From 8fe1387b90679792e411617128d36f7929389069 Mon Sep 17 00:00:00 2001 From: richfitz Date: Tue, 26 Mar 2024 10:29:18 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20mrc-ide/?= =?UTF-8?q?orderly2@5e111236be9b1ced909df3cc938401ae4e99058a=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/collaboration.html | 14 +-- articles/dependencies.html | 56 +++++------ articles/introduction.html | 160 +++++++++++++++--------------- articles/plugins.html | 14 +-- articles/troubleshooting.html | 12 +-- pkgdown.yml | 2 +- reference/orderly_cleanup.html | 10 +- reference/orderly_config.html | 2 +- reference/orderly_config_set.html | 6 +- reference/orderly_example.html | 4 +- reference/orderly_init.html | 2 +- reference/orderly_list_src.html | 4 +- reference/orderly_run.html | 8 +- search.json | 2 +- 14 files changed, 148 insertions(+), 148 deletions(-) diff --git a/articles/collaboration.html b/articles/collaboration.html index 0e8a543f..b09c1af6 100644 --- a/articles/collaboration.html +++ b/articles/collaboration.html @@ -206,7 +206,7 @@

An example
 orderly2::orderly_init(".")
-## ✔ Created orderly root at '/tmp/RtmppNzjZv/file1aa0357cf08a/alice'
+## ✔ Created orderly root at '/tmp/RtmpPKozZG/file1b374789a932/alice'
 ## ✔ Wrote '.gitignore'
 orderly2::orderly_list_src()
 ## [1] "data"
@@ -219,11 +219,11 @@

An example
 id <- orderly2::orderly_run("data")
-## ℹ Starting packet 'data' `20240320-114400-fea30a33` at 2024-03-20 11:44:01.004351
+## ℹ Starting packet 'data' `20240326-102849-cc3d9740` at 2024-03-26 10:28:49.804487
 ## > orderly2::orderly_artefact("Final data", "data.rds")
 ## > saveRDS(mtcars, "data.rds")
 ## ✔ Finished running data.R
-## ℹ Finished 20240320-114400-fea30a33 at 2024-03-20 11:44:01.064851 (0.06049967 secs)
+## ℹ Finished 20240326-102849-cc3d9740 at 2024-03-26 10:28:49.862746 (0.05825949 secs)

Perhaps it takes several goes for Alice to be happy with the analysis, but at some point she has something ready to share. She can then “push” the final packet up onto their server:

@@ -233,7 +233,7 @@

An example
 orderly2::orderly_init(".")
-## ✔ Created orderly root at '/tmp/RtmppNzjZv/file1aa0357cf08a/bob'
+## ✔ Created orderly root at '/tmp/RtmpPKozZG/file1b374789a932/bob'
 ## ✔ Wrote '.gitignore'
 orderly2::orderly_location_add(
@@ -247,7 +247,7 @@ 
An example= "data",
   options = list(allow_remote = TRUE, pull_metadata = TRUE))
 ##                         id name parameters
-## 1 20240320-114400-fea30a33 data
+## 1 20240326-102849-cc3d9740 data

Having seen there is a new “data” packet here, he can pull this down locally (TODO: mrc-4414 makes this nicer):

Now Bob is in a position to develop against the same packet that -Alice ran (20240320-114400-fea30a33)

+Alice ran (20240326-102849-cc3d9740)

Possible working patterns diff --git a/articles/dependencies.html b/articles/dependencies.html index 3abec505..5b64961e 100644 --- a/articles/dependencies.html +++ b/articles/dependencies.html @@ -152,16 +152,16 @@

Basic usevignette("introduction"), to get us started).

 id1 <- orderly2::orderly_run("data")
-## ℹ Starting packet 'data' `20240320-114404-0a5e9a09` at 2024-03-20 11:44:04.043771
+## ℹ Starting packet 'data' `20240326-102852-cdb0f2d0` at 2024-03-26 10:28:52.806702
 ## > d <- read.csv("data.csv")
 ## > d$z <- resid(lm(y ~ x, d))
 ## > saveRDS(d, "data.rds")
 ## ✔ Finished running data.R
-## ℹ Finished 20240320-114404-0a5e9a09 at 2024-03-20 11:44:04.079863 (0.03609133 secs)
+## ℹ Finished 20240326-102852-cdb0f2d0 at 2024-03-26 10:28:52.841872 (0.0351696 secs)
 id2 <- orderly2::orderly_run("analysis")
-## ℹ Starting packet 'analysis' `20240320-114404-1c5ebd4c` at 2024-03-20 11:44:04.113964
+## ℹ Starting packet 'analysis' `20240326-102852-df007fb1` at 2024-03-26 10:28:52.874111
 ## > orderly2::orderly_dependency("data", "latest()", "data.rds")
-## ℹ Depending on data @ `20240320-114404-0a5e9a09` (via latest(name == "data"))
+## ℹ Depending on data @ `20240326-102852-cdb0f2d0` (via latest(name == "data"))
 ## > d <- readRDS("data.rds")
 ## > png("analysis.png")
 ## > plot(y ~ x, d)
@@ -169,14 +169,14 @@ 
Basic use## agg_png 
 ##       2
 ## ✔ Finished running analysis.R
-## ℹ Finished 20240320-114404-1c5ebd4c at 2024-03-20 11:44:04.419673 (0.3057096 secs)
+## ℹ Finished 20240326-102852-df007fb1 at 2024-03-26 10:28:53.003847 (0.1297367 secs)

