I get this error when running devtools::check().
Error in processx::run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout), :
System command error
The check runs and completes just fine if I remove the underscore from my package name. How do I create a package name with underscore?
The manual on writing R extensions describes that this is not permitted.
The mandatory ‘Package’ field gives the name of the package. This should contain only (ASCII) letters, numbers and dot, have at least two characters and start with a letter and not end in a dot. If it needs explaining, this should be done in the ‘Description’ field (and not the ‘Title’ field).
https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Creating-R-packages
See also this question: What's a good R package name?
Related
I am building my own package, and I keep running into encoding issues because the functions in my package has non-english (non-ASCII) characters.
Inherently, Korean characters are a part of many of the functions in my package. A sample function:
library(rvest)
sampleprob <- function(url) {
# sample url: "http://dart.fss.or.kr/dsaf001/main.do?rcpNo=20200330003851"
result <- grepl("연결재무제표 주석", html_text(read_html(url)))
return(result)
}
However, when installing the package I run into encoding problems.
I created a sample package (https://github.com/hyk0127/KorEncod/) with just one function (what is shown above) and uploaded it onto my github page for a reproducible example. I run the following code to install:
library(devtools)
install_github("hyk0127/KorEncod")
Below is the error message that I see
Error : (converted from warning) unable to re-encode 'hello.R' line 7
ERROR: unable to collate and parse R files for package 'KorEncod'
* removing 'C:/Users/myname/Documents/R/win-library/3.6/KorEncod'
* restoring previous 'C:/Users/myname/Documents/R/win-library/3.6/KorEncod'
Error: Failed to install 'KorEncod' from GitHub:
(converted from warning) installation of package ‘C:/Users/myname/AppData/Local/Temp/RtmpmS5ZOe/file48c02d205c44/KorEncod_0.1.0.tar.gz’ had non-zero exit status
The error message about line 7 refers to the Korean characters in the function.
It is possible to locally install the package with tar.gz file, but then the function does not run as intended, because the Korean characters are recognized in broken encoding.
This cannot be the first time that someone has tried building a package that has non-english (or non-ASCII) characters, and yet I couldn't find a solution to this. Any help will be deeply appreciated.
A few pieces of info that I think are related:
Currently the DESCRIPTION file specifies "Encoding: UTF-8".
I have used sys.setlocale to set the locale into Korean and back to no avail.
I have specified #encoding UTF-8 to the function to no avail as well.
I am currently using Windows where the administrative language is set to English. I have tried using a different laptop with Windows & administrative language set to Korean, and the same problem appears.
The key trick is replacing the non-ASCII characters with their unicode codes - the \uxxxx encoding.
These can be generated via stringi::stri_escape_unicode() function.
Note that since it will be necessary to completely get rid of the Korean characters in your code in order to pass the R CMD check it will be necessary to perform a manual copy & re-encode via {stringi} on the command line & paste back operation on all your R scripts included in the package.
I am not aware of an available automated solution for this problem.
In the specific use case of the example provided the unicode would read like this:
sampleprob <- function(url) {
# stringi::stri_escape_unicode("연결재무제표 주석") to get the \uxxxx codes
result <- grepl("\uc5f0\uacb0\uc7ac\ubb34\uc81c\ud45c \uc8fc\uc11d",
rvest::html_text(xml2::read_html(url)))
return(result)
}
sampleprob("http://dart.fss.or.kr/dsaf001/main.do?rcpNo=20200330003851")
[1] TRUE
This will be a hassle, but it seems to be the only way to make your code platform neutral (which is a key CRAN requirement, and thus subject to R CMD check).
Adding for the future value (for those facing similar problems), you can also solve this problem by saving the non-ASCII characters in a data file, then loading the value & using it.
So save the character as a data file (using standard package folder names and roxygen2 package)
# In your package, save as a separate file within .\data-raw
kor_chrs <- list(sampleprob = "연결재무제표 주석")
usethis::use_data(kor_chrs)
Then in your functions load the data and use them.
# This is your R file for the function within ./R folder
#' #importFrom rvest html_text
#' #importFrom xml2 read_html
#' #export
sampleprob <- function(url) {
# sample url: "http://dart.fss.or.kr/dsaf001/main.do?rcpNo=20200330003851"
result <- grepl(kor_chrs$sampleprob[1], html_text(read_html(url)))
return(result)
}
This, yes, is still a workaround, but it runs in Windows machines without any troubles.
