orderly2::orderly_init(".")
-## ✔ Created orderly root at '/tmp/RtmpXFj1Og/file1a6b795204b0/alice'
+## ✔ Created orderly root at '/tmp/RtmpAhPB8U/file1a08583bdeb7/alice'
## ✔ Wrote '.gitignore'
orderly2::orderly_list_src()
## [1] "data"
@@ -206,11 +206,11 @@
id <- orderly2::orderly_run("data")
-## ℹ Starting packet 'data' `20240905-080221-6b00c525` at 2024-09-05 08:02:21.423466
+## ℹ Starting packet 'data' `20240905-155204-ee6992a0` at 2024-09-05 15:52:04.937049
## > orderly2::orderly_artefact("data.rds", description = "Final data")
## > saveRDS(mtcars, "data.rds")
## ✔ Finished running data.R
-## ℹ Finished 20240905-080221-6b00c525 at 2024-09-05 08:02:21.478472 (0.05500579 secs)
+## ℹ Finished 20240905-155204-ee6992a0 at 2024-09-05 15:52:04.996184 (0.05913496 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:
@@ -220,7 +220,7 @@
orderly2::orderly_init(".")
-## ✔ Created orderly root at '/tmp/RtmpXFj1Og/file1a6b795204b0/bob'
+## ✔ Created orderly root at '/tmp/RtmpAhPB8U/file1a08583bdeb7/bob'
## ✔ Wrote '.gitignore'
orderly2::orderly_location_add(
@@ -234,18 +234,18 @@ An example= "data",
options = list(allow_remote = TRUE, pull_metadata = TRUE))
## id name parameters
-## 1 20240905-080221-6b00c525 data
Having seen there is a new “data” packet here, he can pull this down locally (TODO: mrc-4414 makes this nicer):
orderly2::orderly_location_pull_packet(id)
## ℹ Looking for suitable files already on disk
## ℹ Need to fetch 2 files (1.3 kB) from 1 location
-## ⠙ Fetching file 1/2 (95 B) from 'server' | ETA: 0s [2ms]
-## ✔ Fetched 2 files (1.3 kB) from 'server' in 19ms.
+## ⠙ Fetching file 1/2 (95 B) from 'server' | ETA: 0s [3ms]
+## ✔ Fetched 2 files (1.3 kB) from 'server' in 20ms.
## Now Bob is in a position to develop against the same packet that -Alice ran (20240905-080221-6b00c525)
+Alice ran (20240905-155204-ee6992a0)Create an orderly store with a file store and a complete tree. See
orderly2::orderly_init() for more details.
id1 <- orderly2::orderly_run("data")
-## ℹ Starting packet 'data' `20240905-080224-b9674449` at 2024-09-05 08:02:24.726524
+## ℹ Starting packet 'data' `20240905-155208-4ed119f9` at 2024-09-05 15:52:08.310439
## > d <- read.csv("data.csv")
## > d$z <- resid(lm(y ~ x, d))
## > saveRDS(d, "data.rds")
## ✔ Finished running data.R
-## ℹ Finished 20240905-080224-b9674449 at 2024-09-05 08:02:24.761707 (0.03518271 secs)
+## ℹ Finished 20240905-155208-4ed119f9 at 2024-09-05 15:52:08.349091 (0.03865218 secs)
id2 <- orderly2::orderly_run("analysis")
-## ℹ Starting packet 'analysis' `20240905-080224-c961843d` at 2024-09-05 08:02:24.788789
+## ℹ Starting packet 'analysis' `20240905-155208-60507729` at 2024-09-05 15:52:08.378635
## > orderly2::orderly_dependency("data", "latest()", "data.rds")
-## ℹ Depending on data @ `20240905-080224-b9674449` (via latest(name == "data"))
+## ℹ Depending on data @ `20240905-155208-4ed119f9` (via latest(name == "data"))
## > d <- readRDS("data.rds")
## > png("analysis.png")
## > plot(y ~ x, d)
@@ -155,14 +155,14 @@ Basic use## agg_png
## 2
## ✔ Finished running analysis.R
-## ℹ Finished 20240905-080224-c961843d at 2024-09-05 08:02:24.896412 (0.1076229 secs)
When we look at the metadata for the packet created from the
analysis report, we can see it has used
-20240905-080224-b9674449 as its dependency:
20240905-155208-4ed119f9 as its dependency:
orderly2::orderly_metadata(id2)$depends
## packet query files
-## 1 20240905-080224-b9674449 latest(name == "data") data.rds....(indeed it had to, there is only one copy of the data
packet to pick from).
