when i try to add (data.table/ggplot2)code in slidify, i got error.
Here is my code in slidify:
## data.table
```{r}
library(data.table)
DT = data.table(x = 1:5, y=6:10)
setkey(DT, x)
DT[J(1)] # Error: No J function
```
---
## ggplot2
```{r}
library(ggplot2)
a = b = shape = 1:5
ggplot(data=DT, aes(a, b, col=shape)) + geom_point() # Error: can not find object a
```
All the code can run outside slidify, so i guess there is something about variable namespace wrong with slidify.
I also find this link:data.table error when used through knitr, gWidgetsWWW which might be similar with my problem, but still don't know how to fix.
Just to add an answer to follow up on the comments on the question. The dev version of data.table fixed it and is now on CRAN (data.table v1.9.4). But this broke kable() in knitr which knitr v1.7 (on CRAN too) fixes.
So basically, upgrade to latest CRAN versions of knitr and data.table and you should be fine. Please let us know if not.
More detail for the curious ...
I've made another change to data.table in v1.9.5 to make it more robust for packages that evaluate user code (like knitr, slidify and gWidgetsWWW) but don't know about data.table themselves. So that they don't need to know in future. Here is the item :
knitr::kable() works again without needing to upgrade from knitr v1.6 to v1.7. Packages which evaluate user code and don't wish to import data.table need to be added to data.table:::cedta.pkgEvalsUserCode and now only the eval part is made data.table-aware (the rest of such package's code is left data.table-unaware). data.table:::cedta.override is now empty and will be deprecated if no need for it arises.
And here is the item in v1.9.4 that was a little too over-reaching and broke knitr::kable in knitr v1.6 and knitr v1.7 fixes (but shouldn't have needed to) :
Added shiny, rmarkdown and knitr to the data.table whitelist. Packages which take user code as input and run it in their own environment (so do not Depend or Import data.table themselves) either need to be added here, or they can define a variable .datatable.aware <- TRUE in their namepace, so that data.table can work correctly in those packages. Users can also add to data.table's whitelist themselves using assignInNamespace() but these additions upstream remove the need to do that for these packages.
Related
I'm using Rstudio 2022.22.1 on MacOS Monterey 12.3.1.
I load libraries at the begininning by doing:
knitr::opts_chunk$set(echo = TRUE)
library("tidyverse", "here", "magrittr")
library("pastecs", "psych")
## dlf<-read.delim("data/DownloadFestival(No Outlier).dat", header=TRUE)
dlf<-here::here("data/DownloadFestival(No Outlier).dat") %>% readr::read_delim(col_names = TRUE)
I also check the thick for the library "psych" in the Packages section of RStudio.
The issue is that, from a certain point (after Knitting) I wasn't unable to use the command describe, this is the error:
could not find function "describe"
I could bypass this, by typing each time I use the function:
psych::describe
instead of describe alone
How can I use describe without specifying the psych:: prefix each time ?
Your problem is that library("pastecs", "psych") isn't doing what you think. Weirdly enough, there isn't an obvious idiom for "load a bunch of packages at once": I wish there were an easier way to do this, but try
invisible(lapply(c("psych", "pastecs"), library, character.only = TRUE))
The answers to this question provide a bunch of different ways to load many packages at once (the accepted answer is the same as the one given here).
I may not be using the terminology correctly here so please forgive me...
I have a case of one package 'overwriting' a function with the same name loaded by another package and thus changing the behavior (breaking) of a function.
The specific case:
X <- data.frame ( y = rnorm(100), x1 = rnorm(100), x2 = rnorm(100) )
library(CausalImpact)
a <- CausalImpact::CausalImpact( X, c(1,75), c(76, 100) ) # works
library(bfast) # imports quantmod which loads crappy version of as.zoo.data.frame
b <- CausalImpact::CausalImpact( X, c(1,75), c(76, 100) ) # Error
I know the error comes from two versions of the function as.zoo.data.frame.
The problematic version is imported by bfast from the package 'quantmod' (see https://github.com/joshuaulrich/quantmod/issues/168). Unfortunately their hotfix did not prevent this error. Super annoying.
I can hack around this specific problem, but I was wondering if there is a general way to like 'de-register' this function variant from the search path. Neither detach nor unloadNamespace remove the offending function (same behavior after). An explanation and similar problem is discussed here and here, but I wasn't able to find a general solution. For instance I'd rather just remove this function than clone and re-write CausalImpact to deal with this behavior.
From R 3.6.0 onwards, there is a new option called "conflicts.policy" to handle this within an established framework. For small issues like this, you can use the new arguments to library(). If you aren't yet to 3.6, the easiest solution might be to explicitly namespace CausalImpact when you need it, i.e. CausalImpact::CausalImpact. That's a mouthful, so you could do causal_impact <- CausalImpact::CausalImpact and use that alias.
