eplusr error on upgrade data.table

[mattdowle]

eplusr_0.12.0.tar.gz
./eplusr.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/eplusr.Rcheck’
./eplusr.Rcheck/00check.log:* using R Under development (unstable) (2020-07-14 r78854)
./eplusr.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit)
./eplusr.Rcheck/00check.log:* using session charset: UTF-8
./eplusr.Rcheck/00check.log:* checking for file ‘eplusr/DESCRIPTION’ ... OK
./eplusr.Rcheck/00check.log:* this is package ‘eplusr’ version ‘0.12.0’
./eplusr.Rcheck/00check.log:* package encoding: UTF-8
./eplusr.Rcheck/00check.log:* checking package namespace information ... OK
./eplusr.Rcheck/00check.log:* checking package dependencies ... OK
./eplusr.Rcheck/00check.log:* checking if this is a source package ... OK
./eplusr.Rcheck/00check.log:* checking if there is a namespace ... OK
./eplusr.Rcheck/00check.log:* checking for executable files ... OK
./eplusr.Rcheck/00check.log:* checking for hidden files and directories ... OK
./eplusr.Rcheck/00check.log:* checking for portable file names ... OK
./eplusr.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK
./eplusr.Rcheck/00check.log:* checking whether package ‘eplusr’ can be installed ... OK
./eplusr.Rcheck/00check.log:* checking installed package size ... OK
./eplusr.Rcheck/00check.log:* checking package directory ... OK
./eplusr.Rcheck/00check.log:* checking ‘build’ directory ... OK
./eplusr.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK
./eplusr.Rcheck/00check.log:* checking top-level files ... OK
./eplusr.Rcheck/00check.log:* checking for left-over files ... OK
./eplusr.Rcheck/00check.log:* checking index information ... OK
./eplusr.Rcheck/00check.log:* checking package subdirectories ... OK
./eplusr.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK
./eplusr.Rcheck/00check.log:* checking R files for syntax errors ... OK
./eplusr.Rcheck/00check.log:* checking whether the package can be loaded ... OK
./eplusr.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK
./eplusr.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK
./eplusr.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK
./eplusr.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK
./eplusr.Rcheck/00check.log:* checking loading without being on the library search path ... OK
./eplusr.Rcheck/00check.log:* checking dependencies in R code ... OK
./eplusr.Rcheck/00check.log:* checking S3 generic/method consistency ... OK
./eplusr.Rcheck/00check.log:* checking replacement functions ... OK
./eplusr.Rcheck/00check.log:* checking foreign function calls ... OK
./eplusr.Rcheck/00check.log:* checking R code for possible problems ... OK
./eplusr.Rcheck/00check.log:* checking Rd files ... OK
./eplusr.Rcheck/00check.log:* checking Rd metadata ... OK
./eplusr.Rcheck/00check.log:* checking Rd cross-references ... OK
./eplusr.Rcheck/00check.log:* checking for missing documentation entries ... OK
./eplusr.Rcheck/00check.log:* checking for code/documentation mismatches ... OK
./eplusr.Rcheck/00check.log:* checking Rd \usage sections ... OK
./eplusr.Rcheck/00check.log:* checking Rd contents ... OK
./eplusr.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK
./eplusr.Rcheck/00check.log:* checking R/sysdata.rda ... OK
./eplusr.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK
./eplusr.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK
./eplusr.Rcheck/00check.log:* checking examples ... OK
./eplusr.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK
./eplusr.Rcheck/00check.log:* checking tests ... ERROR
./eplusr.Rcheck/00check.log:  Running ‘testthat.R’
./eplusr.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed.
./eplusr.Rcheck/00check.log:Last 13 lines of output:
./eplusr.Rcheck/00check.log:  trying URL 'https://raw.githubusercontent.com/NREL/EnergyPlus/v9.2.0/idd/V8-9-0-Energy%2B.idd'
./eplusr.Rcheck/00check.log:  Content type 'text/plain; charset=utf-8' length 4390209 bytes (4.2 MB)
./eplusr.Rcheck/00check.log:  ==================================================
./eplusr.Rcheck/00check.log:  downloaded 4.2 MB
./eplusr.Rcheck/00check.log:  
./eplusr.Rcheck/00check.log:  ══ testthat results  ═══════════════════════════════════════════════════════════
./eplusr.Rcheck/00check.log:  [ OK: 1103 | SKIPPED: 11 | WARNINGS: 0 | FAILED: 5 ]
./eplusr.Rcheck/00check.log:  1. Error: table (@test_impl-idf.R#314) 
./eplusr.Rcheck/00check.log:  2. Error: Set (@test_impl-idf.R#773) 
./eplusr.Rcheck/00check.log:  3. Failure: Update (@test_impl-idf.R#947) 
./eplusr.Rcheck/00check.log:  4. Failure: Update (@test_impl-idf.R#950) 
./eplusr.Rcheck/00check.log:  5. Error: Update (@test_impl-idf.R#955) 
./eplusr.Rcheck/00check.log:  
./eplusr.Rcheck/00check.log:  Error: testthat unit tests failed
./eplusr.Rcheck/00check.log:  Execution halted
./eplusr.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK
./eplusr.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK
./eplusr.Rcheck/00check.log:* checking running R code from vignettes ... NONE
./eplusr.Rcheck/00check.log:  ‘eplusr.Rmd’ using ‘UTF-8’... OK
./eplusr.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING
./eplusr.Rcheck/00check.log:Error(s) in re-building vignettes:
./eplusr.Rcheck/00check.log:  ...
./eplusr.Rcheck/00check.log:--- re-building ‘eplusr.Rmd’ using rmarkdown
./eplusr.Rcheck/00check.log:trying URL 'https://github.com/NREL/EnergyPlus/releases/download/v8.8.0/EnergyPlus-8.8.0-7c3bbe4830-Linux-x86_64.tar.gz'
./eplusr.Rcheck/00check.log:Content type 'application/octet-stream' length 101420148 bytes (96.7 MB)
./eplusr.Rcheck/00check.log:==================================================
./eplusr.Rcheck/00check.log:downloaded 96.7 MB
./eplusr.Rcheck/00check.log:Quitting from lines 884-885 (eplusr.Rmd) 
./eplusr.Rcheck/00check.log:Error: processing vignette 'eplusr.Rmd' failed with diagnostics:
./eplusr.Rcheck/00check.log:object 'field' not found
./eplusr.Rcheck/00check.log:--- failed re-building ‘eplusr.Rmd’
./eplusr.Rcheck/00check.log:SUMMARY: processing the following file failed:
./eplusr.Rcheck/00check.log:  ‘eplusr.Rmd’
./eplusr.Rcheck/00check.log:Error: Vignette re-building failed.
./eplusr.Rcheck/00check.log:Execution halted
./eplusr.Rcheck/00check.log:* checking PDF version of manual ... OK
./eplusr.Rcheck/00check.log:* DONE
./eplusr.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING

