I have just upgraded to R 3.6.0 and when building and checking my
package, R CMD check passes all the checks, including running the
examples, but devtools::check reports a failure when running the
examples. I have also run the example successfully manually in RStudio.
I would appreciate help in understanding what devtools::check is doing
that R CMD check is not doing, or help in understanding the failure
report that devtools::check provides.
Here are somewhat abbreviated outputs from each:
~/git/rdtLite.check/rdtLite.Rcheck/00_pkg_src/rdtLite -> R CMD check .
* using log directory
‘/Users/blerner/git/rdtLite.check/rdtLite.Rcheck/00_pkg_src/rdtLite/..Rcheck’
* using R version 3.6.0 (2019-04-26)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘./DESCRIPTION’ ... OK
* this is package ‘rdtLite’ version ‘1.0.3’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.commit
..Rcheck
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rdtLite’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Found the following directory with the name of a check directory:
./..Rcheck
Most likely, these were included erroneously.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies
... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘gtools’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
~/git/rdtLite.check/rdtLite.Rcheck/00_pkg_src/rdtLite -> Rscript -e
"devtools::check()"
Updating rdtLite documentation
Warning: roxygen2 requires Encoding: UTF-8
Writing NAMESPACE
Loading rdtLite
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Writing NAMESPACE
── Building ─────────────────────────────────────────────────────────
rdtLite ──
Setting env vars:
● CFLAGS : -Wall -pedantic -fdiagnostics-color=always
● CXXFLAGS : -Wall -pedantic -fdiagnostics-color=always
● CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always
────────────────────────────────────────────────────────────────────────────────
checking for file
‘/Users/blerner/git/rdtLite.check/rdtLite.Rcheck/00_pkg_src✔ checking
for file
‘/Users/blerner/git/rdtLite.check/rdtLite.Rcheck/00_pkg_src/rdtLite/DESCRIPTION’
─ preparing ‘rdtLite’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘rdtLite_1.0.3.tar.gz’
── Checking ─────────────────────────────────────────────────────────
rdtLite ──
Setting env vars:
● _R_CHECK_CRAN_INCOMING_REMOTE_: FALSE
● _R_CHECK_CRAN_INCOMING_ : FALSE
● _R_CHECK_FORCE_SUGGESTS_ : FALSE
── R CMD check
─────────────────────────────────────────────────────────────────
─ using log directory
‘/private/var/folders/66/3lfdj29j1wb48v_s298qtbwm0000gn/T/Rtmpln2xE0/rdtLite.Rcheck’
─ using R version 3.6.0 (2019-04-26)
─ using platform: x86_64-apple-darwin15.6.0 (64-bit)
─ using session charset: UTF-8
─ using options ‘--no-manual --as-cran’
✔ checking for file ‘rdtLite/DESCRIPTION’
─ this is package ‘rdtLite’ version ‘1.0.3’
✔ checking package namespace information ...
✔ checking package dependencies (3.1s)
✔ checking if this is a source package
✔ checking if there is a namespace
✔ checking for executable files (439ms)
N checking for hidden files and directories
Found the following hidden files and directories:
.commit
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
✔ checking for portable file names
✔ checking for sufficient/correct file permissions
✔ checking whether package ‘rdtLite’ can be installed (3s)
✔ checking installed package size ...
✔ checking package directory ...
✔ checking for future file timestamps ...
✔ checking DESCRIPTION meta-information ...
✔ checking top-level files
✔ checking for left-over files
✔ checking index information
✔ checking package subdirectories ...
✔ checking R files for non-ASCII characters ...
✔ checking R files for syntax errors ...
✔ checking whether the package can be loaded ...
✔ checking whether the package can be loaded with stated dependencies ...
✔ checking whether the package can be unloaded cleanly ...
✔ checking whether the namespace can be loaded with stated dependencies ...
✔ checking whether the namespace can be unloaded cleanly ...
✔ checking dependencies in R code (800ms)
✔ checking S3 generic/method consistency (760ms)
✔ checking replacement functions ...
✔ checking foreign function calls (437ms)
✔ checking R code for possible problems (5.5s)
✔ checking Rd files ...
✔ checking Rd metadata ...
✔ checking Rd line widths ...
✔ checking Rd cross-references ...
✔ checking for missing documentation entries ...
✔ checking for code/documentation mismatches (563ms)
✔ checking Rd \usage sections (879ms)
✔ checking Rd contents ...
✔ checking for unstated dependencies in examples ...
E checking examples (2s)
Running examples in ‘rdtLite-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: prov.json
> ### Title: Provenance Access Functions
> ### Aliases: prov.json prov.dir prov.visualize prov.summarize
>
> ### ** Examples
>
> prov.init()
> a <- 1
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
rdtLite
--- call from context ---
.ddg.proc.node("Operation", cmd@abbrev, cmd@abbrev, functions.called
= cmd@functions.called,
cmd = cmd)
--- call from argument ---
!is.null(functions.called) && !is.na(functions.called)
--- R stacktrace ---
where 1: .ddg.proc.node("Operation", cmd@abbrev, cmd@abbrev,
functions.called = cmd@functions.called,
cmd = cmd)
where 2: .ddg.parse.commands(as.expression(task), environ = .GlobalEnv,
run.commands = FALSE)
where 3: (function (task, result, success, printed)
{
.ddg.parse.commands(as.expression(task), environ = .GlobalEnv,
run.commands = FALSE)
return(TRUE)
})(base::quote(a <- 1), 1, TRUE, FALSE)
--- value of length: 3 type: logical ---
[1] TRUE TRUE TRUE
.... more lines omitted ...
----------- END OF FAILURE REPORT --------------
Fatal error: length > 1 in coercion to logical
✔ checking for unstated dependencies in ‘tests’ ...
─ checking tests ...
✔ Running ‘test-all.R’ (685ms)
--
<http://www.getpostbox.com>Barbara Lerner
Professor
Computer Science Department
Mount Holyoke College
<http://www.getpostbox.com>
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