[R-pkg-devel] Package builds, installs, and runs but does not pass devtools::check()
Thanks to John and Zhian for their recent and informative comments. Regarding check() and NSE: the moral seems to be that a little learning is a dangerous thing. I'm off to try to bring quosure to this issue. -- Mike
On Mon, Jul 16, 2018 at 2:38 PM, Zhian Kamvar <zkamvar at gmail.com> wrote:
Using dplyr like that is for exploratory data analysis. You'll want to refer to dplyr's "Programming with dplyr" vignette for using dplyr in a package: https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html Hope that helps. On Jul 16, 2018, at 22:13 , Michael Hannon <jmhannon.ucdavis at gmail.com> wrote: 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 at 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 at r-project.org] on behalf of
Michael Hannon [jmhannon.ucdavis at gmail.com]
Sent: 15 July 2018 02:13
To: r-package-devel at 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)
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