Hello,
The CRAN checks for the drake package (4.1.0) fail for
r-devel-linux-x86_64-debian-clang. This happened right when crayon 1.3.4 was
released, but I suspect the problem is not with crayon or drake, but with base
R-devel. I cannot reproduce the error myself, but I have copied a minimal
working example (MWE) below that should theoretically isolate the problem.
`find_namespaced_functions()` is an internal function in drake that should work
as long as base R is working, and all the failures appear to trace back there.
Below the MWE is part of an existing email thread on this.
Will
# Walk through the body of f
# and find functions called with `::` or `:::`.
find_namespaced_functions <- function(f, found = character(0)){
if (is.function(f)){
return(find_namespaced_functions(body(f), found))
} else if (is.call(f) && deparse(f[[1]]) %in% c("::", ":::")){
found <- c(found, deparse(f))
} else if (is.recursive(f)){
v <- lapply(as.list(f), find_namespaced_functions, found)
found <- unique(c(found, unlist(v)))
}
found
}
f <- function(x){
digest::digest("Should be found.")
digest:::digest("Should also be found.")
digest("Should NOT be found.")
}
print(find_namespaced_functions(f))
# Expected output:
# [1] "digest::digest" "digest:::digest"
From: Will Landau
Sent: Saturday, September 16, 2017 11:16 PM
To: 'Gábor Csárdi' <csardi.ga...@gmail.com>; 'lig...@statistik.tu-dortmund.de'
<lig...@statistik.tu-dortmund.de>
Subject: RE: [EXTERNAL] Re: CRAN submission crayon 1.3.4
Gabor and Uwe,
Thank you for promptly notifying me. I saw the
https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/drake-00check.html,
and I could not reproduce it either. I tried:
• Ubuntu 17.04 with gcc (though drake has no complied code)
• a fresh copy of 64-bit R-devel r73293 (2017-09-16)
• the latest version of all required packages, including crayon 1.3.4
• `R CMD check --as-cran drake_4.1.0.tar.gz` with a
https://cran.r-project.org/src/contrib/drake_4.1.0.tar.gz
From looking at the
https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/drake-00check.html
(which are exactly the ones Uwe mentioned), I strongly believe that the
problem has nothing to do with Gabor’s `crayon` package. Rather, all the CRAN
errors are closely related to a function in drake 4.1.0 called
https://github.com/wlandau-lilly/drake/blob/master/R/dependencies.R#L73, which
only depends on base R. I have attached a minimal working example that should
theoretically isolate and reproduce the
https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/drake-00check.html.
Please let me know how you think we can proceed. I am actively maintaining
`drake`, and I have a strong desire to fix all the problems and keep a clean
production version on CRAN.
Will
-----Original Message-----
From: Gábor Csárdi [mailto:csardi.ga...@gmail.com]
Sent: Saturday, September 16, 2017 3:43 PM
To: Will Landau <mailto:will.lan...@lilly.com>
Subject: [EXTERNAL] Re: CRAN submission crayon 1.3.4
Hi,
I am sorry, the new crayon version, coming to CRAN, seems to break your
package, drake. Hopefully CRAN can tell you on which platform and which R
version this happens. I cannot reproduce this, unfortunately.
Let me know if you think this is my fault.
Gabor
On Sat, Sep 16, 2017 at 8:17 PM, Uwe Ligges
<mailto:lig...@statistik.tu-dortmund.de> wrote:
> Thanks, we see in reverse dependencies:
>
> Package: drake
> Check: tests
> New result: ERROR
> Running ‘testthat.R’ [55s/138s]
> Running the tests in ‘tests/testthat.R’ failed.
> Complete output:
> > Sys.setenv("R_TESTS" = "")
> >
> > library(testthat)
> > library(drake)
> >
> > test_check("drake")
> 1. Failure: function_dependencies() works on :: and :::
> (@test-namespaced.R#19)
> sort(find_namespaced_functions(crazy)) not equal to `ns`.
> Lengths differ: 0 vs 7
>
>
> 2. Failure: function_dependencies() works on :: and :::
> (@test-namespaced.R#20)
> function_dependencies(crazy) not equal to list(functions =
> sort(c(ns, "g", "runif", "sqrt")), variables = character(0)).
> Component "functions": Lengths (3, 10) differ (string compare on
> first
> 3)
> Component "functions": 3 string mismatches
>
>
> 3. Failure: function_dependencies() works on :: and :::
> (@test-namespaced.R#25)
> `d` not equal to sort(c("digest::digest", "runif", "stats::rnorm",
> "stats::rpois")).