# only attach select
library(dplyr, include.only = "select")
# exclude slice/arrange from being attached.
library(dplyr, exclude = c("slice", "arrange"))
library(bfast, exclude = "CausalImpact") should solve your problem.
Attach means that they are available for use without explicit prefixing with their package. In either of these cases, something like dplyr::slice would work just fine.
For more information, you can see ?library. Also, the R-Core member Luke Tierney wrote a blog explaining how the conflicts.policy works. You can find that here
Here's an answer that works, but is less preferable than de-registering a S3 method because it involves replacing the registered version in the S3 Methods table with the desired method:
library(CausalImpact)
library(bfast)
assignInNamespace("as.zoo.data.frame", zoo:::as.zoo.data.frame, ns = asNamespace("zoo"))
based partially on #smingerson's suggestion in the comments
I am running R 3.4.3 and 3.5.1 (non-Microsoft version) and RStudio version 1.1.456. I am trying to knit some code into RMarkdown. However, I get the following error:
Error in library(p, character.only = TRUE) : there is no package called 'RevoUtilsMath'Calls: <Anonymous> ... suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
The package RevoUtilsMath is part of the MKL install with Microsoft R. I cannot install it as a supplemental package with 'regular R'. The script itself runs fine, it just does not work in R Markdown.
The following libraries are loaded:
```{r loadLibraries, echo=FALSE, warning=FALSE}
library(RODBC)
library(dplyr)
library(markovchain)
library(DT)
library(reshape2)
library(knitr)
library(ggplot2)
library(scales)
library(PerformanceAnalytics)
library(plotly)```
The missing package error happens when executing the code below in Markdown. It is called using this code.
```{r histogram1, echo=FALSE, cache=TRUE}```
The histogram1 code is below (very standard ggplot).
g <- ggplot(dataClean, aes(x = IncSnapshotDay, fill = Represent)) +
geom_histogram(bins=70, alpha = .8) +
scale_fill_manual(values = colors) +
scale_x_continuous(labels = comma, limits = c(0,40000)) +
facet_wrap(~SnapshotDay) +
ylim(0,4000) +
theme_bryan()
g
I thought that maybe one of these packages has a dependency, so I ran the following to find out.
library(tools)
> dependsOnPkgs('RevoUtilsMath')
It returns character(0) which indicates that none of the packages depend on it. I did a test of the function on ggplot2, and it works
dependsOnPkgs('ggplot2')
[1] "dendextend" "GGally" "ggthemes" "plotly" "viridis" "caret" "crosstalk"
[8] "DT"
So why does R Markdown/knitr generate this error since the code itself runs fine outside of Markdown, and how do I fix this?
I think you are experiencing a problem similar to one I just had though, without more detail, it is hard for me to know.
In my case, the problem was caused by knitr caching the list of packages used by a previous author (using Microsoft R). The immediate solution was to simply clear the knitr cache (via the "Knit" drop down menu in RStudio) before attempting to knit the code.
I still don't really understand why this is happening or how to avoid it in future situations, but this at least provides a way to create the document even in the face of this behavior.
I am trying to knit a chunk embedded in a latex file with extension Rnw.
library(ggplot2)
library(flexclust)
library(arules)
data(Groceries)
Gr <- Groceries[, itemFrequency(Groceries) > 0.02]
grc <- as(Gr, "matrix")
I get this error:
#Error in as(Gr, "matrix") could not find function "as"
The same commands work perfectly well in R
Any ideas?
When in doubt, try to upgrade your software packages. If you are using a recent version of R (>= 3.5.0), you should not need to library(methods), because it will be loaded (attached) by default. This problem (Rscript does not load methods) has existed in base R for many years until this year and surprised/confused many users. If you have to use an old version of R, you will need library(methods) explicitly.
I am trying to get the latest version of my package (https://github.com/jmcurran/relSim) on CRAN. This has been rejected because of the use of a data set that is included in the package in a function which is not exported (i.e. the user cannot use it unless they use the ::: operator. A code snippet:
testIS = function(nc = c(3, 2), locus = 1, seed = 123456){
set.seed(seed)
np = 2 * nc[2]
freqs = USCaucs$freqs
The dataset is included in the package, and as per Hadley's advice I have LazyData: true in my DESCRIPTION file. However I get this note from https://win-builder.r-project.org which I don't know how to resolve.
* checking R code for possible problems ... [11s] NOTE
testIS: no visible binding for global variable 'USCaucs'
Undefined global functions or variables::
USCaucs
I find this especially frustrating, since, as I said, this function is not even exported (it also works without complaint because the package loads this dataset). All help appreciated
The solution appears to involve a little duplication. At the suggestion of Thomas Lumley, I placed the object in R/sysdata.rda as well as having it in data/USCaucs.rda. I followed Hadley Wickham's suggestion to use devtools::use_data with the argument internal set to TRUE so that it was saved in the correct manner for a package.
As noted, this solution involves duplicating the data. This isn't an issue for a small object such as the one I have here, but I'd like to think there is a more elegant solution out there.