Re: [R-pkg-devel] R CMD check works but with devtools::check() examples fail
Why do you think so? Don't the lines below the "-- Building" header mean that devtools/rcmdcheck is building the package? I saw (the last part of) this: > ~/git/rdtLite.check/rdtLite.Rcheck/00_pkg_src/rdtLite -> R CMD check . Sorry if I added some confusion: on closer inspection, it does look like this is R CMD check doing its normal thing. G. [...] ── 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 ─ [...] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R CMD check works but with devtools::check() examples fail
Barbara, On 5/15/19 5:09 PM, Barbara Lerner wrote: 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 . Agree with Dirk, and also you are running R CMD check on the current directory, whereas Writing R Extensions recommends/insists on checking a tarball created using R CMD build: "It is strongly recommended that the final checks are run on a tar archive prepared by R CMD build." I've no idea how this might change checks (does it still look at .Rbuildignore?) but this might introduce additional problems. Jack * 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 ──
Re: [R-pkg-devel] active bindings in package namespace
This is a good point. I would prefer to include all the data in the
package, but CRAN has strict limitations on package and subdirectory
size, which the potential data would easily exceed. Whether it is an
active binding or a get function, dynamically downloaded data will
always suffer this problem. Also, there are potential copyright issues
which may prevent including all the relevant data in a package, no
matter how the package is distributed.
For this particular package of ICD data, the biggest risk is not the
data changing, but the data not being made available in the future, or
not being provided in a useful format.
I do allow the user to set the cache directory, which eventually
includes all the raw and processed data, and this could be archived by
the user for reproducibilty. In addition, the test suite covers
potential changes to the source data.
On 3/24/19 11:21 AM, Hong Ooi wrote:
Don't want to turn this into a pile-on, but I also think this isn't a very good idea. As
I understand it, accessing the symbol "foo" will pull the latest version of foo
from the remote site. This has consequences for reproducibility, because now your code
could be exactly the same, and your local environment exactly the same, and yet running
the code at different times can yield different results because the remote data has been
updated.
-Original Message-
From: R-package-devel On Behalf Of Jack
Wasey
Sent: Sunday, 24 March 2019 9:57 AM
To: Kirill Müller ; R Development
Subject: Re: [R-pkg-devel] active bindings in package namespace
Thanks both, this is helpful advice.
On 3/23/19 5:14 PM, Kirill Müller wrote:
Dear Jack
This doesn't answer your question, but I would advise against this design.
- Users do not expect side effects (such as network access) from accessing a
symbol.
- A function gives you much more flexibility to change the interface
later on. (Arguments for fetching the data, tokens for API access,
...)
- You already encountered a few quirks that make this an "interesting" problem.
A function call only needs a pair of parentheses.
Best regards
Kirill
On 23.03.19 16:50, Jack O. Wasey wrote:
Dear all,
I am developing a package which is a front for various online data (icd.data
https://github.com/jackwasey/icd.data/ ). The current CRAN version just has
lazy-loaded data, but now the package encompasses far more current and historic
ICD codes from different countries, these can't be included in the CRAN package
even with maximal compression.
Other authors have solved this using functions to get the data, with or without
a local cache of the retrieved data. No CRAN or other packages I have found
after extensive searching use the attractive active binding feature of R.
The goal is simple: for the user to refer to the data by its symbol, e.g.,
'icd10fr2019', or 'icd.data::icd10fr2019', and it will be downloaded and parsed
transparently (if the user has already granted permission, or after prompt if
they haven't).
The bindings are set using commands alongside the function definitions in R/*.R
.E.g.
makeActiveBinding("icd10cm_latest", .icd10cm_latest_binding,
environment()) lockBinding("icd10cm_latest", environment())
For non-interactive use, CI and CRAN tests, no data should be downloaded, and
no cache directory set up without user consent. For interactive use, I ask
permission to create a local data cache before downloading data.
This works fine... until R CMD check. The following steps seems to 'get' or
'source' everything from the package namespace, which results in triggering the
active bindings, and this fails if I am unable to get consent to download data,
and want to 'stop' on this error condition.
- checking dependencies in R code
- checking S3 generic/method consistency
- checking foreign function calls
- checking R code for possible problems
Debugging CI-specific binding bugs is a nightmare because these occur in
different R sessions initiated by R CMD check.
There may be legitimate reasons to evaluate everything in the
namespace, but I've no idea what they are. Incidentally, Rstudio also
does 'mget' on the whole package namespace and triggers bindings
during autocomplete. https://github.com/rstudio/rstudio/issues/4414
Is this something I should raise as an issue with R? Or does anyone have any
idea of a sensible approach to this. Currently I have a set of workarounds, but
this complicates the code, and has taken an awful lot of time. Does anyone know
of any CRAN package which has active bindings in the package namespace?
Any ideas appreciated.
Jack Wasey
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[R-pkg-devel] active bindings in package namespace
Dear all,
I am developing a package which is a front for various online data
(icd.data https://github.com/jackwasey/icd.data/ ). The current CRAN
version just has lazy-loaded data, but now the package encompasses far
more current and historic ICD codes from different countries, these
can't be included in the CRAN package even with maximal compression.
Other authors have solved this using functions to get the data, with or
without a local cache of the retrieved data. No CRAN or other packages I
have found after extensive searching use the attractive active binding
feature of R.
The goal is simple: for the user to refer to the data by its symbol,
e.g., 'icd10fr2019', or 'icd.data::icd10fr2019', and it will be
downloaded and parsed transparently (if the user has already granted
permission, or after prompt if they haven't).
The bindings are set using commands alongside the function definitions
in R/*.R .E.g.
makeActiveBinding("icd10cm_latest", .icd10cm_latest_binding, environment())
lockBinding("icd10cm_latest", environment())
For non-interactive use, CI and CRAN tests, no data should be
downloaded, and no cache directory set up without user consent. For
interactive use, I ask permission to create a local data cache before
downloading data.
This works fine... until R CMD check. The following steps seems to 'get'
or 'source' everything from the package namespace, which results in
triggering the active bindings, and this fails if I am unable to get
consent to download data, and want to 'stop' on this error condition.
- checking dependencies in R code
- checking S3 generic/method consistency
- checking foreign function calls
- checking R code for possible problems
Debugging CI-specific binding bugs is a nightmare because these occur in
different R sessions initiated by R CMD check.
There may be legitimate reasons to evaluate everything in the namespace,
but I've no idea what they are. Incidentally, Rstudio also does 'mget'
on the whole package namespace and triggers bindings during
autocomplete. https://github.com/rstudio/rstudio/issues/4414
Is this something I should raise as an issue with R? Or does anyone have
any idea of a sensible approach to this. Currently I have a set of
workarounds, but this complicates the code, and has taken an awful lot
of time. Does anyone know of any CRAN package which has active bindings
in the package namespace?
Any ideas appreciated.
Jack Wasey
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