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Add reverse dependency checks (all look good)
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‎.Rbuildignore

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^windows$
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^a\.out\.dSYM$
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^NEWS\.md$
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^revdep$

‎revdep/.gitignore

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**/

‎revdep/check.R

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library("devtools")
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res <- revdep_check()
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revdep_check_save_summary(res)
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revdep_check_save_logs(res)

‎revdep/summary.md

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# Setup
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## Platform
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|setting |value |
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|:--------|:----------------------------|
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|version |R version 3.1.2 (2014-10-31) |
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|system |x86_64, darwin13.4.0 |
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|ui |RStudio (0.99.104) |
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|language |(EN) |
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|collate |en_US.UTF-8 |
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|tz |Pacific/Auckland |
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## Packages
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|package |* |version |date |source |
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|:--------|:--|:-------|:----------|:--------------|
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|DBI | |0.3.1 |2014-09-24 |CRAN (R 3.1.1) |
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|testthat | |0.9.1 |2014-10-01 |CRAN (R 3.1.1) |
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# Check results
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10 checked out of 10 dependencies
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## Causata (4.2-0)
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Maintainer: Justin Hemann <justinh@causata.com>
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```
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checking top-level files ... NOTE
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Non-standard file/directory found at top level:
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‘integration_tests’
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```
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```
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checking R code for possible problems ... NOTE
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GetMetadata.Connect: no visible global function definition for
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‘dbGetQuery’
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GetRawData.Connect: no visible global function definition for
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‘dbGetQuery’
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```
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```
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checking Rd cross-references ... WARNING
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Missing link or links in documentation object 'Connect.Rd':
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‘RMySQL’
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See the information in section 'Cross-references' of the 'Writing R
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Extensions' manual.
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```
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```
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checking files in ‘vignettes’ ... NOTE
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The following files look like leftovers/mistakes:
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‘Causata-vignette.log’
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Please remove them from your package.
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```
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## compendiumdb (0.1.0)
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Maintainer: Umesh Nandal <u.k.nandal@amc.uva.nl>
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```
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checking package dependencies ... NOTE
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Packages suggested but not available for checking:
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‘inSilicoDb’ ‘hgu133a.db’ ‘GSVA’ ‘GSVAdata’
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```
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## db.r (0.1.3)
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Maintainer: Greg Lamp <greg@yhathq.com>
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Bug reports: https://github.com/yhat/db.r/issues
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```
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checking package dependencies ... NOTE
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Package suggested but not available for checking: ‘RPostgreSQL’
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```
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## dbConnect (1.0)
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Maintainer: Dason Kurkiewicz <dasonk@iastate.edu>
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```
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checking package dependencies ... ERROR
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Package required but not available: ‘gWidgets’
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Package suggested but not available for checking: ‘gWidgetsRGtk2’
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See the information on DESCRIPTION files in the chapter ‘Creating R
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packages’ of the ‘Writing R Extensions’ manual.
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```
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## dplyr (0.3.0.2)
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Maintainer: Hadley Wickham <hadley@rstudio.com>
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Bug reports: https://github.com/hadley/dplyr/issues
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```
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checking package dependencies ... NOTE
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Packages suggested but not available for checking:
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‘RSQLite.extfuns’ ‘RPostgreSQL’
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```
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```
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checking dependencies in R code ... NOTE
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Namespace in Imports field not imported from: ‘R6’
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All declared Imports should be used.
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See the information on DESCRIPTION files in the chapter ‘Creating R
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packages’ of the ‘Writing R Extensions’ manual.
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```
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```
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checking examples ... ERROR
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Running examples in ‘dplyr-Ex.R’ failed
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The error most likely occurred in:
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> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
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> ### Name: src_mysql
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> ### Title: Connect to mysql/mariadb.
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> ### Aliases: src_mysql tbl.src_mysql
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>
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> ### ** Examples
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>
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> ## Not run:
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> ##D # Connection basics ---------------------------------------------------------
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> ##D # To connect to a database first create a src:
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> ##D my_db <- src_mysql(host = "blah.com", user = "hadley",
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> ##D password = "pass")
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> ##D # Then reference a tbl within that src
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> ##D my_tbl <- tbl(my_db, "my_table")
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> ## End(Not run)
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>
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> # Here we'll use the Lahman database: to create your own local copy,
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> # create a local database called "lahman", or tell lahman_mysql() how to
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> # a database that you can write to
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>
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> if (!has_lahman("postgres") && has_lahman("mysql")) {
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+ # Methods -------------------------------------------------------------------
