[R-pkg-devel] R CMD check works but with devtools::check() examples fail

[Barbara Lerner]

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 using abbrev, cmd using abbrev, functions.called 
= cmd using functions.called,
        cmd = cmd)
     --- call from argument ---
    !is.null(functions.called) && !is.na(functions.called)
     --- R stacktrace ---
    where 1: .ddg.proc.node("Operation", cmd using abbrev, cmd using abbrev, 
functions.called = cmd using 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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