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Advanced R: a book
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Exploratory data analysis for large datasets (10-100 million observations)
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An R package containing US baby names from the SSA
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issue commentRConsortium/OOP-WG
Ah, got it — so method would error when giving anything other than a class object?
I think there's one scenario where we might want to take a string:
method(mean, "pkg::A") <- function(x) 10
This would be shorthand for something like:
if (isNamespaceLoaded("pkg")) {
method(generic, getExportedValue(pkg, class)) <- value
}
setHook(
packageEvent(package, "onLoad"),
function(...) {
method(generic, getExportedValue(pkg, class)) <- value
}
)
which would make it easy to register methods for suggested packages.
OTOH it might be more general to create a base helper that runs code when a package is loaded, and then you'd just do:
whenLoaded("pkg", {
method(mean, pkg::A) <- function() 10
method(sum, pkg::A) <- function() 5
})
That would make the semantics of method<- simpler.
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pull request commentr-lib/pkgload
Allow pkgload to reload usethis
I tested this by repeatedly reloading rlang, devtools, pkgload, and usethis.
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issue closedr-lib/pkgload
Why does pkgload:::print.dev_topic() set no_links = TRUE?
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hadley
issue commentr-lib/pkgload
Why does pkgload:::print.dev_topic() set no_links = TRUE?
Ah because RStudio uses Rdconv and the no_links argument has "logical: suppress hyperlinks to other help topics. Used by R CMD Rdconv."
So I don't think this is possible to fix.
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issue commentr-lib/pkgload
Why does pkgload:::print.dev_topic() set no_links = TRUE?
This code isn't usually called because we use RStudio's previewRd. I took a quick look through the RStudio source code and couldn't find any use of Rd2HTML or no_links.
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PR closed r-lib/pkgload
In favour of using rlang function with same implementation
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pull request commentr-lib/pkgload
Ooops, this makes it impossible to reload rlang
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Update docs
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PR opened r-lib/pkgload
The root cause is that when unloadNamespace() errors, it errors before the package is detached from the search path. I also cleaned up the failure detection and tweaking the messaging
cc @jennybc
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PR opened r-lib/pkgload
In favour of using rlang function with same implementation
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issue commentRConsortium/OOP-WG
Yeah but in your scenario above there’s no object called A — so I assume that would just be an error?
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Document main methods Fixes #395
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issue commentRConsortium/OOP-WG
I think it has to create some sort of UUID; the class argument is purely informative.
It's also worth thinking about whether this would work:
method(mean, "A") <- function(x) 10
And if so, what does it do?
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issue commentRConsortium/OOP-WG
Do you have a few examples of where you'd use class unions? I have never used them.
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issue openedtidyverse/dbplyr
select()andrename()need to use new tidyeval form- need to document that doesn't currently support predict functions
- implement
rename_with()method
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issue commenttidyverse/dbplyr
Database semi_join() doesn't match R's NA semantics
Could provide sql_is_distinct(con, x, y) generic and then use that in sql_join_tbls() when na_matches is TRUE. I think we'd want to preserve the existing behaviour (clearly documented) and then allow people to choose the R behaviour if desired.
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Reduce a little more duplication in sql_select methods
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Re-organise sql_clause_ functions
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issue commentr-lib/pkgdown
@jangorecki it was deliberate because we want people's plot to look as good as they possibly can.
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Delete unnest.html as it is a 2 year old version (#1048) #1042 #1047
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pull request commenttidyverse/tidyr
Delete unnest.html as it is a 2 year old version
It never occurred to me to do this directly 😆
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Move arrange tests to test-arrange
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Remove redundant tests
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commit sha 269cdda12c3d3a51b9799545f9819764f0c387c1
Omit ORDER BY in subqueries (#501) Fixes #276. Closes #471
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PR closed tidyverse/dbplyr
arrange()can now only be used at the end of a pipe or followed byhead(), otherwise it has no effect and raises a warning.window_order()can be used repeatedly but only affects the verb that follows immediately.- All other verbs reset the sort order, with warning.
