[R-pkg-devel] Not a bug in checks in R-devel
On 28/10/2019 1:01 p.m., William Dunlap wrote:
The Matrix package explicitly sets LazyData to "no" with a note saying
that it is necessary.
LazyData: no
LazyDataNote: not possible, since we use data/*.R *and* our classes
My notes on implementing install.packages() in TERR include
When R's install.packages() processes *.R files in the package's
data directory, they may use functions defined in the package's R
directory, whether or not LazyData is yes or no.
If LazyData is no (but not if yes), then the *.R files in data can
refer to files copied from pkg/inst/blah to pkg/blah.
TERR must be able to do this to install the Matrix package from source.
Hence changing the default to "yes" may break the installation of some
packages.
Thanks! This also shows another solution to Luis-Miguel's problem. He had
\usage{growth.curves}
in his .Rd file, but that doesn't work unless LazyData: yes is used (as
pointed out earlier). In fact, it is incorrect: running
growth.curves
in the R console gives the error
Error: object 'growth.curves' not found
Since data is not lazy-loaded, the approach used by Matrix is needed,
i.e. an explicit call to data():
\usage{
data(growth.curves)
}
So this isn't a bug in the checks after all, it was an error in the
package and was being reported correctly.
Duncan Murdoch
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Sun, Oct 27, 2019 at 12:35 PM Duncan Murdoch
mailto:murdoch.dun...@gmail.com>> wrote:
On 27/10/2019 6:04 a.m., Luis-Miguel Rodríguez Rojas wrote:
> Thanks a lot Xavier!
> This solved my issue.
This seems like a simple workaround for the bug. Perhaps "LazyData:
yes" should become the default. I don't know what are the
advantages of
the current "LazyData: no" default.
BTW, another issue is that the environment variable controlling this
test, "_R_CHECK_CODOC_VARIABLES_IN_USAGES_", doesn't appear to be
documented. I did a fairly rough search through the sources for other
undocumented check variables, and found this list:
[1] "_R_CHECK_CODOC_VARIABLES_IN_USAGES_"
[2] "_R_CHECK_CRAN_INCOMING_ASPELL_RECHECK_MAYBE_"
[3] "_R_CHECK_CRAN_INCOMING_ASPELL_RECHECK_START_"
[4] "_R_CHECK_CRAN_INCOMING_CHECK_FILE_URIS_"
[5] "_R_CHECK_CRAN_INCOMING_DESCR_BAD_START_RECHECK_MAYBE_"
[6] "_R_CHECK_CRAN_INCOMING_DESCR_BAD_START_RECHECK_START_"
[7] "_R_CHECK_CRAN_INCOMING_GNU_MAKE_RECHECK_MAYBE_"
[8] "_R_CHECK_CRAN_INCOMING_GNU_MAKE_RECHECK_START_"
[9] "_R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_"
[10] "_R_CHECK_CRAN_INCOMING_SKIP_DATES_"
[11] "_R_CHECK_CRAN_INCOMING_SKIP_DOI_CHECKS_"
[12] "_R_CHECK_CRAN_INCOMING_SKIP_URL_CHECKS_IF_REMOTE_"
[13] "_R_CHECK_CRAN_INCOMING_SKIP_VERSIONS_"
[14] "_R_CHECK_CRAN_INCOMING_TITLE_CASE_RECHECK_MAYBE_"
[15] "_R_CHECK_CRAN_INCOMING_TITLE_CASE_RECHECK_START_"
[16] "_R_CHECK_CRAN_INCOMING_TITLE_INCLUDES_NAME_RECHECK_MAYBE_"
[17] "_R_CHECK_CRAN_INCOMING_TITLE_INCLUDES_NAME_RECHECK_START_"
[18] "_R_CHECK_CRAN_INCOMING_USE_ASPELL_"
[19] "_R_CHECK_CRAN_STATUS_SUMMARY_"
[20] "_R_CHECK_FF_AS_CRAN_"
[21] "_R_CHECK_FILE_TIMES_TOL_"
[22] "_R_CHECK_FUTURE_FILE_TIMESTAMPS_LEEWAY_"
[23] "_R_CHECK_MAINTAINER_ADDRESS_"
[24] "_R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_"
[25] "_R_CHECK_PACKAGE_DEPENDS_IGNORE_MISSING_ENHANCES_"
[26] "_R_CHECK_PACKAGES_USED_CRAN_INCOMING_NOTES_"
[27] "_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_"
[28] "_R_CHECK_RD_CONTENTS_KEYWORDS_"
[29] "_R_CHECK_SIZE_OF_TARBALL_"
[30] "_R_CHECK_SRC_MINUS_W_SOMETIMES_UNINITIALIZED_"
[31] "_R_CHECK_STANGLE_WARNINGS_"
[32] "_R_CHECK_SUPPRESS_RANDR_MESSAGE_"
[33] "_R_CHECK_UNLOAD_NAMESPACES_"
[34] "_R_CHECK_URLS_USE_CURL_"
[35] "_R_CHECK_VIGNETTE_TITLES_"
[36] "_R_CHECK_VIGNETTES_SKIP_RUN_MAYBE_"
Some of these (including _R_CHECK_CODOC_VARIABLES_IN_USAGES_) may be
intended for internal use only; I'm not even certain the others are
used
in the checks. All I was looking for were patterns in the source using
grep -r _R_CHECK_ *
and within those lines I assumed ones with the pattern
Sys.getenv("...")
