
=C2=A0
=20
All works fine, except the functions calling GRASS. When I run the examples=
form my local computer everything works, but in the Github actions it does=
not run, apparently because the command
=20
=C2=A0
system("grass78 --config path", intern =3D T)=20
to find the GRASS folder and use within rgrass::initGRASS does not work, so=
the connection between R and GRASS do not exist.
=20
=C2=A0
=20
Does someone in the group has experience with that and could help with hint=
s to solve it?
=20
Is there a recommended way to make sure Github actions know where GRASS is =
and use it?
=20
=C2=A0
=20
Best
=20
Bernardo
=20
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<html><head></head><body><div class=3D"ydp2e917366yahoo-style-wrap" style=
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rif;"><div style=3D"font-family: Helvetica Neue, Helvetica, Arial, sans-ser=
if;"></div>
<div dir=3D"ltr" data-setdir=3D"false" style=3D"font-family: Helvet=
ica Neue, Helvetica, Arial, sans-serif;">Hi Stefan,</div><div dir=3D"ltr" d=
ata-setdir=3D"false" style=3D"font-family: Helvetica Neue, Helvetica, Arial=
, sans-serif;">(and thanks Roger and Floris for replying as well)</div><div=
dir=3D"ltr" data-setdir=3D"false" style=3D"font-family: Helvetica Neue, He=
lvetica, Arial, sans-serif;"><br></div><div dir=3D"ltr" data-setdir=3D"fals=
e" style=3D"font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">You=
r solution worked perfectly, Stefan. Thanks a lot!</div><div dir=3D"ltr" da=
ta-setdir=3D"false" style=3D"font-family: Helvetica Neue, Helvetica, Arial,=
sans-serif;">In the case of continuous integration within Github as it is =
the case, it seems we must ask GRASS to be installed in the virtual machine=
.</div><div dir=3D"ltr" data-setdir=3D"false" style=3D"font-family: Helveti=
ca Neue, Helvetica, Arial, sans-serif;"><br></div><div dir=3D"ltr" data-set=
dir=3D"false" style=3D"font-family: Helvetica Neue, Helvetica, Arial, sans-=
serif;">This could be done with Stefan's suggestion, adding these lines to =
the yaml file within .github/workflows:</div><div dir=3D"ltr" data-setdir=
=3D"false" style=3D""><div style=3D""><div style=3D"font-family: Helvetica =
Neue, Helvetica, Arial, sans-serif;"><br></div><div style=3D""><font face=
=3D"courier new, courier, monaco, monospace, sans-serif">- name: Install GR=
ASS GIS and other dependencies</font></div><div style=3D""><font face=3D"co=
urier new, courier, monaco, monospace, sans-serif"> &nb=
sp; run: |</font></div><div style=3D""><font face=3D"courier new, courier, =
monaco, monospace, sans-serif"> sudo apt-=
get update -qq</font></div><div style=3D""><font face=3D"courier new, couri=
er, monaco, monospace, sans-serif"> sudo =
apt-get install -y -qq grass grass-dev grass-doc wget</font></div></div></d=
iv><div dir=3D"ltr" data-setdir=3D"false" style=3D"font-family: Helvetica N=
eue, Helvetica, Arial, sans-serif;"><br></div><div dir=3D"ltr" data-setdir=
=3D"false" style=3D"font-family: Helvetica Neue, Helvetica, Arial, sans-ser=
if;">You can also see it here: <span><a href=3D"https://github.com/NIN=
Anor/oneimpact/pull/11/commits/8c77deaa92cbae2cf2dd909c47b67ad356801b9b" re=
l=3D"nofollow" target=3D"_blank">Install GRASS for CI by ninsbl =C2=B7 Pull=
Request #11 =C2=B7 NINAnor/oneimpact (github.com)</a></span></div><div dir=
=3D"ltr" data-setdir=3D"false" style=3D"font-family: Helvetica Neue, Helvet=
ica, Arial, sans-serif;"><br></div><div dir=3D"ltr" data-setdir=3D"false" s=
tyle=3D"font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">I guess=
this could be documented for GRASS/R users somewhere? Maybe in some wiki?<=