- An empty
arrange()can be used to undo the effects of the lastarrange(). - This change leads to fewer subqueries and fewer redundant
ORDER BYclauses. - The documentation for
arrange()andwindow_order()has been expanded.
Each commit is self-contained and passes tests. Happy to split into separate pull requests if it helps.
Closes #276, closes #373.
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issue closedtidyverse/dbplyr
Rethink optimization of ORDER BY
ORDER BY clauses in subqueries are problematic:
- MSSQL outrights forbids them (#275)
- Other DBMS sometimes ignore them (see reprex) and are not obliged to follow either (https://mariadb.com/kb/en/library/why-is-order-by-in-a-from-subquery-ignored/, https://dba.stackexchange.com/a/83500/6934)
As a stop gap, we could remove ORDER BY clauses from inner queries if we don't combine the inner and the outer query. With a warning. This would also solve #275. I wonder if this generates spurious warnings, e.g., for window functions.
Alternatively, we could allow arrange() only at the very last step in the pipe, and transform it to window_order() if additional verbs are added, with a warning. This will be a problem later when we want to support lazy operations for data frames.
For a true solution, we cannot simply delay the computation due to aliasing (https://github.com/tidyverse/dbplyr/issues/94#issuecomment-395599454). A few examples, and a reprex illustrating the problem (using #277), are below. This might well be out of scope.
# Input:
lazy_frame(a = 1:3, b = 4:2) %>%
mutate(a = -a) %>%
arrange(a) %>%
mutate(a = -a)
# Equivalent with `arrange()` delayed:
lazy_frame(a = 1:3, b = 4:2) %>%
mutate(a = -a) %>%
mutate(zzz_001 = a) %>%
mutate(a = -a) %>%
arrange(zzz_001) %>%
select(-zzz_001)
# Input:
lazy_frame(a = 1:3, b = 4:2) %>%
arrange(a) %>%
group_by(b) %>%
mutate(c = cumsum(a)) %>%
ungroup()
# Equivalent with `arrange()` delayed:
lazy_frame(a = 1:3, b = 4:2) %>%
window_order(a) %>%
group_by(b) %>%
mutate(c = cumsum(a)) %>%
ungroup() %>%
arrange(a)
library(tidyverse)
devtools::load_all("~/git/R/dbplyr")
#> Loading dbplyr
#>
#> Attaching package: 'testthat'
#> The following object is masked from 'package:dplyr':
#>
#> matches
#> The following object is masked from 'package:purrr':
#>
#> is_null
#> Registering testing src: df OK
#> Registering testing src: sqlite OK
#> Registering testing src: mysql OK
#> Registering testing src: MariaDB OK
#> Registering testing src: postgres OK
#> Registering testing src: MSSQL OK
test_frame(a = 1:3, b = 4:2) %>%
map(
. %>%
mutate(a = -a) %>%
arrange(a) %>%
mutate(a = -a)
)
#> Created a temporary table named: ##dbplyr_001
#> $df
#> # A tibble: 3 x 2
#> a b
#> <int> <int>
#> 1 3 2
#> 2 2 3
#> 3 1 4
#>
#> $sqlite
#> # Source: lazy query [?? x 2]
#> # Database: sqlite 3.25.3 [:memory:]
#> # Ordered by: a
#> a b
#> <int> <int>
#> 1 3 2
#> 2 2 3
#> 3 1 4
#>
#> $mysql
#> # Source: lazy query [?? x 2]
#> # Database: mysql 5.5.5-10.1.38-MariaDB-0ubuntu0.18.04.1
#> # [kirill@localhost:/test]
#> # Ordered by: a
#> a b
#> <dbl> <int>
#> 1 1 4
#> 2 2 3
#> 3 3 2
#>
#> $MariaDB
#> # Source: lazy query [?? x 2]
#> # Database: mysql 5.5.5-10.1.38-MariaDB-0ubuntu0.18.04.1
#> # [kirill@localhost:/test]
#> # Ordered by: a
#> a b
#> <S3: integer64> <int>
#> 1 1 4
#> 2 2 3
#> 3 3 2
#>
#> $postgres
#> # Source: lazy query [?? x 2]
#> # Database: postgres 9.6.9 [kirill@/var/run/postgresql:5432/kirill]
#> # Ordered by: a
