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
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