/div><div dir=3D"ltr" data-setdir=3D"false" style=3D"font-family: Helvetica=
Neue, Helvetica, Arial, sans-serif;">Any suggestion on where to add this?<=
br></div><div dir=3D"ltr" data-setdir=3D"false" style=3D"font-family: Helve=
tica Neue, Helvetica, Arial, sans-serif;"><br></div><div dir=3D"ltr" data-s=
etdir=3D"false" style=3D"font-family: Helvetica Neue, Helvetica, Arial, san=
s-serif;">Best</div><div dir=3D"ltr" data-setdir=3D"false" style=3D"font-fa=
mily: Helvetica Neue, Helvetica, Arial, sans-serif;">Bernardo</div><div dir=
=3D"ltr" data-setdir=3D"false" style=3D"font-family: Helvetica Neue, Helvet=
ica, Arial, sans-serif;"><br></div><div style=3D"font-family: Helvetica Neu=
e, Helvetica, Arial, sans-serif;"><br></div>
=20
</div><div id=3D"yahoo_quoted_1896614575" class=3D"yahoo_quoted">
<div style=3D"font-family:'Helvetica Neue', Helvetica, Arial, s=
ans-serif;font-size:13px;color:#26282a;">
=20
<div>
Em sexta-feira, 26 de agosto de 2022 13:27:46 GMT+2, St=
efan Blumentrath <[email protected]> escreveu:
</div>
<div><br></div>
<div><br></div>
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<div>
<div class=3D"yiv0852532148WordSection1">
<p class=3D"yiv0852532148MsoNormal"><span style=3D"">Hi Bernardo,</span></p=
>=20
<p class=3D"yiv0852532148MsoNormal"><span style=3D""> </span></p>=20
<p class=3D"yiv0852532148MsoNormal"><span lang=3D"EN-US" style=3D"">Seems l=
ike GRASS GIS isn`t installed on the CI VM.</span></p>=20
<p class=3D"yiv0852532148MsoNormal"><span lang=3D"EN-US" style=3D""> =
</span></p>=20
<p class=3D"yiv0852532148MsoNormal"><span lang=3D"EN-US" style=3D"">Please =
see:</span></p>=20
<p class=3D"yiv0852532148MsoNormal"><span lang=3D"EN-US" style=3D""><a rel=
=3D"nofollow noopener noreferrer" target=3D"_blank" href=3D"https://github.=
com/NINAnor/oneimpact/pulls">https://github.com/NINAnor/oneimpact/pulls</a>=
</span></p>=20
<p class=3D"yiv0852532148MsoNormal"><span lang=3D"EN-US" style=3D""> =
</span></p>=20
<p class=3D"yiv0852532148MsoNormal"><span lang=3D"EN-US" style=3D"">You may=
add UbuntuGIS PPAs if you want other versions than shipped by plain Ubuntu=
.</span></p>=20
<p class=3D"yiv0852532148MsoNormal"><span lang=3D"EN-US" style=3D""> =
</span></p>=20
<p class=3D"yiv0852532148MsoNormal"><span lang=3D"EN-US" style=3D"">Cheers<=
/span></p>=20
<p class=3D"yiv0852532148MsoNormal"><span lang=3D"EN-US" style=3D"">Stefan<=
/span></p>=20
<p class=3D"yiv0852532148MsoNormal"><span lang=3D"EN-US" style=3D""> =
</span></p>=20
<div>
<div style=3D"border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm =
0cm 0cm;">
<p class=3D"yiv0852532148MsoNormal"><b><span lang=3D"EN-US">From:</span></b=
><span lang=3D"EN-US"> grass-user <[email protected]>=
;
<b>On Behalf Of </b>Bernardo Santos via grass-user<br>
<b>Sent:</b> fredag 26. august 2022 12:56<br>
<b>To:</b> [email protected]; GRASS User List <grass-user@list=
s.osgeo.org><br>
<b>Subject:</b> [GRASS-user] Running r-grass examples when building a R pac=
kage</span></p>=20
</div>
</div>
<p class=3D"yiv0852532148MsoNormal"> </p>=20
<div>
<div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;">Dear all,</span></p>=20
</div>
<div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;"> </span></p>=20
</div>
<div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;">I am building a R package and some of the functions use rgrass=
to connect to a GRASS project and run thingfs within GRASS.</span></p>=20
</div>
<div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;">I have now set up a webpage for the package using pkgdown in i=
ntegrated to Github actions. This means when I push new commits all the exa=