> Lengths differ: 1 vs 4
>
>
> 4. Error: namespaced workflow works (@test-namespaced.R#40)
> --------------------
> key 'base::list' ('objects') not found
> 1: readd("base::list", character_only = TRUE) at
> testthat/test-namespaced.R:40
> 2: cache$get(target)
> 3: self$get_value(self$get_hash(key, namespace), use_cache)
> 4: exists0(hash, envir)
> 5: vlapply(name, exists, envir = envir, inherits = FALSE,
> USE.NAMES =
> FALSE)
> 6: vapply(X, FUN, logical(1), ...)
> 7: self$get_hash(key, namespace)
>
> testthat results
> ================================================================
> OK: 358 SKIPPED: 0 FAILED: 4
> 1. Failure: function_dependencies() works on :: and :::
> (@test-namespaced.R#19)
> 2. Failure: function_dependencies() works on :: and :::
> (@test-namespaced.R#20)
> 3. Failure: function_dependencies() works on :: and :::
> (@test-namespaced.R#25)
> 4. Error: namespaced workflow works (@test-namespaced.R#40)
>
> Error: testthat unit tests failed
> Execution halted
>
>
> Is this expected and has the author been informed?
>
> Best,
> Uwe
>
>
>
>
>
>
>
> On 15.09.2017 20:15, CRAN submission wrote:
>>
>> [This was generated from CRAN.R-project.org/submit.html]
>>
>> The following package was uploaded to CRAN:
>> ===========================================
>>
>> Package Information:
>> Package: crayon
>> Version: 1.3.4
>> Title: Colored Terminal Output
>> Author(s): Gábor Csárdi [aut, cre], Brodie Gaslam [ctb]
>> Maintainer: Gábor Csárdi <mailto:csardi.ga...@gmail.com>
>> Suggests: mockery, rstudioapi, testthat, withr
>> Description: Colored terminal output on terminals that support 'ANSI'
>> color and highlight codes. It also works in 'Emacs' 'ESS'.
>> 'ANSI' color support is automatically detected. Colors and
>> highlighting can be combined and nested. New styles can also
>> be created easily. This package was inspired by the 'chalk'
>> 'JavaScript' project.
>> License: MIT + file LICENSE
>> Imports: grDevices, methods, utils
>>
>>
>> The maintainer confirms that he or she has read and agrees to the
>> CRAN policies.
>>
>> Submitter's comment: Please publish this one instead of the previously
>> submitted 1.3.3 version, that one has a bug that
>> breaks colors on some platforms.
>>
>> =================================================
>>
>> Original content of DESCRIPTION file:
>>
>> Package: crayon
>> Title: Colored Terminal Output
>> Version: 1.3.4
>> Authors@R: c(
>> person("Gábor", "Csárdi", , "mailto:csardi.ga...@gmail.com";,
>> role = c("aut", "cre")),
>> person(
>> "Brodie", "Gaslam", email="mailto:brodie.gas...@yahoo.com";,
>> role=c("ctb"))
>> )
>> Description: Colored terminal output on terminals that support 'ANSI'
>> color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI'
>> color support is automatically detected. Colors and highlighting can
>> be combined and nested. New styles can also be created easily.
>> This package was inspired by the 'chalk' 'JavaScript' project.
>> License: MIT + file LICENSE
>> LazyData: true
>> URL: https://github.com/r-lib/crayon#readme
>> BugReports: https://github.com/r-lib/crayon/issues
>> Collate: 'ansi-256.r' 'combine.r' 'string.r' 'utils.r'
>> 'crayon-package.r' 'disposable.r' 'has_ansi.r' 'has_color.r'
>> 'styles.r' 'machinery.r' 'parts.r' 'print.r' 'style-var.r'
>> 'show.r' 'string_operations.r'
>> Imports: grDevices, methods, utils
>> Suggests: mockery, rstudioapi, testthat, withr
>> RoxygenNote: 6.0.1.9000
>> Encoding: UTF-8
>> Roxygen: list(markdown = TRUE)
>> NeedsCompilation: no
>> Packaged: 2017-09-15 18:14:04 UTC; gaborcsardi
>> Author: Gábor Csárdi [aut, cre],
>> Brodie Gaslam [ctb]
>> Maintainer: Gábor Csárdi <mailto:csardi.ga...@gmail.com>
>>
>
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