cyl:
orderly2::orderly_run("data", list(cyl = 4))
-## ℹ Starting packet 'data' `20240905-080225-40f9c854` at 2024-09-05 08:02:25.256076
+## ℹ Starting packet 'data' `20240905-155208-d7439145` at 2024-09-05 15:52:08.84341
## ℹ Parameters:
## • cyl: 4
## > orderly2::orderly_parameters(cyl = NULL)
## > d <- mtcars[mtcars$cyl == cyl, ]
## > saveRDS(d, "data.rds")
## ✔ Finished running data.R
-## ℹ Finished 20240905-080225-40f9c854 at 2024-09-05 08:02:25.286214 (0.03013873 secs)
-## [1] "20240905-080225-40f9c854"
+## ℹ Finished 20240905-155208-d7439145 at 2024-09-05 15:52:08.876495 (0.03308415 secs)
+## [1] "20240905-155208-d7439145"
orderly2::orderly_run("data", list(cyl = 6))
-## ℹ Starting packet 'data' `20240905-080225-4da56319` at 2024-09-05 08:02:25.30542
+## ℹ Starting packet 'data' `20240905-155208-e5c4ca41` at 2024-09-05 15:52:08.899926
## ℹ Parameters:
## • cyl: 6
## > orderly2::orderly_parameters(cyl = NULL)
## > d <- mtcars[mtcars$cyl == cyl, ]
## > saveRDS(d, "data.rds")
## ✔ Finished running data.R
-## ℹ Finished 20240905-080225-4da56319 at 2024-09-05 08:02:25.332333 (0.02691317 secs)
-## [1] "20240905-080225-4da56319"
+## ℹ Finished 20240905-155208-e5c4ca41 at 2024-09-05 15:52:08.930287 (0.0303607 secs)
+## [1] "20240905-155208-e5c4ca41"
orderly2::orderly_run("data", list(cyl = 8))
-## ℹ Starting packet 'data' `20240905-080225-59e680b0` at 2024-09-05 08:02:25.353485
+## ℹ Starting packet 'data' `20240905-155208-f3619169` at 2024-09-05 15:52:08.953167
## ℹ Parameters:
## • cyl: 8
## > orderly2::orderly_parameters(cyl = NULL)
## > d <- mtcars[mtcars$cyl == cyl, ]
## > saveRDS(d, "data.rds")
## ✔ Finished running data.R
-## ℹ Finished 20240905-080225-59e680b0 at 2024-09-05 08:02:25.378441 (0.02495623 secs)
-## [1] "20240905-080225-59e680b0"Our follow-on analysis contains:
orderly2::orderly_parameters(cyl = NULL) @@ -233,7 +233,7 @@).Filtering candidates by parametersthis:cyl
+## ℹ Finished 20240905-155209-23026439 at 2024-09-05 15:52:09.190904 (0.05169082 secs) +## [1] "20240905-155209-23026439"orderly2::orderly_run("analysis", list(cyl = 4)) -## ℹ Starting packet 'analysis' `20240905-080225-8719a52e` at 2024-09-05 08:02:25.530097 +## ℹ Starting packet 'analysis' `20240905-155209-23026439` at 2024-09-05 15:52:09.139214 ## ℹ Parameters: ## • cyl: 4 ## > orderly2::orderly_parameters(cyl = NULL) @@ -241,7 +241,7 @@Filtering candidates by parameters## + "data", ## + "latest(parameter:cyl == this:cyl)", ## + "data.rds") -## ℹ Depending on data @ `20240905-080225-40f9c854` (via latest(parameter:cyl == this:cyl && name == "data")) +## ℹ Depending on data @ `20240905-155208-d7439145` (via latest(parameter:cyl == this:cyl && name == "data")) ## > d <- readRDS("data.rds") ## > png("analysis.png") ## > plot(mpg ~ disp, d) @@ -249,8 +249,8 @@
Filtering candidates by parameters## agg_png ## 2 ## ✔ Finished running analysis.R -## ℹ Finished 20240905-080225-8719a52e at 2024-09-05 08:02:25.579071 (0.04897404 secs) -## [1] "20240905-080225-8719a52e"
orderly2::orderly_run("analysis", list(cyl = 9000))
-## ℹ Starting packet 'analysis' `20240905-080225-a81e462f` at 2024-09-05 08:02:25.658968
+## ℹ Starting packet 'analysis' `20240905-155209-45ac12a6` at 2024-09-05 15:52:09.274588
## ℹ Parameters:
## • cyl: 9000
## > orderly2::orderly_parameters(cyl = NULL)
@@ -267,7 +267,7 @@ Interpreting errors## + "latest(parameter:cyl == this:cyl)",
## + "data.rds")
## ✖ Error running analysis.R
-## ℹ Finished 20240905-080225-a81e462f at 2024-09-05 08:02:25.717692 (0.05872464 secs)
+## ℹ Finished 20240905-155209-45ac12a6 at 2024-09-05 15:52:09.336643 (0.06205487 secs)
## Error in `orderly2::orderly_run()`:
## ! Failed to run report
## Caused by error in `outpack_packet_use_dependency()`:
@@ -324,8 +324,8 @@ Interpreting errors## [1] 3
##
## $found
-## [1] "20240905-080225-40f9c854" "20240905-080225-4da56319"
-## [3] "20240905-080225-59e680b0"
(this would have worked with
rlang::last_error()$explanation$parts$A too).