When we look at the metadata for the packet created from the analysis report, we can see it has used -20240320-114404-0a5e9a09 as its dependency:

+20240326-102852-cdb0f2d0 as its dependency:

 orderly2::orderly_metadata(id2)$depends
 ##                     packet                  query        files
-## 1 20240320-114404-0a5e9a09 latest(name == "data") data.rds....
+## 1 20240326-102852-cdb0f2d0 latest(name == "data") data.rds....

(indeed it had to, there is only one copy of the data packet to pick from).

@@ -201,35 +201,35 @@

Filtering candidates by parametersWe can run this for several values of cyl:

 orderly2::orderly_run("data", list(cyl = 4))
-## ℹ Starting packet 'data' `20240320-114404-c9fa1de5` at 2024-03-20 11:44:04.792111
+## ℹ Starting packet 'data' `20240326-102853-5f4a8dc0` at 2024-03-26 10:28:53.375361
 ## ℹ Parameters:
 ## • cyl: 4
 ## > orderly2::orderly_parameters(cyl = NULL)
 ## > d <- mtcars[mtcars$cyl == cyl, ]
 ## > saveRDS(d, "data.rds")
 ## ✔ Finished running data.R
-## ℹ Finished 20240320-114404-c9fa1de5 at 2024-03-20 11:44:04.822163 (0.03005242 secs)
-## [1] "20240320-114404-c9fa1de5"
+## ℹ Finished 20240326-102853-5f4a8dc0 at 2024-03-26 10:28:53.405129 (0.02976799 secs)
+## [1] "20240326-102853-5f4a8dc0"
 orderly2::orderly_run("data", list(cyl = 6))
-## ℹ Starting packet 'data' `20240320-114404-d7cd3c46` at 2024-03-20 11:44:04.846072
+## ℹ Starting packet 'data' `20240326-102853-6cf7ce7b` at 2024-03-26 10:28:53.428689
 ## ℹ Parameters:
 ## • cyl: 6
 ## > orderly2::orderly_parameters(cyl = NULL)
 ## > d <- mtcars[mtcars$cyl == cyl, ]
 ## > saveRDS(d, "data.rds")
 ## ✔ Finished running data.R
-## ℹ Finished 20240320-114404-d7cd3c46 at 2024-03-20 11:44:04.873492 (0.02742004 secs)
-## [1] "20240320-114404-d7cd3c46"
+## ℹ Finished 20240326-102853-6cf7ce7b at 2024-03-26 10:28:53.455681 (0.02699184 secs)
+## [1] "20240326-102853-6cf7ce7b"
 orderly2::orderly_run("data", list(cyl = 8))
-## ℹ Starting packet 'data' `20240320-114404-e5705533` at 2024-03-20 11:44:04.899273
+## ℹ Starting packet 'data' `20240326-102853-7a65244d` at 2024-03-26 10:28:53.481173
 ## ℹ Parameters:
 ## • cyl: 8
 ## > orderly2::orderly_parameters(cyl = NULL)
 ## > d <- mtcars[mtcars$cyl == cyl, ]
 ## > saveRDS(d, "data.rds")
 ## ✔ Finished running data.R
-## ℹ Finished 20240320-114404-e5705533 at 2024-03-20 11:44:04.926691 (0.0274179 secs)
-## [1] "20240320-114404-e5705533"
+## ℹ Finished 20240326-102853-7a65244d at 2024-03-26 10:28:53.508787 (0.02761459 secs) +## [1] "20240326-102853-7a65244d"

Our follow-on analysis contains:

Interpreting errors @@ -272,7 +272,7 @@

Interpreting errors
 orderly2::orderly_run("analysis", list(cyl = 9000))
-## ℹ Starting packet 'analysis' `20240320-114405-378e3479` at 2024-03-20 11:44:05.220121
+## ℹ Starting packet 'analysis' `20240326-102853-cbd2039f` at 2024-03-26 10:28:53.799244
 ## ℹ Parameters:
 ## • cyl: 9000
 ## > orderly2::orderly_parameters(cyl = NULL)
@@ -281,7 +281,7 @@ 
Interpreting errors## +   "latest(parameter:cyl == this:cyl)",
 ## +   "data.rds")
 ## ✖ Error running analysis.R
-## ℹ Finished 20240320-114405-378e3479 at 2024-03-20 11:44:05.285748 (0.06562686 secs)
+## ℹ Finished 20240326-102853-cbd2039f at 2024-03-26 10:28:53.864053 (0.06480861 secs)
 ## Error in `orderly2::orderly_run()`:
 ## ! Failed to run report
 ## Caused by error in `outpack_packet_use_dependency()`:
@@ -338,8 +338,8 @@ 
Interpreting errors## [1] 3
 ## 
 ## $found
-## [1] "20240320-114404-c9fa1de5" "20240320-114404-d7cd3c46"
-## [3] "20240320-114404-e5705533"