[MichaelChirico]

This is a regression. Still haven't quite nailed down an MRE but it's do do with using a variable in j from the same environment, which is causing the eval used for #4159 to fail.

[hongyuanjia]

I am the author of eplusr package. Maybe I can help to provide a MRE here. But I did not know how to install the version that cause this error. Can I directly install the dev version of data.table via remote::install_github("Rdatatable/data.table")?

[eddelbuettel]

@hongyuanjia That is correct. The release candidate version in current development is in the main branch, and with that install_github() call you will get it.

[MichaelChirico]

Thanks @hongyuanjia , yes the latest dev reproduced the error for me. However it stopped reproducing as the eplusr vignette stopped compiling. I think maybe I was pinging GitHub to download the EPlus binary a few too many times

[eddelbuettel]

I think maybe I was pinging GitHub to download the EPlus binary a few too many times

I can recommend registering a GITHUB_PAT and setting it as an environment variable.

[hongyuanjia]

Below is a MRE. Seems like a scoping issue:

library(data.table)

dt <- data.table(id = c(1, 1, 2), value = c("a", "b", "c"))

fun <- function (dt, tag = c("A", "B")) {
    dt[, var := tag[[.GRP]], by = "id"]
}

fun(dt)
#> Error in eval(call("is.atomic", jsub[[2L]]), envir = x): object 'tag' not found

^{Created on 2020-07-20 by the reprex package (v0.3.0)}

[hongyuanjia]

Interesting. Inside [.data.table, [[ does not work but [ does:

library(data.table)

dt <- data.table(id = c(1, 1, 2), value = c("a", "b", "c"))

fun1 <- function (dt, tag = c("A", "B")) {
    # using "[[" does not work
    dt[, var := tag[[.GRP]], by = "id"]
}

fun1(dt)[]
#> Error in eval(call("is.atomic", jsub[[2L]]), envir = x): object 'tag' not found

fun2 <- function (dt, tag = c("A", "B")) {
    # using "[" works
    dt[, var := tag[.GRP], by = "id"]
}

fun2(dt)[]
#>    id value var
#> 1:  1     a   A
#> 2:  1     b   A
#> 3:  2     c   B

^{Created on 2020-07-20 by the reprex package (v0.3.0)}

[hongyuanjia]

The error comes from:

data.table/R/data.table.R

Line 1545 in 1a8a390

(jsub[[1L]] == "[[" && is.name(jsub[[2L]]) && eval(call('is.atomic', jsub[[2L]]), envir = x))) &&

where [.data.table tries to evaluate the name inside the data.table.

[hongyuanjia]

I can confirm that all errors are caused by this issue. After I temporarily getting workaround on this, all check errors are gone and eplusr can work well with dev version of data.table.

[MichaelChirico]

Thanks @hongyuanjia for the MRE. I do think data.table should be able to work without any change on your end in this case. It is a bug introduced by the fix for #4159.

[ColeMiller1]

@MichaelChrico I looked into this - it looks like simply adding enclos = parent.frame() within the eval statement fixes the issue. I recompiled and the (great!) MRE no longer errors and there are no tests that fail on our end. Not sure why it works, that should be the default enclosure.