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

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