+## [1] "20240326-102853-5f4a8dc0" "20240326-102853-6cf7ce7b" +## [3] "20240326-102853-7a65244d"

(this would have worked with rlang::last_error()$explanation$parts$A too).

You can also use orderly2::orderly_metadata_extract to @@ -349,9 +349,9 @@

Interpreting errors= "data", extract = c(cyl = "parameters.cyl is number")) ## id cyl -## 1 20240320-114404-c9fa1de5 4 -## 2 20240320-114404-d7cd3c46 6 -## 3 20240320-114404-e5705533 8 +## 1 20240326-102853-5f4a8dc0 4 +## 2 20240326-102853-6cf7ce7b 6 +## 3 20240326-102853-7a65244d 8

Filtering candidates in other ways @@ -365,7 +365,7 @@

Filtering candidates in other wayslatest(parameter:cyl == environment:cyl) to match against whatever value cyl took in the evaluating environment.

Instead of a query, you can provide a single id (e.g, -20240320-114405-13266176), which would mean that even as +20240326-102853-a824ca4a), which would mean that even as new copies of the data packet are created, this dependency will always resolve to the same value.

You can chain together logical operations with diff --git a/articles/introduction.html b/articles/introduction.html index e0d1cc02..5085d9dc 100644 --- a/articles/introduction.html +++ b/articles/introduction.html @@ -121,7 +121,7 @@

Creating an empty orderly reposito 
 path <- tempfile() # we'll use a temporary directory here - see note below
 orderly2::orderly_init(path)
-## ✔ Created orderly root at '/tmp/RtmptDk5Eq/file1b2c4b9e6cfe'
+## ✔ Created orderly root at '/tmp/RtmplUlPtF/file1bc221f2f847'

which creates a few files:

## .
 ## ├── .outpack
@@ -183,14 +183,14 @@ 
Creating your first orderly reportorderly2::orderly_run():

 
 id <- orderly2::orderly_run("incoming_data")
-## ℹ Starting packet 'incoming_data' `20240320-114408-8c55377d` at 2024-03-20 11:44:08.553096
+## ℹ Starting packet 'incoming_data' `20240326-102857-15d0e6c6` at 2024-03-26 10:28:57.090209
 ## > d <- read.csv("data.csv")
 ## > d$z <- resid(lm(y ~ x, d))
 ## > saveRDS(d, "data.rds")
 ## ✔ Finished running incoming_data.R
-## ℹ Finished 20240320-114408-8c55377d at 2024-03-20 11:44:08.615441 (0.06234455 secs)
+## ℹ Finished 20240326-102857-15d0e6c6 at 2024-03-26 10:28:57.154431 (0.06422257 secs)
 id
-## [1] "20240320-114408-8c55377d"

+## [1] "20240326-102857-15d0e6c6"

The id that is created is a new identifier for the packet that will be both unique among all packets (within reason) and chronologically sortable. A packet that has an id that sorts after @@ -199,7 +199,7 @@

Creating your first orderly report## . ## ├── archive ## │ └── incoming_data -## │ └── 20240320-114408-8c55377d +## │ └── 20240326-102857-15d0e6c6 ## │ ├── data.csv ## │ ├── data.rds ## │ └── incoming_data.R @@ -212,7 +212,7 @@

Creating your first orderly report## └── incoming_data.R

A few things have changed here:

    -
  • we have a directory archive/incoming_data/20240320-114408-8c55377d; +
  • we have a directory archive/incoming_data/20240326-102857-15d0e6c6; this directory contains
    • the file that was created when we ran the report @@ -284,10 +284,10 @@

      Depending on packets from anot orderly2::orderly_run():

       id <- orderly2::orderly_run("analysis")
-## ℹ Starting packet 'analysis' `20240320-114409-111623d9` at 2024-03-20 11:44:09.06988
+## ℹ Starting packet 'analysis' `20240326-102857-9975d1e8` at 2024-03-26 10:28:57.602746
 ## > orderly2::orderly_dependency("incoming_data", "latest()",
 ## +                              c("incoming.rds" = "data.rds"))
-## ℹ Depending on incoming_data @ `20240320-114408-8c55377d` (via latest(name == "incoming_data"))
+## ℹ Depending on incoming_data @ `20240326-102857-15d0e6c6` (via latest(name == "incoming_data"))
 ## > d <- readRDS("incoming.rds")
 ## > png("analysis.png")
 ## > plot(y ~ x, d)
@@ -295,7 +295,7 @@ 
      Depending on packets from anot
 ## agg_png 
 ##       2
 ## ✔ Finished running analysis.R
-## ℹ Finished 20240320-114409-111623d9 at 2024-03-20 11:44:09.148942 (0.07906246 secs)
      +## ℹ Finished 20240326-102857-9975d1e8 at 2024-03-26 10:28:57.683402 (0.08065653 secs)

      For more information on dependencies, see vignette("dependencies").