You can also use orderly2::orderly_metadata_extract to
@@ -335,9 +335,9 @@
cyl took in the evaluating environment.
Instead of a query, you can provide a single id (e.g,
-20240905-080225-8719a52e), which would mean that even as
+20240905-155209-23026439), 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 15db74de..0674a433 100644 --- a/articles/introduction.html +++ b/articles/introduction.html @@ -107,7 +107,7 @@
path <- tempfile() # we'll use a temporary directory here - see note below
orderly2::orderly_init(path)
-## ✔ Created orderly root at '/tmp/RtmpqAQMea/file1af65b7c91e8'which creates a few files:
## . ## ├── .outpack @@ -169,14 +169,14 @@:Creating your first orderly reportorderly2::orderly_run()
+## [1] "20240905-155212-78e3f681"id <- orderly2::orderly_run("incoming_data") -## ℹ Starting packet 'incoming_data' `20240905-080228-ca5e5af6` at 2024-09-05 08:02:28.794513 +## ℹ Starting packet 'incoming_data' `20240905-155212-78e3f681` at 2024-09-05 15:52:12.476331 ## > d <- read.csv("data.csv") ## > d$z <- resid(lm(y ~ x, d)) ## > saveRDS(d, "data.rds") ## ✔ Finished running incoming_data.R -## ℹ Finished 20240905-080228-ca5e5af6 at 2024-09-05 08:02:28.855893 (0.06137991 secs) +## ℹ Finished 20240905-155212-78e3f681 at 2024-09-05 15:52:12.53853 (0.06219864 secs) id -## [1] "20240905-080228-ca5e5af6"
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
@@ -185,7 +185,7 @@
## .
## ├── archive
## │ └── incoming_data
-## │ └── 20240905-080228-ca5e5af6
+## │ └── 20240905-155212-78e3f681
## │ ├── data.csv
## │ ├── data.rds
## │ └── incoming_data.R
@@ -198,7 +198,7 @@ Creating your first orderly report## └── incoming_data.R
A few things have changed here:
orderly2::orderly_run():
id <- orderly2::orderly_run("analysis")
-## ℹ Starting packet 'analysis' `20240905-080229-4bf6295e` at 2024-09-05 08:02:29.299062
+## ℹ Starting packet 'analysis' `20240905-155212-fa93a12e` at 2024-09-05 15:52:12.981231
## > orderly2::orderly_dependency("incoming_data", "latest()",
## + c("incoming.rds" = "data.rds"))
-## ℹ Depending on incoming_data @ `20240905-080228-ca5e5af6` (via latest(name == "incoming_data"))
+## ℹ Depending on incoming_data @ `20240905-155212-78e3f681` (via latest(name == "incoming_data"))
## > d <- readRDS("incoming.rds")
## > png("analysis.png")
## > plot(y ~ x, d)
@@ -281,7 +281,7 @@ Depending on packets from anot
## agg_png
## 2
## ✔ Finished running analysis.R
-## ℹ Finished 20240905-080229-4bf6295e at 2024-09-05 08:02:29.375767 (0.07670498 secs)
For more information on dependencies, see
vignette("dependencies").