#> a b
#> <int> <int>
#> 1 3 2
#> 2 2 3
#> 3 1 4
#>
#> $MSSQL
#> # Source: lazy query [?? x 2]
#> # Database: Microsoft SQL Server 12.00.1300[@cynkra-mssql/main]
#> # Ordered by: a
#> a b
#> <int> <int>
#> 1 1 4
#> 2 2 3
#> 3 3 2
<sup>Created on 2019-04-09 by the reprex package (v0.2.1.9000)</sup>
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krlmlr
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Update docs
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commit sha a7a813a659c82e9f25b51749c022fee6fa573d45
Fix optimisation bug
commit sha 079729e544231e5d79a99a593702f7a4841d87ff
Also need to warn during optimisation
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Port translation to other backends
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pull request commenttidyverse/dbplyr
Once complete, need to move arrange tests out of test-select.R
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pull request commenttidyverse/dbplyr
To do:
# Needs to warn
lf <- lazy_frame(a = 1)
lf %>% mutate(a = -a) %>% arrange(a) %>% mutate(a = -a)
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commit sha 877491afba0da05aceb5534712c7c9f4f70b01ba
Clarify purpose of bare_identifer_ok argument It's really about whether or not we're in a subquery
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issue closedtidyverse/dbplyr
Retaining too optimistic order information when manipulating after arrange()
It seems that op_sort() is a tad too optimistic in some cases.
Related: #338 #337. I think arrange() should only have an effect if it's the last verb in a pipe (or can be bubbled down safely), or to define the window order for window functions.
library(tidyverse)
library(dbplyr)
tbl <- memdb_frame(a = 1:3, b = 3:1)
tbl
#> # Source: table<dbplyr_001> [?? x 2]
#> # Database: sqlite 3.29.0 [:memory:]
#> a b
#> <int> <int>
#> 1 1 3
#> 2 2 2
#> 3 3 1
tbl_a <- tbl %>% arrange(a)
tbl_a
#> # Source: table<dbplyr_001> [?? x 2]
#> # Database: sqlite 3.29.0 [:memory:]
#> # Ordered by: a
#> a b
#> <int> <int>
#> 1 1 3
#> 2 2 2
#> 3 3 1
# Sort order wrong, the database won't guarantee lexical ordering
tbl_ab <- tbl %>% arrange(a) %>% arrange(b)
tbl_ab %>% sql_render()
#> <SQL> SELECT *
#> FROM (SELECT *
#> FROM `dbplyr_001`
#> ORDER BY `a`)
#> ORDER BY `b`
# a no longer exists, confusing
tbl_aba <- tbl %>% arrange(a) %>% select(-a)
tbl_aba
#> # Source: lazy query [?? x 1]
#> # Database: sqlite 3.29.0 [:memory:]
#> # Ordered by: a
#> b
#> <int>
#> 1 3
#> 2 2
#> 3 1
# How can I un-arrange?
tbl_aa <- tbl_aba %>% arrange(a) %>% arrange()
tbl_aa
#> # Source: lazy query [?? x 1]
#> # Database: sqlite 3.29.0 [:memory:]
#> # Ordered by: a, a
#> b
#> <int>
#> 1 3
#> 2 2
#> 3 1
# The ordering leaks to the lag() call
tbl_ac <- tbl_aba %>% collapse() %>% mutate(c = lag(b))
tbl_ac
#> Error: no such column: a
tbl_ac %>% sql_render()
#> <SQL> SELECT `b`, LAG(`b`, 1, NULL) OVER (ORDER BY `a`) AS `c`
#> FROM (SELECT `b`
#> FROM (SELECT *
#> FROM `dbplyr_001`
#> ORDER BY `a`))
<sup>Created on 2019-11-01 by the reprex package (v0.3.0)</sup>
closed time in a day
krlmlr
issue commenttidyverse/dbplyr
Retaining too optimistic order information when manipulating after arrange()
Ok, I'm comfortable that the current behaviour here is "correct". dbplyr is simulating what happens if you arrange a regular data frame — this may have been a mistake but I don't think it's worth revisiting at this point.
