Questions/suggestions about new staged installation

On 4/25/19 3:11 AM, Pages, Herve wrote:

Hi,

I was playing around with inotifywait (great tool!) to see the new
staged installation of source packages in action. In one terminal I'm
monitoring the create/delete/move events of the installation library 
with:

? ? inotifywait -m --timefmt '%F %T' --format '%T -- %w %e %f' -e create
-e delete -e move path/to/R/library/

While in another terminal I install CRAN package abc with:

? ? R CMD INSTALL abc_2.1.tar.gz

All deps are already installed.

## With R 3.5

When installing abc the first time with R 3.5 inotifywait reports the
following events:

2019-04-24 16:57:42 -- /home/hpages/R/R-3.5.r75051/library/ CREATE,ISDIR
00LOCK-abc
2019-04-24 16:57:42 -- /home/hpages/R/R-3.5.r75051/library/ 
CREATE,ISDIR abc
2019-04-24 16:57:45 -- /home/hpages/R/R-3.5.r75051/library/ DELETE,ISDIR
00LOCK-

Then on subsequent times:

2019-04-24 16:58:14 -- /home/hpages/R/R-3.5.r75051/library/ CREATE,ISDIR
00LOCK-abc
2019-04-24 16:58:14 -- /home/hpages/R/R-3.5.r75051/library/
MOVED_FROM,ISDIR abc
2019-04-24 16:58:14 -- /home/hpages/R/R-3.5.r75051/library/ 
CREATE,ISDIR abc
2019-04-24 16:58:17 -- /home/hpages/R/R-3.5.r75051/library/ DELETE,ISDIR
00LOCK-abc

IIUC the additional 'MOVED_FROM,ISDIR abc'? event on subsequent installs
is triggered by the backing up of the earlier installation in case the
new installation fails.

## With R 3.6

First installation:

2019-04-24 17:09:04 -- /home/hpages/R/R-3.6.r76385/library/ CREATE,ISDIR
00LOCK-abc
2019-04-24 17:09:04 -- /home/hpages/R/R-3.6.r76385/library/ 
CREATE,ISDIR abc
2019-04-24 17:09:08 -- /home/hpages/R/R-3.6.r76385/library/
MOVED_TO,ISDIR abc
2019-04-24 17:09:09 -- /home/hpages/R/R-3.6.r76385/library/ DELETE,ISDIR
00LOCK-abc

Subsequent installations:

2019-04-24 17:09:59 -- /home/hpages/R/R-3.6.r76385/library/ CREATE,ISDIR
00LOCK-abc
2019-04-24 17:09:59 -- /home/hpages/R/R-3.6.r76385/library/
MOVED_FROM,ISDIR abc
2019-04-24 17:09:59 -- /home/hpages/R/R-3.6.r76385/library/ 
CREATE,ISDIR abc
2019-04-24 17:10:02 -- /home/hpages/R/R-3.6.r76385/library/
MOVED_TO,ISDIR abc
2019-04-24 17:10:03 -- /home/hpages/R/R-3.6.r76385/library/ DELETE,ISDIR
00LOCK-abc

IIUC the new 'MOVED_TO,ISDIR abc' event is triggered by the package
installation folder being moved from the temporary location to the final
location.

However I wonder about the CREATE,ISDIR abc event. It looks like even
for a staged installation tools:::.install_packages() still creates the
empty abc dir. This should no longer be necessary because this empty
folder is replaced later by the 'MOVED_TO,ISDIR abc' event. Am I missing
somethin

Yes, the final directory location gets created before the 
installation. I did this to minimize the added cognitive complexity to 
the code. I could explore if this could be changed, if the 
installation could work without that directory (which would mean 
implementing and testing on all CRAN/BIOC, installing in different 
modes, so certainly some effort).? Is the current implementation 
causing any problem?

Another thing: the times indicate that the 'MOVED_TO,ISDIR abc' event
(move from temp to final location) happens about 3-4 seconds after the
'MOVED_FROM,ISDIR abc' event (backing up). In this interval of time, the
abc package is missing. Wouldn't it be safer to leave the earlier
installation where it is and to replace it when the new installation
folder is moved from the temporary location to the final location? Said
otherwise, the backing up step no longer seems necessary with staged
installs. So inotifywait would report something like this:

2019-04-24 17:09:59 -- /home/hpages/R/R-3.6.r76385/library/ CREATE,ISDIR
00LOCK-abc
2019-04-24 17:10:02 -- /home/hpages/R/R-3.6.r76385/library/
MOVED_TO,ISDIR abc
2019-04-24 17:10:03 -- /home/hpages/R/R-3.6.r76385/library/ DELETE,ISDIR
00LOCK-abc

That is, only 3 events. On first and subsequent installation.

I don't think that would be possible. The package is test-loaded also 
from the final installation directory, and if that fails, restored 
from a back-up. This test-loading is useful as it can detect some 
problems with hard-coded directories possibly not detected before on 
test-loading from the temporary installation directory.

Best,
Tomas

Cheers,

H.


? > sessionInfo()
R version 3.6.0 beta (2019-04-12 r76385)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS:?? /home/hpages/R/R-3.6.r76385/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.6.r76385/lib/libRlapack.so

locale:
? ?[1] LC_CTYPE=en_US.UTF-8?????? LC_NUMERIC=C
? ?[3] LC_TIME=en_US.UTF-8??????? LC_COLLATE=en_US.UTF-8
? ?[5] LC_MONETARY=en_US.UTF-8??? LC_MESSAGES=en_US.UTF-8
? ?[7] LC_PAPER=en_US.UTF-8?????? LC_NAME=C
? ?[9] LC_ADDRESS=C?????????????? LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats???? graphics? grDevices utils???? datasets? methods base

loaded via a namespace (and not attached):
[1] compiler_3.6.0