      @@ -369,7 +369,7 @@

      Available in-report orderly comman available at that point (see below).

       id <- orderly2::orderly_run("incoming_data")
-## ℹ Starting packet 'incoming_data' `20240320-114409-5bf65b71` at 2024-03-20 11:44:09.361205
+## ℹ Starting packet 'incoming_data' `20240326-102857-e5a007e2` at 2024-03-26 10:28:57.898934
 ## > orderly2::orderly_strict_mode()
 ## > orderly2::orderly_resource("data.csv")
 ## > orderly2::orderly_artefact("Processed data", "data.rds")
@@ -377,7 +377,7 @@ 
      Available in-report orderly comman
 ## > d$z <- resid(lm(y ~ x, d))
 ## > saveRDS(d, "data.rds")
 ## ✔ Finished running incoming_data.R
-## ℹ Finished 20240320-114409-5bf65b71 at 2024-03-20 11:44:09.393691 (0.0324862 secs)
      +## ℹ Finished 20240326-102857-e5a007e2 at 2024-03-26 10:28:57.925488 (0.02655435 secs)

      Parameterised reports @@ -419,7 +419,7 @@

      Parameterised reports 
       id <- orderly2::orderly_run("random", list(n_samples = 15))
-## ℹ Starting packet 'random' `20240320-114409-9bb4e1c9` at 2024-03-20 11:44:09.611324
+## ℹ Starting packet 'random' `20240326-102858-23e6aecf` at 2024-03-26 10:28:58.143521
 ## ℹ Parameters:
 ## • n_samples: 15
 ## > orderly2::orderly_parameters(n_samples = 10)
@@ -427,7 +427,7 @@ 
      Parameterised reports## > d <- data.frame(x = x, y = x + rnorm(n_samples))
 ## > saveRDS(d, "data.rds")
 ## ✔ Finished running random.R
-## ℹ Finished 20240320-114409-9bb4e1c9 at 2024-03-20 11:44:09.640507 (0.02918339 secs)
      +## ℹ Finished 20240326-102858-23e6aecf at 2024-03-26 10:28:58.173673 (0.03015208 secs)

      Our resulting file has 15 rows, as the parameter we passed in affected the report:

      @@ -435,30 +435,30 @@ 
      Parameterised reports                             dest = dest)
 readRDS(file.path(dest, "random.rds"))
 ##     x          y
-## 1   1 -0.6445119
-## 2   2  1.7742788
-## 3   3  2.8678077
-## 4   4  3.7376916
-## 5   5  4.3717520
-## 6   6  6.3204476
-## 7   7  6.1215173
-## 8   8  6.3457428
-## 9   9  9.9784759
-## 10 10 10.4910966
-## 11 11  9.2635225
-## 12 12 11.9968438
-## 13 13 13.1277617
-## 14 14 13.1773673
-## 15 15 15.0977809
      +## 1 1 -0.8864689 +## 2 2 0.7549000 +## 3 3 4.5097307 +## 4 4 4.4705757 +## 5 5 5.4987667 +## 6 6 4.8851789 +## 7 7 6.8787464 +## 8 8 7.2021611 +## 9 9 8.8381048 +## 10 10 9.2982084 +## 11 11 11.2325857 +## 12 12 13.0650189 +## 13 13 13.3954358 +## 14 14 13.4552431 +## 15 15 13.3141654

      You can use these parameters in orderly’s search functions. For example we can find the most recent version of a packet by running:

       orderly2::orderly_search('latest(name == "random")')
-## [1] "20240320-114409-9bb4e1c9"
      +## [1] "20240326-102858-23e6aecf"

      But we can also pass in parameter queries here:

       orderly2::orderly_search('latest(name == "random" && parameter:n_samples > 10)')
-## [1] "20240320-114409-9bb4e1c9"
      +## [1] "20240326-102858-23e6aecf"

      These can be used within orderly2::orderly_dependency() (the name == "random" part is implied by the first name argument), for example