I think the main problem is allowing ORDER BY clauses in subqueries, which is the subject of #276.
comment created time in a day
issue closedtidyverse/dbplyr
Forget window_frame() after next verb
for consistency with window_order(): https://github.com/tidyverse/dbplyr/pull/471#discussion_r430614610.
closed time in a day
krlmlr
issue commenttidyverse/dbplyr
Forget window_frame() after next verb
The more I think about this, the less I like it. (And it doesn't affect existing code, just code in a PR).
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commit sha c4072d784439180fc016283541488cde940836b9
Implement slice methods Fixes #394
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issue closedtidyverse/dbplyr
Provide methods for new slice helpers
And provide an informative error for the slice() method.
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hadley
issue commenttidyverse/dbplyr
Provide methods for new slice helpers
slice_head(),slice_tail()slice_min(),slice_max(),slice_sample()
All also work on groups, so I think will be translated into filter() calls.
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Bump version Next release will be 2.0.0
commit sha 2399899126a940acc21ad52c2254ac5c07f0dd88
Start on vignette describing backend conversion process #385
commit sha 4b1b21f2bf24a61e31ef9b28f627d759edfd8b3a
Implement relocate method Fixes #494
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issue closedtidyverse/dplyr
Export implementation of relocate
So that other packages (e.g. dbplyr, dtplyr) can use it.
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hadley
issue commenttidyverse/dplyr
Export implementation of relocate
Hmmmm, maybe that's not necessary since you can just pass a one row data frame to the default method
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issue openedtidyverse/dplyr
Export implementation of relocate
So that other packages (e.g. dbplyr, dtplyr) can use it.
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issue openedtidyverse/dplyr
So that dbplyr can override with own implementation
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issue commenttidyverse/dbplyr
Replace database generics from dplyr
Need some way for developers to opt-in so that they get warnings/errors without affecting released packages. Maybe provide dbplyr_edition() generic?
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Add missing character (#666)
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Typo in 8.1.3 (#269)
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PR merged hadley/mastering-shiny
In the sentence "This is important for inputText() which may trigger....", shouldn't it be textInput() instead of inputText()?
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issue closedr-lib/downlit
Prepare for release:
- [x] Check current CRAN check results
- [x]
devtools::check(remote = TRUE, manual = TRUE) - [x]
devtools::check_win_devel() - [x]
revdepcheck::revdep_check(num_workers = 4) - [x] Update
cran-comments.md - [x] Polish NEWS
- [x] Review pkgdown reference index for, e.g., missing topics
Submit to CRAN:
- [x]
usethis::use_version('minor') - [x]
devtools::submit_cran() - [x] Approve email
Wait for CRAN...
- [x] Accepted :tada:
- [x]
usethis::use_github_release() - [x]
usethis::use_dev_version()
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Increment version number
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Update to 1.74" stickers (#48) * Update to 1.74" stickers * Add updated date * Update stickermule.md
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All pandoc tests need 2.0.0
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issue openedr-lib/downlit
Prepare for release:
- [ ] Check current CRAN check results
- [ ]
devtools::check(remote = TRUE, manual = TRUE) - [ ]
devtools::check_win_devel() - [ ]
rhub::check_for_cran() - [ ]
revdepcheck::revdep_check(num_workers = 4) - [ ] Update
cran-comments.md - [ ] Polish NEWS
- [ ] Review pkgdown reference index for, e.g., missing topics
- [ ] Draft blog post
Submit to CRAN:
- [ ]
usethis::use_version('minor') - [ ]
devtools::submit_cran() - [ ] Approve email
Wait for CRAN...
