[R-pkg-devel] Package builds, installs, and runs but does not pass devtools::check()

Fox, John jfox @ending from mcm@@ter@c@
Mon Jul 16 23:29:34 CEST 2018 

Dear Michael,

You could add a call to globalVariables() in the package sources for cases like this.

I hope this helps,
 John

-----------------------------------------------------------------
John Fox
Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
Web: https://socialsciences.mcmaster.ca/jfox/



> -----Original Message-----
> From: R-package-devel [mailto:r-package-devel-bounces using r-project.org] On
> Behalf Of Michael Hannon
> Sent: Monday, July 16, 2018 2:14 PM
> To: Georgi Boshnakov <georgi.boshnakov using manchester.ac.uk>
> Cc: r-package-devel using r-project.org
> Subject: Re: [R-pkg-devel] Package builds, installs, and runs but does not pass
> devtools::check()
> 
> Thanks, Georgi.  I've changed my approach and now do what I gather is
> recommended practice: put all external package names into the "Imports"
> section of the DESCRIPTION file and then use the fully-qualified names for
> functions from those packages, as:
> 
>     dplyr::select()
> 
> The "check" operation is still not entirely "happy" with me, but it doesn't flag
> any errors, and the package builds and runs.
> 
> BTW, one source of "complaints" from "check()" is evidently the use of NSE in
> the tidyverse functions.  For instance, the line:
> 
>     next_data_frame %>% dplyr::select(-amount,
> 
> generates the message:
> 
>     standardize_format: no visible binding for global variable ‘amount’
> 
> where, of course, "amount" is one of the column headings in
> "next_data_frame".  There seems to be no harm done by this, and I plan to
> ignore such messages, but if there's some additional wisdom that applies
> here, I'd be happy to receive it.
> 
> -- Mike
> 
> 
> On Sun, Jul 15, 2018 at 12:05 AM, Georgi Boshnakov
> <georgi.boshnakov using manchester.ac.uk> wrote:
> >
> > It seems that the R session used by 'check' doesn't look in the library used by
> your interactive session. This discrepancy may happen since the check tools
> do not load the same Renviron files as interactive sessions. This may result in
> different libraries in interactive and 'check' sessions. See ?Startup, especially
> section Note.
> > It is difficult to give more specific advice without details of your setup.
> >
> >
> > Hope this helps,
> > Georgi Boshnakov
> >
> >
> > ________________________________________
> > From: R-package-devel [r-package-devel-bounces using r-project.org] on
> > behalf of Michael Hannon [jmhannon.ucdavis using gmail.com]
> > Sent: 15 July 2018 02:13
> > To: r-package-devel using r-project.org
> > Subject: [R-pkg-devel] Package builds, installs, and runs but does not
> > pass devtools::check()
> >
> > Greetings.  I'm working on a small package, and I'm using the devtools
> > functions to create, build, etc., the package.
> >
> > As indicated in the subject line, I get no errors when I do:
> >
> >     > build()
> >     > install()
> >
> > When I run a separate R session and load the package, i.e.,
> >
> >     > library(my_pkg)
> >
> > the package loads without error, and the two exported functions appear
> > to work as advertised.
> >
> > OTOH, if I include devtools::check() in the construction of the
> > package, I consistently get an error:
> >
> >     * installing *source* package ‘my_pkg’ ...
> >     ** R
> >     ** preparing package for lazy loading
> >     Error in loadNamespace(from, lib.loc = .library) :
> >       there is no package called ‘dplyr’
> >     Error : unable to load R code in package 'my_pkg'
> >
> > Clearly there *is* a package called "dplyr" on my system (see the
> > session info below, for instance).  And, as I've mentioned, the code
> > *does* run, and I can watch it successfully reading CSV files.
> >
> > Here's the relevant part of my DESCRIPTION file:
> >
> >     Depends: R (>= 3.4.4)
> >     Imports: readr,
> >             dplyr,
> >             ggplot2,
> >             purrr,
> >             magrittr
> >
> > I suspect the problem may be that I'm misunderstanding something about
> > the `import::from()` function, which I'm using for the first time to
> > load required functions into my code.  In each of the three files that
> > use dplyr I have the line:
> >
> >     import::from(dplyr, mutate, filter, rename, select, setdiff,
> > slice, "%>%")
> >
> > I've tried:
> >
> >     (1) putting that line in just one of the files (the lexically first one)
> >     (2) including different subsets of dplyr functions, as needed, in
> > the various files
> >
> > Needless to say, I haven't seen any improvement with any of the above
> > (or any of the other thrashing I've done).
> >
> > If you can point me in the right direction, I'd appreciate it.  Thanks.
> >
> > -- Mike
> >
> >
> >> session_info()
> > Session info
> > ------------------------------------------------------------------
> >  setting  value
> >  version  R version 3.4.4 (2018-03-15)
> >  system   x86_64, linux-gnu
> >  ui       X11
> >  language en_US
> >  collate  en_US.UTF-8
> >  tz       America/Los_Angeles
> >  date     2018-07-14
> >
> > Packages ----------------------------------------------------------------------
> >  package    * version date       source
> >  assertthat   0.2.0   2017-04-11 CRAN (R 3.3.3)
> >  base       * 3.4.4   2018-03-16 local
> >  bindr        0.1.1   2018-03-13 CRAN (R 3.4.3)
> >  bindrcpp     0.2.2   2018-03-29 CRAN (R 3.4.4)
> >  compiler     3.4.4   2018-03-16 local
> >  crayon       1.3.4   2017-09-16 CRAN (R 3.4.1)
> >  datasets   * 3.4.4   2018-03-16 local
> >  devtools   * 1.13.6  2018-06-27 CRAN (R 3.4.4)
> >  digest       0.6.15  2018-01-28 CRAN (R 3.4.3)
> >  dplyr      * 0.7.6   2018-06-29 CRAN (R 3.4.4)
> >  glue         1.2.0   2017-10-29 CRAN (R 3.4.2)
> >  graphics   * 3.4.4   2018-03-16 local
> >  grDevices  * 3.4.4   2018-03-16 local
> >  magrittr     1.5     2014-11-22 CRAN (R 3.2.2)
> >  memoise      1.1.0   2017-04-21 CRAN (R 3.3.3)
> >  methods    * 3.4.4   2018-03-16 local
> >  pillar       1.3.0   2018-07-14 CRAN (R 3.4.4)
> >  pkgconfig    2.0.1   2017-03-21 CRAN (R 3.4.0)
> >  purrr        0.2.5   2018-05-29 CRAN (R 3.4.4)
> >  R6           2.2.2   2017-06-17 CRAN (R 3.4.0)
> >  Rcpp         0.12.17 2018-05-18 CRAN (R 3.4.4)
> >  rlang        0.2.1   2018-05-30 CRAN (R 3.4.4)
> >  stats      * 3.4.4   2018-03-16 local
> >  tibble       1.4.2   2018-01-22 CRAN (R 3.4.3)
> >  tidyselect   0.2.4   2018-02-26 CRAN (R 3.4.3)
> >  utils      * 3.4.4   2018-03-16 local
> >  withr        2.1.2   2018-03-15 CRAN (R 3.4.3)
> >>
> >
> > ______________________________________________
> > R-package-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

More information about the R-package-devel mailing list