      @@ -490,21 +490,21 @@

      Shared resources## . ## ├── archive ## │ ├── analysis -## │ │ └── 20240320-114409-111623d9 +## │ │ └── 20240326-102857-9975d1e8 ## │ │ ├── analysis.R ## │ │ ├── analysis.png ## │ │ └── incoming.rds ## │ ├── incoming_data -## │ │ ├── 20240320-114408-8c55377d +## │ │ ├── 20240326-102857-15d0e6c6 ## │ │ │ ├── data.csv ## │ │ │ ├── data.rds ## │ │ │ └── incoming_data.R -## │ │ └── 20240320-114409-5bf65b71 +## │ │ └── 20240326-102857-e5a007e2 ## │ │ ├── data.csv ## │ │ ├── data.rds ## │ │ └── incoming_data.R ## │ └── random -## │ └── 20240320-114409-9bb4e1c9 +## │ └── 20240326-102858-23e6aecf ## │ ├── data.rds ## │ └── random.R ## ├── draft @@ -535,7 +535,7 @@

      Shared resourcesWe can run this:

       id <- orderly2::orderly_run("use_shared")
-## ℹ Starting packet 'use_shared' `20240320-114410-1b53b869` at 2024-03-20 11:44:10.109907
+## ℹ Starting packet 'use_shared' `20240326-102858-a21165f0` at 2024-03-26 10:28:58.636223
 ## > orderly2::orderly_shared_resource(data.csv = "data.csv")
 ## > orderly2::orderly_artefact("analysis", "analysis.png")
 ## > d <- read.csv("data.csv")
@@ -545,11 +545,11 @@ 
      Shared resources## agg_png 
 ##       2
 ## ✔ Finished running use_shared.R
-## ℹ Finished 20240320-114410-1b53b869 at 2024-03-20 11:44:10.143107 (0.03320026 secs)
      +## ℹ Finished 20240326-102858-a21165f0 at 2024-03-26 10:28:58.670165 (0.03394198 secs)

      In the resulting archive, the file that was used from the shared directory is present:

      ## archive/use_shared
-## └── 20240320-114410-1b53b869
+## └── 20240326-102858-a21165f0
 ##     ├── analysis.png
 ##     ├── data.csv
 ##     └── use_shared.R
      @@ -643,49 +643,49 @@

      Deleting things from the archive name = "incoming_data", extract = c(time = "time.start")) ## id time -## 1 20240320-114408-8c55377d 2024-03-20 11:44:08 -## 2 20240320-114409-5bf65b71 2024-03-20 11:44:09 +## 1 20240326-102857-15d0e6c6 2024-03-26 10:28:57 +## 2 20240326-102857-e5a007e2 2024-03-26 10:28:57

      When we run the analysis task, it will pull in the most -recent version (20240320-114409-5bf65b71). However, if you +recent version (20240326-102857-e5a007e2). However, if you had deleted this manually (e.g., to save space or accidentally) or corrupted it (e.g., by opening some output in Excel and letting it save changes) it will not be able to be included, and running analysis will fail:

       orderly2::orderly_run("analysis")
-## ℹ Starting packet 'analysis' `20240320-114410-b763c758` at 2024-03-20 11:44:10.719405
+## ℹ Starting packet 'analysis' `20240326-102859-402253d4` at 2024-03-26 10:28:59.253644
 ## > orderly2::orderly_dependency("incoming_data", "latest()",
 ## +                              c("incoming.rds" = "data.rds"))
 ## ✖ Error running analysis.R
-## ℹ Finished 20240320-114410-b763c758 at 2024-03-20 11:44:10.823049 (0.1036444 secs)
+## ℹ Finished 20240326-102859-402253d4 at 2024-03-26 10:28:59.360183 (0.1065388 secs)
 ## Error in `orderly2::orderly_run()`:
 ## ! Failed to run report
 ## Caused by error in `orderly_copy_files()`:
-## ! Unable to copy files, due to deleted packet 20240320-114409-5bf65b71
-## ℹ Consider 'orderly2::orderly_validate_archive("20240320-114409-5bf65b71",
+## ! Unable to copy files, due to deleted packet 20240326-102857-e5a007e2
+## ℹ Consider 'orderly2::orderly_validate_archive("20240326-102857-e5a007e2",
 ##   action = "orphan")' to remove this packet from consideration
 ## Caused by error:
 ## ! File not found in archive
 ## ✖ data.rds

      The error here tries to be fairly informative, telling us that we failed because when copying files from -20240320-114409-5bf65b71 we found that the packet was +20240326-102857-e5a007e2 we found that the packet was corrupt, because the file data.rds was not found in the archive. It also suggests a fix; we can tell orderly2 that -20240320-114409-5bf65b71 is “orphaned” and should not be +20240326-102857-e5a007e2 is “orphaned” and should not be considered for inclusion when we look for dependencies.