id <- orderly2::orderly_run("incoming_data")
-## ℹ Starting packet 'incoming_data' `20240905-080229-95242471` at 2024-09-05 08:02:29.584198
+## ℹ Starting packet 'incoming_data' `20240905-155213-43dfe003` at 2024-09-05 15:52:13.266759
## > orderly2::orderly_strict_mode()
## > orderly2::orderly_resource("data.csv")
## > orderly2::orderly_artefact("Processed data", "data.rds")
@@ -372,7 +372,7 @@ Available in-report orderly comman
## future versions of orderly, we will change the order of the arguments to
## 'orderly_artefact()' so that 'files' comes first. If you name your calls to
## 'description' then you will be compatible when we make this change.
-## ℹ Finished 20240905-080229-95242471 at 2024-09-05 08:02:29.626847 (0.04264855 secs)
id <- orderly2::orderly_run("random", list(n_samples = 15))
-## ℹ Starting packet 'random' `20240905-080229-d73f20b5` at 2024-09-05 08:02:29.843275
+## ℹ Starting packet 'random' `20240905-155213-85e624a8` at 2024-09-05 15:52:13.525522
## ℹ Parameters:
## • n_samples: 15
## > orderly2::orderly_parameters(n_samples = 10)
@@ -422,7 +422,7 @@ Parameterised reports## > d <- data.frame(x = x, y = x + rnorm(n_samples))
## > saveRDS(d, "data.rds")
## ✔ Finished running random.R
-## ℹ Finished 20240905-080229-d73f20b5 at 2024-09-05 08:02:29.868695 (0.02541995 secs)
Our resulting file has 15 rows, as the parameter we passed in affected the report:
@@ -449,11 +449,11 @@Parameterised reports
+## [1] "20240905-155213-85e624a8"orderly2::orderly_search('latest(name == "random")') -## [1] "20240905-080229-d73f20b5"
But we can also pass in parameter queries here:
orderly2::orderly_search('latest(name == "random" && parameter:n_samples > 10)')
-## [1] "20240905-080229-d73f20b5"These can be used within orderly2::orderly_dependency()
(the name == "random" part is implied by the first
name argument), for example
## .
## ├── archive
## │ ├── analysis
-## │ │ └── 20240905-080229-4bf6295e
+## │ │ └── 20240905-155212-fa93a12e
## │ │ ├── analysis.R
## │ │ ├── analysis.png
## │ │ └── incoming.rds
## │ ├── incoming_data
-## │ │ ├── 20240905-080228-ca5e5af6
+## │ │ ├── 20240905-155212-78e3f681
## │ │ │ ├── data.csv
## │ │ │ ├── data.rds
## │ │ │ └── incoming_data.R
-## │ │ └── 20240905-080229-95242471
+## │ │ └── 20240905-155213-43dfe003
## │ │ ├── data.csv
## │ │ ├── data.rds
## │ │ └── incoming_data.R
## │ └── random
-## │ └── 20240905-080229-d73f20b5
+## │ └── 20240905-155213-85e624a8
## │ ├── data.rds
## │ └── random.R
## ├── draft
@@ -530,7 +530,7 @@ Shared resourcesWe can run this:
id <- orderly2::orderly_run("use_shared")
-## ℹ Starting packet 'use_shared' `20240905-080230-53670258` at 2024-09-05 08:02:30.328211
+## ℹ Starting packet 'use_shared' `20240905-155214-01f628f0` at 2024-09-05 15:52:14.010163
## > orderly2::orderly_shared_resource("data.csv")
## > orderly2::orderly_artefact("analysis", "analysis.png")
## Warning: Please use a named argument for the description in 'orderly_artefact()'
@@ -549,11 +549,11 @@ Shared resources## future versions of orderly, we will change the order of the arguments to