mples of R functions are run again
and the webpage is updated with the results of the examples. Here is the w=
ebpage: <a rel=3D"nofollow noopener noreferrer" target=3D"_blank" href=
=3D"https://eur01.safelinks.protection.outlook.com/?url=3Dhttps%3A%2F%2Fnin=
anor.github.io%2Foneimpact%2F&data=3D05%7C01%7CStefan.Blumentrath%40nin=
a.no%7C4ec863c6b2d14350bafa08da8751a786%7C6cef373021314901831055b3abf02c73%=
7C0%7C0%7C637971082028512352%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLC=
JQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=3DtL=
KgU9W3QU2M9Jyr4lWtCa3qDuvvH%2B4d41sewIzdYPU%3D&reserved=3D0">https://ni=
nanor.github.io/oneimpact/</a></span></p>=20
</div>
<div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;"> </span></p>=20
</div>
<div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;">All works fine, except the functions calling GRASS. When I run=
the examples form my local computer everything works, but in the Github ac=
tions it does not run, apparently
because the command</span></p>=20
</div>
<div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;"> </span></p>=20
</div>
<div>
<div style=3D"border:solid #DEE2E6 1.0pt;padding:0cm 0cm 0cm 0cm;background=
:#F1F3F5;">
<pre style=3D"background:#F1F3F5;border:none;padding:0cm;"><span class=3D"y=
iv0852532148ydpa6a6511efu"><span style=3D"color:#4758AB;"><a rel=3D"nofollo=
w noopener noreferrer" target=3D"_blank" href=3D"https://eur01.safelinks.pr=
otection.outlook.com/?url=3Dhttps%3A%2F%2Frdrr.io%2Fr%2Fbase%2Fsystem.html&=
amp;data=3D05%7C01%7CStefan.Blumentrath%40nina.no%7C4ec863c6b2d14350bafa08d=
a8751a786%7C6cef373021314901831055b3abf02c73%7C0%7C0%7C637971082028512352%7=
CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwi=
LCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=3DXlu8yfS8TnTLHdkRc91AGeQI8fUCDpRd=
CbySjheiaNY%3D&reserved=3D0">system</a></span></span><span class=3D"yiv=
0852532148ydpa6a6511eop"><span style=3D"color:#5E5E5E;">(</span></span><spa=
n class=3D"yiv0852532148ydpa6a6511est"><span style=3D"color:#20794D;">"gras=
s78 --config path"</span></span><span class=3D"yiv0852532148ydpa6a6511er-in=
"><span style=3D"color:#003B4F;">, intern </span></span><span class=3D"yiv0=
852532148ydpa6a6511eop"><span style=3D"color:#5E5E5E;">=3D</span></span><sp=
an class=3D"yiv0852532148ydpa6a6511er-in"><span style=3D"color:#003B4F;"> <=
/span></span><span class=3D"yiv0852532148ydpa6a6511ecn"><span style=3D"colo=
r:#8F5902;">T</span></span><span class=3D"yiv0852532148ydpa6a6511eop"><span=
style=3D"color:#5E5E5E;">)</span></span><span style=3D"font-size:10.5pt;co=
lor:black;"></span></pre>=20
</div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;">to find the GRASS folder and use within rgrass::initGRASS does=
not work, so the connection between R and GRASS do not exist.</span></p>=
=20
</div>
<div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;"> </span></p>=20
</div>
<div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;">Does someone in the group has experience with that and could h=
elp with hints to solve it?</span></p>=20
</div>
<div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;">Is there a recommended way to make sure Github actions know wh=
ere GRASS is and use it?</span></p>=20
</div>
<div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;"> </span></p>=20
</div>
<div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;">Best</span></p>=20
</div>
<div>
<p class=3D"yiv0852532148MsoNormal"><span style=3D"font-size:12.0pt;font-fa=
mily:serif;">Bernardo</span></p>=20
</div>
</div>
</div>
</div>
</div></div>
</div>
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