data.table throws "object not found" error

r data.table devtools

15,411

Great reproducible question! Here's what I get. You didn't post your output as well, so perhaps you don't get the same output at me. I've split the output and placed HERE where the problem might be.

$ R
R version 3.1.0 (2014-04-10) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

> library(devtools)
> setwd(tempdir())
> # make dummy package called foo
> create("foo")
Creating package foo in .
No DESCRIPTION found. Creating with values:

Package: foo
Title: 
Description: 
Version: 0.1
Authors@R: # getOptions('devtools.desc.author')
Depends: R (>= 3.1.0)
License: # getOptions('devtools.desc.license')
LazyData: true
> setwd("foo")
> 
> # add data.table as a package dependency
> a <- readLines("DESCRIPTION")
> depends.idx <- grepl("Depends", a)
> a[depends.idx] <- paste0(a[depends.idx], ", data.table")
> writeLines(a, "DESCRIPTION")
> 
> # create a dummy function 
> writeLines("myfunction <- function() {a <- data.table(b=1); return(a[,b])}",
+             "R/foo.R")
> 
> # check and throw error
> check()
Loading required package: roxygen2
Updating foo documentation
Loading foo

HERE :

Invalid DESCRIPTION:
Authors@R field gives no person with author role.
Authors@R field gives no person with maintainer role and email address.

See the information on DESCRIPTION files in section 'Creating R packages' of the 'Writing R Extensions' manual.

Loading required package: data.table
data.table 1.9.2  For help type: help("data.table")

Attaching package: ‘data.table’

The following object is masked from ‘package:bit’:

    setattr

Updating collate directive in  /tmp/Rtmp0h3yz9/foo/DESCRIPTION 
Updating namespace directives
Writing foo.Rd
'/usr/lib/R/bin/R' --vanilla CMD build '/tmp/Rtmp0h3yz9/foo' --no-manual --no-resave-data 

* checking for file '/tmp/Rtmp0h3yz9/foo/DESCRIPTION' ... OK
* preparing 'foo':

HERE :

* checking DESCRIPTION meta-information ... ERROR
Authors@R field gives no person with author role.
Authors@R field gives no person with maintainer role and email address.

See the information on DESCRIPTION files in section 'Creating R
packages' of the 'Writing R Extensions' manual.

Error: Command failed (1)
> library(foo)
> myfunction()
Error in `[.data.frame`(x, i, j) : object 'b' not found
>

15,411

Abe

Updated on September 16, 2022

Comments

Abe over 1 year
I have a data.table:
```
library(data.table)
mydt <- data.table(index = 1:10)
```
I am getting this to work when I try it in the global environment, but not when I am in the debugger or when I use it in a package test.

The problem is that I can not subset it in the standard ways.
```
Browse[2]> mydt[,index]
Error in `[.data.frame`(x, i, j) : object 'index' not found
Browse[2]> mydt[,list(index)]
Error in `[.data.frame`(x, i, j) : object 'index' not found
```
Here is a reproducible example, in which I create a package and then get the error when I evaluate the function called myfunction:
```
library(devtools)
setwd(tempdir())
# make dummy package called foo
create("foo")
setwd("foo")

# add data.table as a package dependency
a <- readLines("DESCRIPTION")
depends.idx <- grepl("Depends", a)
a[depends.idx] <- paste0(a[depends.idx], ", data.table")
writeLines(a, "DESCRIPTION")

# create a dummy function 
writeLines("myfunction <- function() {a <- data.table(b=1); return(a[,b])}",
            "R/foo.R")

# check and throw error
check()
library(foo)
myfunction()
```
Here is the session info:
```
Browse[2]> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C            LC_COLLATE=C         LC_MONETARY=C       
 [6] LC_MESSAGES=C        LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C         LC_TELEPHONE=C      
[11] LC_MEASUREMENT=C     LC_IDENTIFICATION=C 

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] PEcAn.data.atmosphere_1.3.3 data.table_1.9.2            RPostgreSQL_0.4             PEcAn.settings_1.3.3       
 [5] lubridate_1.3.3             PEcAn.DB_1.3.3              DBI_0.2-7                   PEcAn.utils_1.3.3          
 [9] udunits2_0.6                ncdf4_1.12                  randtoolbox_1.14            rngWELL_0.10-2             
[13] ggplot2_1.0.0               XML_3.98-1.1                plyr_1.8.1                  abind_1.4-0                
[17] testthat_0.8.1              devtools_1.5.0.99          

loaded via a namespace (and not attached):
 [1] MASS_7.3-29      RCurl_1.95-4.1   Rcpp_0.11.2      colorspace_1.2-4 digest_0.6.4     evaluate_0.5.5   grid_3.0.2      
 [8] gtable_0.1.2     httr_0.3         memoise_0.2.1    munsell_0.4.2    parallel_3.0.2   proto_0.3-10     reshape2_1.4    
[15] roxygen2_4.0.1   scales_0.2.4     stringr_0.6.2    tools_3.0.2      whisker_0.3-2      
```
- Admin almost 10 years
  
  There is no index object in your workspace. Create it first.
- Abe almost 10 years
  
  @Pascal index is a column name for the data.table. If you are not familiar with the data.table package, one feature is that it allows indexing without putting quotes around the column names.
- Admin almost 10 years
  
  I understand. But it is a question of workspace and namespace I guess.
- Abe almost 10 years
  
  @Pascal could you elaborate? How might I get the object to behave as expected?
- mnel almost 10 years
  
  From where are you calling browser? Can you post a reproducible example.
- Abe almost 10 years
  
  @mnel I have provided a reproducible example, it requires putting this all into a dummy package. It doesn't enter the browser; but I would do so in the example by using debugonce(foo)
- MrFlick almost 10 years
  
  Is the a[6] value the "Depends" line?
- Abe almost 10 years
  
  @MrFlick yes ... but now I realize my example is wrong ... I'll try and fix it
- Abe almost 10 years
  
  @MrFlick The reproducible example throws the error now; I've also clarified the indexing
- Admin almost 10 years
  
  Did you notice this lines during checking? * checking dependencies in R code ... NOTE Package in Depends field not imported from: 'data.table' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
- Matt Dowle almost 10 years
  
  Have you followed stackoverflow.com/a/10529888/403310 ?
- Abe almost 10 years
  
  @MattDowle Isn't that demonstrated in the reproducible example that I posted? It says to put data.table in the Depends section of the DESCRIPTION file, correct?
- Matt Dowle almost 10 years
  
  @Abe Sorry my bad. Yes it reproduces (great question!) and I'll add an answer.
- eddi almost 10 years
  
  Seems like data.table:::cedta expects to find a ".Depends" object in the package that would list the dependencies, in particular data.table and doesn't - I don't know if this is smth that has changed in R. Perhaps you can try the import method instead?
- eddi almost 10 years
  
  btw a very simple workaround is to add a global .datatable.aware=TRUE to your package - e.g. writeLines(".datatable.aware=TRUE; myfunction...
- Abe almost 10 years
  
  @eddi it works ... thanks! why not post as an answer?
- Arun almost 10 years
  
  I think this might be the same bug in devtools which is also explained here (if so, I'd mark this as a duplicate).
- Abe almost 10 years
  
  @arun yes, appears to be the same
- krlmlr almost 9 years
  
  Can't replicate this issue anymore: github.com/hadley/devtools/issues/192#issuecomment-105451177
Abe almost 10 years

seems to be an old devtools bug github.com/hadley/devtools/issues/192