- [ ] Accepted :tada:
- [ ]
usethis::use_github_release() - [ ]
usethis::use_dev_version() - [ ] Finish blog post
- [ ] Tweet
- [ ] Add link to blog post in pkgdown news menu
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Use installed pkgdown.yml if present (#30) Fixes #29
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commit sha c90c116d1d563eb081bb3c17a4a4d99065dfbc6a
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Autolink R6 instantiation (#59)
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if not available through the metadata, e.g. if the package doesn't set its url: in its _pkgdown.yml.
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More tweaking
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More class tweaking * Improve overall organisation * Link to sheet with pandoc class names & descriptions * Add missing cases for EQ_SUB, brackets, NE, SLOT
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Match RStudio syntax highlighting (#58) * Colour parens as operators * Match RStudio constants * Match RStudio's handling of special keywords * Tweak classes layout
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Allow for bookdown hacking (#53)
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Don't autolink R6 methods (#55) Fixes #54
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Autolink R6 instantiation (#59)
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Autolink R6 instantiation (#59)
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PR merged r-lib/downlit
I wanted to see how I could get
downlit::highlight("library(crul); HttpClient$new()")
#> [1] "<span class='kr'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='o'>(</span><span class='nv'><a href='https://docs.ropensci.org/crul'>crul</a></span><span class='o'>)</span>; <span class='nv'><a href='https://docs.ropensci.org/crul/reference/HttpClient.html'>HttpClient</a></span><span class='o'>$</span><span class='nf'>new</span><span class='o'>(</span><span class='o'>)</span>"
<sup>Created on 2020-09-21 by the reprex package (v0.3.0.9001)</sup>
But
- it might be adding too much complexity just for the special case of R6 instantiation;
- I can't test it without adding a dependency (or some sort of mocking);
- The usefulness of this is quite limited since downlit doesn't know what packages are really attached (compared to what knitr would know) so I'd probably be better off just namespacing (the reprex below works without any tweak). :sweat_smile:
downlit::highlight("crul::HttpClient$new()")
#> [1] "<span class='nf'>crul</span><span class='nf'>::</span><span class='nv'><a href='https://docs.ropensci.org/crul/reference/HttpClient.html'>HttpClient</a></span><span class='o'>$</span><span class='nf'>new</span><span class='o'>(</span><span class='o'>)</span>"
<sup>Created on 2020-09-21 by the reprex package (v0.3.0.9001)</sup>
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issue commentbrodieG/unitizer
I'd consider it if you did a PR, but as I said, it's a complex part of testthat that I don't really want to mess with. I agree that deprecation would be desirable here, but this is just a place where I have to make a judgement call based on the amount of existing code in the wild that uses it.
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commit sha e082f3c2325b5db880bb68959c9d3e4cc74b2e70
Drop db_drop_table()/sql_drop_table() Since no longer used anywhere. #385
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Standardise sql method names
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Preserve ident() in mssql_table_rename()
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commit sha 1b2b298c88d1745ff7ae9bec94d00e334e3d91ec
Re-document
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Remove db_insert_into method Part of #385
commit sha c29dc1cf8969d3d7358c828136b836a488addfb2
Don't use sql_escape_ident() and sql_escape_string() methods from dplyr #385
commit sha a7f95db0dbac80dfd25ea35cc5bbd7bea4886064
Remove unused db_create_table() method #385
commit sha 3e2c022a7dc8416222e7503d8b92beae657a8526
Implement sql_query_fields() and sql_query_rows() #38
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Update vignette and imports
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Drop db_data_types() #385
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commit sha 777e789f2ca30acab6c6f0f9420452476537e973
Capture all need variables in transmute subqueries Fixes #313.