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+ batting <- tbl(lahman_mysql(), "Batting")
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+ dim(batting)
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+ colnames(batting)
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+ head(batting)
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+
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+ # Data manipulation verbs ---------------------------------------------------
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+ filter(batting, yearID > 2005, G > 130)
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+ select(batting, playerID:lgID)
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+ arrange(batting, playerID, desc(yearID))
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+ summarise(batting, G = mean(G), n = n())
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+ mutate(batting, rbi2 = 1.0 * R / AB)
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+
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+ # note that all operations are lazy: they don't do anything until you
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+ # request the data, either by `print()`ing it (which shows the first ten
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+ # rows), by looking at the `head()`, or `collect()` the results locally.
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+
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+ system.time(recent <- filter(batting, yearID > 2010))
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+ system.time(collect(recent))
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+
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+ # Group by operations -------------------------------------------------------
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+ # To perform operations by group, create a grouped object with group_by
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+ players <- group_by(batting, playerID)
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+ group_size(players)
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+
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+ # MySQL doesn't support windowed functions, which means that only
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+ # grouped summaries are really useful:
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+ summarise(players, mean_g = mean(G), best_ab = max(AB))
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+
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+ # When you group by multiple level, each summarise peels off one level
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+ per_year <- group_by(batting, playerID, yearID)
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+ stints <- summarise(per_year, stints = max(stint))
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+ filter(ungroup(stints), stints > 3)
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+ summarise(stints, max(stints))
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+
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+ # Joins ---------------------------------------------------------------------
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+ player_info <- select(tbl(lahman_mysql(), "Master"), playerID,
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+ birthYear)
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+ hof <- select(filter(tbl(lahman_mysql(), "HallOfFame"), inducted == "Y"),
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+ playerID, votedBy, category)
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+
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+ # Match players and their hall of fame data
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+ inner_join(player_info, hof)
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+ # Keep all players, match hof data where available
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+ left_join(player_info, hof)
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+ # Find only players in hof
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+ semi_join(player_info, hof)
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+ # Find players not in hof
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+ anti_join(player_info, hof)
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+
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+ # Arbitrary SQL -------------------------------------------------------------
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+ # You can also provide sql as is, using the sql function:
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+ batting2008 <- tbl(lahman_mysql(),
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+ sql("SELECT * FROM Batting WHERE YearID = 2008"))
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+ batting2008
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+ }
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Loading required package: RPostgreSQL
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Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
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there is no package called ‘RPostgreSQL’
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Loading required package: RMySQL
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Loading required package: DBI
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Error: select is not a character vector
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Execution halted
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```
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## ProjectTemplate (0.6)
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Maintainer: Kirill Mueller <krlmlr+r@mailbox.org>
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Bug reports: https://github.com/johnmyleswhite/ProjectTemplate/issues
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```
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checking package dependencies ... NOTE
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Packages suggested but not available for checking: ‘RODBC’ ‘RPostgreSQL’
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```
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```
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checking dependencies in R code ... NOTE
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No Java runtime present, requesting install.
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See the information on DESCRIPTION files in the chapter ‘Creating R
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packages’ of the ‘Writing R Extensions’ manual.
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```
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## quantmod (0.4-3)
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Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>
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```
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checking R code for possible problems ... NOTE
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Found the following calls to attach():
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File ‘quantmod/R/attachSymbols.R’:
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attach(NULL, pos = pos, name = DB$name)
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attach(NULL, pos = pos, name = DB$name)
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See section ‘Good practice’ in ‘?attach’.
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```
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## sqldf (0.4-10)
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Maintainer: G. Grothendieck <ggrothendieck@gmail.com>
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Bug reports: http://groups.google.com/group/sqldf
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```
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checking package dependencies ... NOTE
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Package suggested but not available for checking: ‘RPostgreSQL’
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```
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## TSMySQL (2013.9-1)
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Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
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```
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checking package dependencies ... ERROR
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Package required but not available: ‘TSsql’
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See the information on DESCRIPTION files in the chapter ‘Creating R
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packages’ of the ‘Writing R Extensions’ manual.
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```
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## TSsql (2014.4-1)
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Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
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```
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checking R code for possible problems ... NOTE
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TSgetSQL: no visible global function definition for ‘as.zoo’
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TSgetSQL: no visible global function definition for ‘zoo’
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TSgetSQL: no visible global function definition for
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‘changeTSrepresentation’
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TSquery: no visible global function definition for ‘zoo’
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```
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