      We can carry out the suggestion and just validate this packet by running

      -orderly2::orderly_validate_archive("20240320-114409-5bf65b71", action = "orphan")
      +orderly2::orderly_validate_archive("20240326-102857-e5a007e2", action = "orphan")

      or we can validate all the packets we have:

       orderly2::orderly_validate_archive(action = "orphan")
-## ✔ 20240320-114408-8c55377d (incoming_data) is valid
-## ✔ 20240320-114409-111623d9 (analysis) is valid
-## ✖ 20240320-114409-5bf65b71 (incoming_data) is invalid due to its files
-## ✔ 20240320-114409-9bb4e1c9 (random) is valid
-## ✔ 20240320-114410-1b53b869 (use_shared) is valid
      +## ✔ 20240326-102857-15d0e6c6 (incoming_data) is valid +## ✔ 20240326-102857-9975d1e8 (analysis) is valid +## ✖ 20240326-102857-e5a007e2 (incoming_data) is invalid due to its files +## ✔ 20240326-102858-23e6aecf (random) is valid +## ✔ 20240326-102858-a21165f0 (use_shared) is valid

      If we had the option core.require_complete_tree enabled, then this process would also look for any packets that used our now-deleted packet and orphan those too, as we no longer have a complete @@ -772,16 +772,16 @@

      Interaction with the outpack store## │ └── outpack.rds ## ├── location ## │ ├── local -## │ │ ├── 20240320-114408-8c55377d -## │ │ ├── 20240320-114409-111623d9 -## │ │ ├── 20240320-114409-9bb4e1c9 -## │ │ └── 20240320-114410-1b53b869 +## │ │ ├── 20240326-102857-15d0e6c6 +## │ │ ├── 20240326-102857-9975d1e8 +## │ │ ├── 20240326-102858-23e6aecf +## │ │ └── 20240326-102858-a21165f0 ## │ └── orphan ## └── metadata -## ├── 20240320-114408-8c55377d -## ├── 20240320-114409-111623d9 -## ├── 20240320-114409-9bb4e1c9 -## └── 20240320-114410-1b53b869 +## ├── 20240326-102857-15d0e6c6 +## ├── 20240326-102857-9975d1e8 +## ├── 20240326-102858-23e6aecf +## └── 20240326-102858-a21165f0

      As can be perhaps inferred from the filenames, the files .outpack/metadata/<packet-id> are the metadata for each packet as it has been run. The files @@ -799,38 +799,38 @@

      Interaction with the outpack store## │ └── sha256 ## │ ├── 0a ## │ │ └── a82571c21c4e5f1f435e8bef2328dda5ef47e177d78d63d1c4ec647a5a388a -## │ ├── 20 -## │ │ └── b10e2cf5b88678cfdd95092536b4e3c4f6f92d303e2d9dce98f0de6c8f2ca0 ## │ ├── 23 ## │ │ └── 0cb6053c3bc82e67fc339c44b495852c77294bd3b0ccb5c4ba78b06b23e438 -## │ ├── 3f -## │ │ └── a3e41e3c8205942c7f233f5e4e18e8d1511fb3d8a2be8296f56d73c7514123 -## │ ├── 4c -## │ │ └── 9b503a1fe73aa592126ab57ae37315e23e9379f99e46c82504143d16473b33 +## │ ├── 24 +## │ │ └── 4568508dd0dbe711197773943f677b15b787080e7cc5db1ed135e891ba2c02 +## │ ├── 52 +## │ │ └── 2760c61350b6e6ffe334e3ee60eee0bd9e0939456ad30c131574eb21d20763 ## │ ├── 5f ## │ │ └── 96f49230c2791c05706f24cb2335cd0fad5d3625dc6bca124c44a51857f3f8 +## │ ├── af +## │ │ └── 726887d192821d139b9712b9060e456a656045d9f235dd0fc1333a9048ee73 +## │ ├── c9 +## │ │ └── 7483c2eb606db7d4adf4c439c28db00461b3044a7e7b4bbf3f7ee91385f2a8 +## │ ├── d5 +## │ │ └── 48a7f02ebbaf0429ad7f171e7ff7e0b3cae2fa9a6d2a11e51b5a72b1c80f46 ## │ ├── d9 ## │ │ └── 1699ae410cbd811e1f028f8a732e5162b7df854eec08d921141f965851272d -## │ ├── e3 -## │ │ └── 6c1710dac04f53afe583834ab34262199a75fad4582466fe6ecaa88ccc2c89 -## │ ├── e4 -## │ │ └── f953bd0296a25944f81de84813eb93d5852899f15ad5fb2767520169a662cf -## │ └── fb -## │ └── 92c0e5486e03f8fca4df7f4a8a802f34bfcb62e1ecb5ab8cf953187ff2dd4f +## │ └── e9 +## │ └── 030a8bd409eb480b8e9e253a312a29c902b40a226c26e790f499e5ffc1abdc ## ├── index ## │ └── outpack.rds ## ├── location ## │ ├── local -## │ │ ├── 20240320-114408-8c55377d -## │ │ ├── 20240320-114409-111623d9 -## │ │ ├── 20240320-114409-9bb4e1c9 -## │ │ └── 20240320-114410-1b53b869 +## │ │ ├── 20240326-102857-15d0e6c6 +## │ │ ├── 20240326-102857-9975d1e8 +## │ │ ├── 20240326-102858-23e6aecf +## │ │ └── 20240326-102858-a21165f0 ## │ └── orphan ## └── metadata -## ├── 20240320-114408-8c55377d -## ├── 20240320-114409-111623d9 -## ├── 20240320-114409-9bb4e1c9 -## └── 20240320-114410-1b53b869 +## ├── 20240326-102857-15d0e6c6 +## ├── 20240326-102857-9975d1e8 +## ├── 20240326-102858-23e6aecf +## └── 20240326-102858-a21165f0