## 'orderly_artefact()' so that 'files' comes first. If you name your calls to
## 'description' then you will be compatible when we make this change.
-## ℹ Finished 20240905-080230-53670258 at 2024-09-05 08:02:30.372285 (0.04407382 secs)
+## ℹ Finished 20240905-155214-01f628f0 at 2024-09-05 15:52:14.054829 (0.04466653 secs)
In the resulting archive, the file that was used from the shared directory is present:
## archive/use_shared
-## └── 20240905-080230-53670258
+## └── 20240905-155214-01f628f0
## ├── analysis.png
## ├── data.csv
## └── use_shared.RWhen we run the analysis task, it will pull in the most
-recent version (20240905-080229-95242471). However, if you
+recent version (20240905-155213-43dfe003). 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' `20240905-080230-f22cf381` at 2024-09-05 08:02:30.948278
+## ℹ Starting packet 'analysis' `20240905-155214-a0f1c6b9` at 2024-09-05 15:52:14.631023
## > orderly2::orderly_dependency("incoming_data", "latest()",
## + c("incoming.rds" = "data.rds"))
## ✖ Error running analysis.R
-## ℹ Finished 20240905-080230-f22cf381 at 2024-09-05 08:02:31.020346 (0.07206869 secs)
+## ℹ Finished 20240905-155214-a0f1c6b9 at 2024-09-05 15:52:14.705544 (0.07452083 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 20240905-080229-95242471
-## ℹ Consider 'orderly2::orderly_validate_archive("20240905-080229-95242471",
+## ! Unable to copy files, due to deleted packet 20240905-155213-43dfe003
+## ℹ Consider 'orderly2::orderly_validate_archive("20240905-155213-43dfe003",
## action = "orphan")' to remove this packet from consideration
## Caused by error:
## ! File not found in archive
## ✖ data.rdsThe error here tries to be fairly informative, telling us that we
failed because when copying files from
-20240905-080229-95242471 we found that the packet was
+20240905-155213-43dfe003 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
-20240905-080229-95242471 is “orphaned” and should not be
+20240905-155213-43dfe003 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("20240905-080229-95242471", action = "orphan")orderly2::orderly_validate_archive("20240905-155213-43dfe003", action = "orphan")
or we can validate all the packets we have:
orderly2::orderly_validate_archive(action = "orphan")
-## ✔ 20240905-080228-ca5e5af6 (incoming_data) is valid
-## ✔ 20240905-080229-4bf6295e (analysis) is valid
-## ✖ 20240905-080229-95242471 (incoming_data) is invalid due to its files
-## ✔ 20240905-080229-d73f20b5 (random) is valid
-## ✔ 20240905-080230-53670258 (use_shared) is validIf 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
@@ -776,16 +776,16 @@
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
@@ -825,16 +825,16 @@
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 078a6a88..b948d235 100644
--- a/articles/plugins.html
+++ b/articles/plugins.html
@@ -137,7 +137,7 @@
minimum_orderly_version: 1.99.0
plugins:
example.db:
- path: /tmp/Rtmp01esxs/file1be86b7a0ff0Our 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.
orderly2::orderly_run("example", root = path_root)
-## ℹ Starting packet 'example' `20240905-080238-d2ef47f8` at 2024-09-05 08:02:38.827684
+## ℹ Starting packet 'example' `20240905-155222-9e7ed57f` at 2024-09-05 15:52:22.622947
## > dat <- example.db::query("SELECT * FROM mtcars WHERE cyl == 4")
## > orderly2::orderly_artefact("Summary of data", "data.rds")
## Warning: Please use a named argument for the description in 'orderly_artefact()'
@@ -303,8 +303,8 @@ Trying it out## future versions of orderly, we will change the order of the arguments to
## 'orderly_artefact()' so that 'files' comes first. If you name your calls to
## 'description' then you will be compatible when we make this change.
-## ℹ Finished 20240905-080238-d2ef47f8 at 2024-09-05 08:02:39.001563 (0.1738789 secs)
-## [1] "20240905-080238-d2ef47f8"
+## ℹ Finished 20240905-155222-9e7ed57f at 2024-09-05 15:52:22.803447 (0.1805007 secs)
+## [1] "20240905-155222-9e7ed57f"
## .
## ├── archive
## │ └── example
-## │ └── 20240905-080238-d2ef47f8
+## │ └── 20240905-155222-9e7ed57f
## │ ├── data.rds
## │ └── example.R
## ├── draft
@@ -496,7 +496,7 @@ Saving metadata about what th
several).
