R abuild - Revision history

Sertonix: add deletion request

2023-08-25T01:11:01Z

add deletion request

← Older revision	Revision as of 01:11, 25 August 2023
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		{{Delete\|This page is completely unused and therefor can be deleted.}}

Jirutka: Blanked the page

2016-05-30T23:04:22Z

Blanked the page

← Older revision		Revision as of 23:04, 30 May 2016
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	~~This page is just a workspace for issues and needs regarding to R abuild.~~


	~~== CRAN_mirrors.csv ==~~

	~~Alba reported the following issue:~~

	~~<pre>~~
	~~install.packages("ggplot2")~~
	~~--- Please select a CRAN mirror for use in this session ---~~
	~~Warning: failed to download mirrors file (cannot download all files);~~
	~~using local file '/usr/share/doc/R//CRAN_mirrors.csv'~~
	~~Error in file(file, "rt") : cannot open the connection~~
	~~In addition: Warning messages:~~
	~~1: In download.file(url, destfile = f, quiet = TRUE) :~~
	~~URL 'https://cran.r-project.org/CRAN_mirrors.csv': status was~~
	~~'Problem with the SSL CA cert (path? access rights?)'~~
	~~2: In file(file, "rt") :~~
	~~cannot open file '/usr/share/doc/R//CRAN_mirrors.csv': No such file~~
	~~or directory~~
	~~</pre>~~

	~~I can’t reproduce it; when I’ve tried it on fresh Alpine installation, [http://haste.fit.cvut.cz/anowopo.sh\|it works correctly for me].~~

	~~It seems that sometimes R needs CRAN_mirrors.csv, but it apparently installs it into docs, so it’s separated in R-doc subpackage…~~


	~~== Plot and X11 ==~~

	For plotting X11 libs and other graphic libs are needed. Quite huge stuff. Maybe we should provide two packages, something like with OpenJDK – R as a full-blown package with all dependencies and R-base as a lightweight package without X11?


	~~== Installing R packages with C extensions ==~~

	~~Some R packages (like ggplot2) contains C extensions, so it needs header files, make and probably the whole C build environment to build them.~~


	~~== Missing depends_dev ==~~

	~~I forgot to add depends_dev. However, I don’t know how to find what exactly are dev dependencies of R. The same as makedepends?~~


	~~== R_HOME ==~~

	~~I thought that environment variable R_HOME should be set globally. As I found some packages needs this variable. However, R complains:~~

	~~<pre>WARNING: ignoring environment value of R_HOME</pre>~~


	~~Martin Morgan explained me on r-help mailing list, that this variable is really not needed to be set system-wide.~~

	~~<blockquote>~~
	~~R_HOME is set when R starts~~

	~~~$ env\|grep R_HOME~~
	~~~$ R --vanilla -e "Sys.getenv('R_HOME')"~~
	~~> Sys.getenv('R_HOME')~~
	~~[1] "/home/mtmorgan/bin/R-3-3-branch"~~

	~~and (after reading the documentation in ?R_HOME it the R help system)~~

	~~~$ R RHOME~~
	~~/home/mtmorgan/bin/R-3-3-branch~~

	so there is no need to set it in a system-wide profile. It is sometimes referenced inside an R package source tree that uses C or other compiled code in a Makevars file, as described in the 'Writing R Extensions' manual

	~~https://cran.r-project.org/doc/manuals/r-release/R-exts.html~~
	~~e.g., the section on configure and cleanup~~

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

	~~In these circumstances it has been set by the R process that is compiling the source code.~~
	~~</blockquote>~~

Jirutka at 23:05, 13 May 2016

2016-05-13T23:05:35Z

← Older revision		Revision as of 23:05, 13 May 2016
Line 39:		Line 39:

	I forgot to add depends_dev. However, I don’t know how to find what exactly are dev dependencies of R. The same as makedepends?		I forgot to add depends_dev. However, I don’t know how to find what exactly are dev dependencies of R. The same as makedepends?


			== R_HOME ==

			I thought that environment variable R_HOME should be set globally. As I found some packages needs this variable. However, R complains:

			<pre>WARNING: ignoring environment value of R_HOME</pre>


			Martin Morgan explained me on r-help mailing list, that this variable is really not needed to be set system-wide.

			<blockquote>
			R_HOME is set when R starts

			~$ env\|grep R_HOME
			~$ R --vanilla -e "Sys.getenv('R_HOME')"
			> Sys.getenv('R_HOME')
			[1] "/home/mtmorgan/bin/R-3-3-branch"

			and (after reading the documentation in ?R_HOME it the R help system)

			~$ R RHOME
			/home/mtmorgan/bin/R-3-3-branch

			so there is no need to set it in a system-wide profile. It is sometimes referenced inside an R package source tree that uses C or other compiled code in a Makevars file, as described in the 'Writing R Extensions' manual

			https://cran.r-project.org/doc/manuals/r-release/R-exts.html
			e.g., the section on configure and cleanup

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

			In these circumstances it has been set by the R process that is compiling the source code.
			</blockquote>

Jirutka at 23:02, 9 May 2016

2016-05-09T23:02:58Z

← Older revision		Revision as of 23:02, 9 May 2016
Line 34:		Line 34:

	Some R packages (like ggplot2) contains C extensions, so it needs header files, make and probably the whole C build environment to build them.		Some R packages (like ggplot2) contains C extensions, so it needs header files, make and probably the whole C build environment to build them.


			== Missing depends_dev ==

			I forgot to add depends_dev. However, I don’t know how to find what exactly are dev dependencies of R. The same as makedepends?

Jirutka: Created page with "This page is just a workspace for issues and needs regarding to R abuild. == CRAN_mirrors.csv == Alba reported the following issue:

 install.packages("ggplot2") --- P..."

2016-05-09T22:59:55Z

Created page with "This page is just a workspace for issues and needs regarding to R abuild. == CRAN_mirrors.csv == Alba reported the following issue: <pre> install.packages("ggplot2") --- P..."

New page

This page is just a workspace for issues and needs regarding to R abuild.

== CRAN_mirrors.csv ==

Alba reported the following issue:

<pre>
install.packages("ggplot2")
--- Please select a CRAN mirror for use in this session ---
Warning: failed to download mirrors file (cannot download all files);
using local file '/usr/share/doc/R//CRAN_mirrors.csv'
Error in file(file, "rt") : cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile = f, quiet = TRUE) :
URL 'https://cran.r-project.org/CRAN_mirrors.csv': status was
'Problem with the SSL CA cert (path? access rights?)'
2: In file(file, "rt") :
cannot open file '/usr/share/doc/R//CRAN_mirrors.csv': No such file
or directory
</pre>

I can’t reproduce it; when I’ve tried it on fresh Alpine installation, [http://haste.fit.cvut.cz/anowopo.sh|it works correctly for me].

It seems that sometimes R needs CRAN_mirrors.csv, but it apparently installs it into docs, so it’s separated in R-doc subpackage…

== Plot and X11 ==

For plotting X11 libs and other graphic libs are needed. Quite huge stuff. Maybe we should provide two packages, something like with OpenJDK – R as a full-blown package with all dependencies and R-base as a lightweight package without X11?

== Installing R packages with C extensions ==

Some R packages (like ggplot2) contains C extensions, so it needs header files, make and probably the whole C build environment to build them.