I'm installing "getSpatialData" package with following codes:
devtools::install_github("16EAGLE/getSpatialData")
library(getSpatialData)
and when I'm loading library(getSpatialData), I'm getting following in this console:
Enter one or more numbers, or an empty line to skip updates:devtools::install_github("16EAGLE/getSpatialData")
Enter one or more numbers, or an empty line to skip updates:library(getSpatialData)
Also, no functions of getSpatialData package is made availble after loading libraries.
Please someone help! I'm new in R and making terible blunders.
What I have read
I have read this SO question and related answers but I am still a bit at loss of how to document a defunct function properly in my package.
What I have tried
I replaced the code of my defunctfucntion by a call of .Defunct("<pointer to a function to be used instead>", "<my package name>")
I deleted the .Rd file containing the old documentation of my function
I created a mypackage-defunct.Rd file with an alias pointing to my now defunct function name
In mypackage-defunct.Rd I created an \usage entry for my old function and replaced the function arguments by \dots (as I do not see the need to keep track about the old arguments. I followed a bit what is done in base-defunct)
What I have got
When running RCMD CHECK I get the following WARNING:
checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'mypackage-defunct'
'...'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
What I would like to have
How do i get rid of the warning? Do I need to document arguments from defunct functions? Bonus question: What is the recommended way for a defunct function. Should I remove all arguments and replace them by ...? Looking at base-defunct, I see a mix of functions with proper argument names, . and ...arguments and empty argument lists. What is the "correct" way?
In an earlier post, I asked about declaring such functions in R packages and making them work. Having succeeded, I'm now trying to document one such function.
I created an Rd file with the function's name as a title, but when running the CHECK, I get the following warning:
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'%IN%'
I tried several names such as %IN%.Rd or '%IN%'.Rd, to no avail. Any hints on how to make this work?
The goto guide would definitely be section 2.1.1 "Documenting functions"[1] of the "Writing R Extensions" manual. As #joran pointed out in a comment the important part maybe the use of an \alias. According to the "Writing R extensions" manual the %s need to be escaped at least in \alias and in the text. About \name it states: " [name should not contain] ‘!’ ‘|’ nor ‘#’, and to avoid possible problems with the HTML help system it should not contain ‘/’ nor a space. (LaTeX special characters are allowed, but may not be collated correctly in the index.)"[2] and about \alias: " Percent and left brace need to be escaped by a backslash."[3]
I am trying to create a package in R wherein I have created lots of new custom Classes. Each class is in a different file. The Classes inherit from a parent class and inherit to other classes.
While running my codes I call each of them like this
source("package/father.R")
source("package/son.R")
source("package/grandson.R")
Definition for Some of the methods needed by the grandson Class in defined in Son class. I use package.skeleton() to call each of them and create a package and it seems to work fine. But when running R CMD Check(and when trying install into R), it throws an error because the function tries to call the files in the alphabetical order and so the file grandson.R is called before son.R and it shows and error saying that the methods has not been defined. If I change the names to zgrandson.R, R called that file the last, and everything seems to work fine, but this is evidently not a solution for the problem.
I have read tutorials for creating packages, but all of them seem to deal with simple cases where there is no inheritance/calling other files in R. Hope I have made myself clear.
As far as I understand, you can use the Collate field in the DESCRIPTION file to control this.
Quoting from the Writing R Extensions manual:
An ‘Collate’ field can be used for controlling the collation order for
the R code files in a package when these are processed for package
installation. The default is to collate according to the ‘C’ locale.
If present, the collate specification must list all R code files in
the package (taking possible OS-specific subdirectories into account,
see Package subdirectories) as a whitespace separated list of file
paths relative to the R subdirectory. Paths containing white space or
quotes need to be quoted. An OS-specific collation field
(‘Collate.unix’ or ‘Collate.windows’) will be used instead of
‘Collate’.
So, you could specify:
Collate:
father.r
son.R
grandson.r
Or simply rename the files in such a way that lexicographic sorting order will result in the correct collation order, as you indicated in your question.
But also see this answer by #DirkEddelbuettel on a similar question.