id <- orderly2::orderly_run("example", root = path_root)
-## ℹ Starting packet 'example' `20240905-080239-da473a20` at 2024-09-05 08:02:39.855157
+## ℹ Starting packet 'example' `20240905-155223-aab9cdb5` at 2024-09-05 15:52:23.669423
## > dat <- example.db::query("SELECT * FROM mtcars WHERE cyl == 4")
## > orderly2::orderly_artefact("Summary of data", "data.rds")
## Warning: Please use a named argument for the description in 'orderly_artefact()'
@@ -510,7 +510,7 @@ Saving metadata about what th
## future versions of orderly, we will change the order of the arguments to
## 'orderly_artefact()' so that 'files' comes first. If you name your calls to
## 'description' then you will be compatible when we make this change.
-## ℹ Finished 20240905-080239-da473a20 at 2024-09-05 08:02:39.90698 (0.0518229 secs)
+## ℹ Finished 20240905-155223-aab9cdb5 at 2024-09-05 15:52:23.721703 (0.05227947 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 a81c6bb6..b46de14c 100644
--- a/articles/troubleshooting.html
+++ b/articles/troubleshooting.html
@@ -116,21 +116,21 @@ 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' `20240905-080246-3b8cf756` at 2024-09-05 08:02:46.235029
+## ℹ Starting packet 'data' `20240905-155230-0e9ee1eb` at 2024-09-05 15:52:30.059476
## > orderly2::orderly_artefact("data.rds", description = "Final data")
## > saveRDS(mtcars, "data.rds")
## ✔ Finished running data.R
-## ℹ Finished 20240905-080246-3b8cf756 at 2024-09-05 08:02:46.270178 (0.03514838 secs)
-## [1] "20240905-080246-3b8cf756"
+## ℹ Finished 20240905-155230-0e9ee1eb at 2024-09-05 15:52:30.095824 (0.03634834 secs)
+## [1] "20240905-155230-0e9ee1eb"
subsequent calls will not display the warning:
orderly2::orderly_run("data")
-## ℹ Starting packet 'data' `20240905-080246-5a93f4e7` at 2024-09-05 08:02:46.356176
+## ℹ Starting packet 'data' `20240905-155230-2e2063ea` at 2024-09-05 15:52:30.182563
## > orderly2::orderly_artefact("data.rds", description = "Final data")
## > saveRDS(mtcars, "data.rds")
## ✔ Finished running data.R
-## ℹ Finished 20240905-080246-5a93f4e7 at 2024-09-05 08:02:46.376964 (0.02078772 secs)
-## [1] "20240905-080246-5a93f4e7"
+## ℹ Finished 20240905-155230-2e2063ea at 2024-09-05 15:52:30.203949 (0.02138615 secs)
+## [1] "20240905-155230-2e2063ea"
The rest of this section discusses how you might permanently fix the
issue.
diff --git a/pkgdown.yml b/pkgdown.yml
index 128513ef..a76c3141 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
plugins: plugins.html
query: query.html
troubleshooting: troubleshooting.html
-last_built: 2024-09-05T08:02Z
+last_built: 2024-09-05T15:51Z
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 68a4232b..2e707fe9 100644
--- a/reference/orderly_cleanup.html
+++ b/reference/orderly_cleanup.html
@@ -135,24 +135,24 @@ Notes for user of orderly1Examples
# Create a simple example:
path <- orderly2::orderly_example("default")
-#> ✔ Created orderly root at '/tmp/RtmpTXa1jo/file170f43324a93'
+#> ✔ Created orderly root at '/tmp/RtmpiweZAh/file16ac5ea4b156'
# 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/RtmpTXa1jo/file170f43324a93/src/data/data.R': No such file or directory
+#> Warning: cannot open file '/tmp/RtmpiweZAh/file16ac5ea4b156/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/RtmpTXa1jo/file170f43324a93': no such file or directory
+#> Error: [ENOENT] Failed to search directory '/tmp/RtmpiweZAh/file16ac5ea4b156': 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/RtmpTXa1jo/file170f43324a93'
+#> Error: Directory does not exist: '/tmp/RtmpiweZAh/file16ac5ea4b156'
# 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
@@ -161,7 +161,7 @@ Examples
# Do the actual deletion:
orderly2::orderly_cleanup("data", root = path)
-#> Error: Directory does not exist: '/tmp/RtmpTXa1jo/file170f43324a93'
+#> Error: Directory does not exist: '/tmp/RtmpiweZAh/file16ac5ea4b156'
path <- orderly2::orderly_example("default")
-#> ✔ Created orderly root at '/tmp/RtmpTXa1jo/file170f7c5e1acd'
+#> ✔ Created orderly root at '/tmp/RtmpiweZAh/file16ac5f2c0cad'
orderly2::orderly_list_src(root = path)
-#> Error: Directory does not exist: '/tmp/RtmpTXa1jo/file170f7c5e1acd'
+#> Error: Directory does not exist: '/tmp/RtmpiweZAh/file16ac5f2c0cad'