      The files under .outpack/files/ should never be modified or deleted. This approach to storage naturally deduplicates the file archive, so that a large file used in many places is only ever stored diff --git a/articles/plugins.html b/articles/plugins.html index b284a787..a9e2f05a 100644 --- a/articles/plugins.html +++ b/articles/plugins.html @@ -151,7 +151,7 @@

      An example
      minimum_orderly_version: 1.99.0
 plugins:
   example.db:
-    path: /tmp/RtmpodBoFd/file1c1d3e835833
      + path: /tmp/RtmprGqhQu/file1cb3330a0f35

      Our plugin is called example.db and is listed within the plugins section, along with its configuration; in this case indicating the path where the SQLite file can be loaded from.

      @@ -303,13 +303,13 @@

      Trying it out
       orderly2::orderly_run("example", root = path_root)
-## ℹ Starting packet 'example' `20240320-114419-2651f9cf` at 2024-03-20 11:44:19.224923
+## ℹ Starting packet 'example' `20240326-102907-bc684843` at 2024-03-26 10:29:07.818577
 ## > dat <- example.db::query("SELECT * FROM mtcars WHERE cyl == 4")
 ## > orderly2::orderly_artefact("Summary of data", "data.rds")
 ## > saveRDS(summary(dat), "data.rds")
 ## ✔ Finished running example.R
-## ℹ Finished 20240320-114419-2651f9cf at 2024-03-20 11:44:19.318692 (0.09376884 secs)
-## [1] "20240320-114419-2651f9cf"
      +## ℹ Finished 20240326-102907-bc684843 at 2024-03-26 10:29:07.91025 (0.0916729 secs) +## [1] "20240326-102907-bc684843"
      @@ -449,7 +449,7 @@

      Saving metadata about what th 
      ## .
 ## ├── archive
 ## │   └── example
-## │       └── 20240320-114419-2651f9cf
+## │       └── 20240326-102907-bc684843
 ## │           ├── data.rds
 ## │           └── example.R
 ## ├── draft
@@ -501,12 +501,12 @@ 
      Saving metadata about what th
 several).
      
 
       id <- orderly2::orderly_run("example", root = path_root)
-## ℹ Starting packet 'example' `20240320-114420-2d54f63d` at 2024-03-20 11:44:20.180382
+## ℹ Starting packet 'example' `20240326-102908-c63e09e7` at 2024-03-26 10:29:08.777729
 ## > dat <- example.db::query("SELECT * FROM mtcars WHERE cyl == 4")
 ## > orderly2::orderly_artefact("Summary of data", "data.rds")
 ## > saveRDS(summary(dat), "data.rds")
 ## ✔ Finished running example.R
-## ℹ Finished 20240320-114420-2d54f63d at 2024-03-20 11:44:20.219796 (0.03941393 secs)
+## ℹ Finished 20240326-102908-c63e09e7 at 2024-03-26 10:29:08.822044 (0.04431486 secs)
 meta <- orderly2::orderly_metadata(id, root = path_root)
 meta$custom$example.db
 ##                                   sql rows         cols
diff --git a/articles/troubleshooting.html b/articles/troubleshooting.html
index 2c89fa71..3e375def 100644
--- a/articles/troubleshooting.html
+++ b/articles/troubleshooting.html
@@ -130,21 +130,21 @@ 
      Outpack files accidentally
 ##   <https://mrc-ide.github.io/orderly2/articles/troubleshooting.html>
 ## This warning is displayed once per session.
      