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issue closedtidyverse/dbplyr
There is an error in the SQL generation for transmute
library(dplyr)
library(dbplyr)
df <- data.frame(x = 1, y = 2)
# doesn't work
tbl_lazy(df, con = simulate_postgres()) %>%
transmute(x, x2 = x + y, y)
#> <SQL>
#> SELECT `x`, `x` + `y` AS `x2`, `y`
#> FROM (SELECT `x`
#> FROM `df`) `dbplyr_001`
# works
tbl_lazy(df, con = simulate_postgres()) %>%
transmute(x, y, x2 = x + y)
#> <SQL>
#> SELECT `x`, `y`, `x` + `y` AS `x2`
#> FROM (SELECT `x`, `y`
#> FROM `df`) `dbplyr_002`
<sup>Created on 2019-06-04 by the reprex package (v0.3.0)</sup>
<sup>Created on 2019-06-04 by the reprex package (v0.3.0)</sup>
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mgirlich
issue commenttidyverse/dbplyr
select,renamemutatesummarisedistinctfilterarrangeneeds to mention impact on window functionspull()window_frame()/window_order()need more details
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commit sha a03d7d13342e8f527fec9f2a659e1cc1f3953195
Store pool, not connection (#107)
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PR merged rstudio/pool
Fixes https://github.com/tidyverse/dbplyr/issues/457
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issue closedtidyverse/dbplyr
It appears that the tbl(con, ...) with a pool connection will derive the underlying server-specific connection instead. While doing this is certainly understandable, it suffers from issues that pool is intended to remedy (e.g., reconnects).
con <- pool::dbPool(...)
copy_to(con, mtcars, name = "r2mtcars", temporary = FALSE)
mt_tbl <- tbl(con, "r2mtcars")
mt_tbl
# # Source: table<r2mtcars> [?? x 11]
# # Database: Microsoft SQL Server 13.00.1742[bevans@FPTC-DATA01/racers]
# mpg cyl disp hp drat wt qsec vs am gear carb
# <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
# 1 21 6 160 110 3.9 2.62 16.5 0 1 4 4
# 2 21 6 160 110 3.9 2.88 17.0 0 1 4 4
# 3 22.8 4 108 93 3.85 2.32 18.6 1 1 4 1
# 4 21.4 6 258 110 3.08 3.22 19.4 1 0 3 1
# 5 18.7 8 360 175 3.15 3.44 17.0 0 0 3 2
# 6 18.1 6 225 105 2.76 3.46 20.2 1 0 3 1
# 7 14.3 8 360 245 3.21 3.57 15.8 0 0 3 4
# 8 24.4 4 147. 62 3.69 3.19 20 1 0 4 2
# 9 22.8 4 141. 95 3.92 3.15 22.9 1 0 4 2
# 10 19.2 6 168. 123 3.92 3.44 18.3 1 0 4 4
# # ... with more rows
pause, allow the connection to time out
mt_tbl
# Error in new_result(connection@ptr, statement, immediate) :
# external pointer is not valid
DBI::dbGetQuery(con, "select top 1 * from r2mtcars")
# mpg cyl disp hp drat wt qsec vs am gear carb
# 1 21 6 160 110 3.9 2.62 16.46 0 1 4 4
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r2evans
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Align test and R file names
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commit sha fb4c20c3171f991e7e0bf2b63d4097eff0493407
Doc fixes * Use actual dplyr API in example * Remove old param
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commit sha fdf8c22b7f3e1be48ceea85f86f1c97d7770432f
Redocument
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PR opened rstudio/pool
Fixes https://github.com/tidyverse/dbplyr/issues/457
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commit sha e5150d6b681c61047402122b72be474f6c0bfd3e
Tidy up docs and description (#104) * Use latest roxygen2 * Generate all docs with roxygen2 * Update package doc to modern style * Use markdown in roxygen * Improve documentation of S4 methods * use_tidy_description()
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PR merged rstudio/pool
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commit sha e98f09cd00693c2bf6948bba7c6fd134190df743
use_tidy_github_actions() (#105)
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Merge commit 'e98f09cd00693c2bf6948bba7c6fd134190df743' Conflicts: DESCRIPTION
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use_tidy_github_actions() (#105)
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