R help - Apr 2017 - rdb and rds files include abolute file paths / help understanding how lazy-load dbs are created

Hi,

On 12.04.2017 at 08:09, Jeff Newmiller wrote:
> Someone might respond here anyway, but I think this is more of an R-devel
> question.
I tired R-devel before[1] with no response :(.
> Anyway, as long as the package file after installation has appropriate file
> names for where it is installed, what does it matter what is in the files
> before installation?
That's actually the point. In the installed .rd[bs] files the absolute file
paths
are still present but often[2] the referenced files don't even exist on the
computer the packaged is installed. My approach therefore is to replace those
absolute paths by relative[3] paths. But to do so I need to understand where
exactly those absolute paths are injected in the files - that's why I asked
for
help in my fist mail - sorry for not being clear enough.

Best,
Philip


[1] https://stat.ethz.ch/pipermail/r-devel/2017-April/074016.html
[2] At least on Linux for packages installed via the distribution packages
system.
And I think this also holds for prebuild windows/mac builds from cran.
[3] Relative to teh root directory of the package source

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I think we are (I certainly am) going to need a more concrete example. As in,
point us at a specific package and filename in this package that illustrates
your concern. Such precision would also be expected on R-devel, so the lack of
response may have been self-inflicted.

Are you aware of the system.file and file.path functions?  File names that YOU
enter into your package code should be referenced using these functions. I have
been assuming so far that you were referring to filenames picked up by R as it
builds the package, which appear to be handled just fine however they are stored
though I don't know the details.
-- 
Sent from my phone. Please excuse my brevity.

On April 19, 2017 2:40:05 PM PDT, Philip Rinn <rinni at inventati.org>
wrote:
>Hi,
>
>On 12.04.2017 at 08:09, Jeff Newmiller wrote:
>
>> Someone might respond here anyway, but I think this is more of an
>R-devel
>> question.
>
>I tired R-devel before[1] with no response :(.
>
>> Anyway, as long as the package file after installation has
>appropriate file
>> names for where it is installed, what does it matter what is in the
>files
>> before installation?
>
>That's actually the point. In the installed .rd[bs] files the absolute
>file paths
>are still present but often[2] the referenced files don't even exist on
>the
>computer the packaged is installed. My approach therefore is to replace
>those
>absolute paths by relative[3] paths. But to do so I need to understand
>where
>exactly those absolute paths are injected in the files - that's why I
>asked for
>help in my fist mail - sorry for not being clear enough.
>
>Best,
>Philip
>
>
>[1] https://stat.ethz.ch/pipermail/r-devel/2017-April/074016.html
>[2] At least on Linux for packages installed via the distribution
>packages system.
>And I think this also holds for prebuild windows/mac builds from cran.
>[3] Relative to teh root directory of the package source

Hi,

Am 20.04.2017 um 00:32 schrieb Jeff Newmiller:
> I think we are (I certainly am) going to need a more concrete example. As
in,
> point us at a specific package and filename in this package that
illustrates
> your concern. Such precision would also be expected on R-devel, so the lack
of
> response may have been self-inflicted.
Ok, let's give you an example:

philip at debian:~$ wget https://cran.r-project.org/src/contrib/ald_1.1.tar.gz
philip at debian:~$ mkdir test
philip at debian:~$ mkdir test1
philip at debian:~$ cp ald_1.1.tar.gz test/
philip at debian:~$ cp ald_1.1.tar.gz test1/
philip at debian:~$ cd test
philip at debian:~/test$ R CMD INSTALL --build ald_1.1.tar.gz
philip at debian:~/test$ tar -zxvf ald_1.1_R_x86_64-pc-linux-gnu.tar.gz
ald/help/paths.rds
philip at debian:~/test$ cd ../test1
philip at debian:~/test1$ R CMD INSTALL --build ald_1.1.tar.gz
philip at debian:~/test1$ tar -zxvf ald_1.1_R_x86_64-pc-linux-gnu.tar.gz
ald/help/paths.rds
philip at debian:~/test1$ cd ..
philip at debian:~$ Rscript -e
"readRDS('test/ald/help/paths.rds')"
[1] "/tmp/RtmpXhF0y3/R.INSTALLd717b7b387a/ald/man/ALD.Rd"
[2] "/tmp/RtmpXhF0y3/R.INSTALLd717b7b387a/ald/man/ald-package.Rd"
[3] "/tmp/RtmpXhF0y3/R.INSTALLd717b7b387a/ald/man/likALD.Rd"
[4] "/tmp/RtmpXhF0y3/R.INSTALLd717b7b387a/ald/man/mleALD.Rd"
[5] "/tmp/RtmpXhF0y3/R.INSTALLd717b7b387a/ald/man/momentsALD.Rd"
attr(,"first")
[1] 46
philip at debian:~$ Rscript -e
"readRDS('test1/ald/help/paths.rds')"
[1] "/tmp/RtmpqjNKva/R.INSTALLe362823e45a/ald/man/ALD.Rd"
[2] "/tmp/RtmpqjNKva/R.INSTALLe362823e45a/ald/man/ald-package.Rd"
[3] "/tmp/RtmpqjNKva/R.INSTALLe362823e45a/ald/man/likALD.Rd"
[4] "/tmp/RtmpqjNKva/R.INSTALLe362823e45a/ald/man/mleALD.Rd"
[5] "/tmp/RtmpqjNKva/R.INSTALLe362823e45a/ald/man/momentsALD.Rd"
attr(,"first")
[1] 46

As you see, the file help/paths.rds contains absolute paths which doe not exist
(after compilation) on the PC. I therefore try to find a way to replace these
absolute paths by relative. My favorite output would be:

philip at debian:~$ Rscript -e
"readRDS('test2/ald/help/paths.rds')"
[1] "./ald/man/ALD.Rd"
[2] "./ald/man/ald-package.Rd"
[3] "./ald/man/likALD.Rd"
[4] "./ald/man/mleALD.Rd"
[5] "./ald/man/momentsALD.Rd"
attr(,"first")
[1] 46

I just ask for help to understand where those paths got inject (see my first
mail
for details). I'm willing to write/test the patches needed.

Hope that helps to understand my idea.

Best,
Philip

I would have thunk that the right list would be

https://stat.ethz.ch/mailman/listinfo/r-package-devel

Best
David 

Sent from my iPhone
> On Apr 19, 2017, at 3:40 PM, Philip Rinn <rinni at inventati.org>
wrote:
> 
> Hi,
> 
>> On 12.04.2017 at 08:09, Jeff Newmiller wrote:
>> 
>> Someone might respond here anyway, but I think this is more of an
R-devel
>> question.
> 
> I tired R-devel before[1] with no response :(.
> 
>> Anyway, as long as the package file after installation has appropriate
file
>> names for where it is installed, what does it matter what is in the
files
>> before installation?
> 
> That's actually the point. In the installed .rd[bs] files the absolute
file paths
> are still present but often[2] the referenced files don't even exist on
the
> computer the packaged is installed. My approach therefore is to replace
those
> absolute paths by relative[3] paths. But to do so I need to understand
where
> exactly those absolute paths are injected in the files - that's why I
asked for
> help in my fist mail - sorry for not being clear enough.
> 
> Best,
> Philip
> 
> 
> [1] https://stat.ethz.ch/pipermail/r-devel/2017-April/074016.html
> [2] At least on Linux for packages installed via the distribution packages
system.
> And I think this also holds for prebuild windows/mac builds from cran.
> [3] Relative to teh root directory of the package source
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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http://www.R-project.org/posting-guide.html
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