 
      ## ✔ Wrote '.gitignore'
      
-
      ## ℹ Starting packet 'data' `20240320-114426-aec3f3c0` at 2024-03-20 11:44:26.685751
      
+
      ## ℹ Starting packet 'data' `20240326-102915-53d4d1d3` at 2024-03-26 10:29:15.330637
      
 
      ## > orderly2::orderly_artefact("Final data", "data.rds")
 ## > saveRDS(mtcars, "data.rds")
      
 
      ## ✔ Finished running data.R
      
-
      ## ℹ Finished 20240320-114426-aec3f3c0 at 2024-03-20 11:44:26.719405 (0.03365374 secs)
      
-
      ## [1] "20240320-114426-aec3f3c0"
      
+
      ## ℹ Finished 20240326-102915-53d4d1d3 at 2024-03-26 10:29:15.364546 (0.03390884 secs)
      
+
      ## [1] "20240326-102915-53d4d1d3"
      
 
      subsequent calls will not display the warning:
      
 
       orderly2::orderly_run("data")
      
-
      ## ℹ Starting packet 'data' `20240320-114426-ce9944c4` at 2024-03-20 11:44:26.810406
      
+
      ## ℹ Starting packet 'data' `20240326-102915-738ddbdb` at 2024-03-26 10:29:15.454582
      
 
      ## > orderly2::orderly_artefact("Final data", "data.rds")
 ## > saveRDS(mtcars, "data.rds")
      
 
      ## ✔ Finished running data.R
      
-
      ## ℹ Finished 20240320-114426-ce9944c4 at 2024-03-20 11:44:26.833797 (0.02339005 secs)
      
-
      ## [1] "20240320-114426-ce9944c4"
      
+
      ## ℹ Finished 20240326-102915-738ddbdb at 2024-03-26 10:29:15.476465 (0.02188277 secs)
      
+
      ## [1] "20240326-102915-738ddbdb"
      
 
      The rest of this section discusses how you might permanently fix the
 issue.
      
 
      
diff --git a/pkgdown.yml b/pkgdown.yml
index 1e739341..c7ade873 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
   plugins: plugins.html
   query: query.html
   troubleshooting: troubleshooting.html
-last_built: 2024-03-20T11:43Z
+last_built: 2024-03-26T10:28Z
 urls:
   reference: https://mrc-ide.github.io/orderly2/reference
   article: https://mrc-ide.github.io/orderly2/articles
diff --git a/reference/orderly_cleanup.html b/reference/orderly_cleanup.html
index fb4e9221..ba25ca4d 100644
--- a/reference/orderly_cleanup.html
+++ b/reference/orderly_cleanup.html
@@ -150,24 +150,24 @@ 
      Notes for user of orderly1Examples
      
     
      # Create a simple example:
 path <- orderly2::orderly_example("default")
-#> ✔ Created orderly root at '/tmp/Rtmp3h50Ab/file17a024b47b4e'
+#> ✔ Created orderly root at '/tmp/RtmpB7oElW/file18356e529db5'
 
 # We simulate running a packet interactively by using 'source';
 # you might have run this line-by-line, or with the "Source"
 # button in Rstudio.
 source(file.path(path, "src/data/data.R"), chdir = TRUE)
-#> Warning: cannot open file '/tmp/Rtmp3h50Ab/file17a024b47b4e/src/data/data.R': No such file or directory
+#> Warning: cannot open file '/tmp/RtmpB7oElW/file18356e529db5/src/data/data.R': No such file or directory
 #> Error in file(filename, "r", encoding = encoding): cannot open the connection
 
 # Having run this, the output of the report is present in the
 # source directory:
 fs::dir_tree(path)
-#> Error: [ENOENT] Failed to search directory '/tmp/Rtmp3h50Ab/file17a024b47b4e': no such file or directory
+#> Error: [ENOENT] Failed to search directory '/tmp/RtmpB7oElW/file18356e529db5': no such file or directory
 
 # We can detect what might want cleaning up by running
 # "orderly_cleanup_status":
 orderly2::orderly_cleanup_status("data", root = path)
-#> Error: Directory does not exist: '/tmp/Rtmp3h50Ab/file17a024b47b4e'
+#> Error: Directory does not exist: '/tmp/RtmpB7oElW/file18356e529db5'
 
 # Soon this will print more nicely to the screen, but for now you
 # can see that the status of "data.rds" is "derived", which means
@@ -176,7 +176,7 @@ 
      Examples
 # Do the actual deletion:
 orderly2::orderly_cleanup("data", root = path)
-#> Error: Directory does not exist: '/tmp/Rtmp3h50Ab/file17a024b47b4e'
+#> Error: Directory does not exist: '/tmp/RtmpB7oElW/file18356e529db5'

      diff --git a/reference/orderly_list_src.html b/reference/orderly_list_src.html index 63dcf6b8..508c6e30 100644 --- a/reference/orderly_list_src.html +++ b/reference/orderly_list_src.html @@ -114,9 +114,9 @@

      See also

      Examples

      path <- orderly2::orderly_example("default")
-#> ✔ Created orderly root at '/tmp/Rtmp3h50Ab/file17a012e26376'
+#> ✔ Created orderly root at '/tmp/RtmpB7oElW/file183572fb2271'
 orderly2::orderly_list_src(root = path)
-#> Error: Directory does not exist: '/tmp/Rtmp3h50Ab/file17a012e26376'
+#> Error: Directory does not exist: '/tmp/RtmpB7oElW/file183572fb2271'