were actually environment variables being used, and ones in files in
the
doc directory were documented. The ones listed above appear to be used
but not documented.
Duncan Murdoch
>
> Best,
> Miguel.
>
> --
> Luis M. Rodriguez-R, Ph.D.
> [ https://rodriguez-r.com
Re: [R-pkg-devel] Bug in checks in R-devel (was: Data docs)
The Matrix package explicitly sets LazyData to "no" with a note saying that
it is necessary.
LazyData: no
LazyDataNote: not possible, since we use data/*.R *and* our classes
My notes on implementing install.packages() in TERR include
When R's install.packages() processes *.R files in the package's data
directory, they may use functions defined in the package's R directory,
whether or not LazyData is yes or no.
If LazyData is no (but not if yes), then the *.R files in data can refer to
files copied from pkg/inst/blah to pkg/blah.
TERR must be able to do this to install the Matrix package from source.
Hence changing the default to "yes" may break the installation of some
packages.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Sun, Oct 27, 2019 at 12:35 PM Duncan Murdoch
wrote:
> On 27/10/2019 6:04 a.m., Luis-Miguel Rodríguez Rojas wrote:
> > Thanks a lot Xavier!
> > This solved my issue.
>
> This seems like a simple workaround for the bug. Perhaps "LazyData:
> yes" should become the default. I don't know what are the advantages of
> the current "LazyData: no" default.
>
> BTW, another issue is that the environment variable controlling this
> test, "_R_CHECK_CODOC_VARIABLES_IN_USAGES_", doesn't appear to be
> documented. I did a fairly rough search through the sources for other
> undocumented check variables, and found this list:
>
> [1] "_R_CHECK_CODOC_VARIABLES_IN_USAGES_"
> [2] "_R_CHECK_CRAN_INCOMING_ASPELL_RECHECK_MAYBE_"
> [3] "_R_CHECK_CRAN_INCOMING_ASPELL_RECHECK_START_"
> [4] "_R_CHECK_CRAN_INCOMING_CHECK_FILE_URIS_"
> [5] "_R_CHECK_CRAN_INCOMING_DESCR_BAD_START_RECHECK_MAYBE_"
> [6] "_R_CHECK_CRAN_INCOMING_DESCR_BAD_START_RECHECK_START_"
> [7] "_R_CHECK_CRAN_INCOMING_GNU_MAKE_RECHECK_MAYBE_"
> [8] "_R_CHECK_CRAN_INCOMING_GNU_MAKE_RECHECK_START_"
> [9] "_R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_"
> [10] "_R_CHECK_CRAN_INCOMING_SKIP_DATES_"
> [11] "_R_CHECK_CRAN_INCOMING_SKIP_DOI_CHECKS_"
> [12] "_R_CHECK_CRAN_INCOMING_SKIP_URL_CHECKS_IF_REMOTE_"
> [13] "_R_CHECK_CRAN_INCOMING_SKIP_VERSIONS_"
> [14] "_R_CHECK_CRAN_INCOMING_TITLE_CASE_RECHECK_MAYBE_"
> [15] "_R_CHECK_CRAN_INCOMING_TITLE_CASE_RECHECK_START_"
> [16] "_R_CHECK_CRAN_INCOMING_TITLE_INCLUDES_NAME_RECHECK_MAYBE_"
> [17] "_R_CHECK_CRAN_INCOMING_TITLE_INCLUDES_NAME_RECHECK_START_"
> [18] "_R_CHECK_CRAN_INCOMING_USE_ASPELL_"
> [19] "_R_CHECK_CRAN_STATUS_SUMMARY_"
> [20] "_R_CHECK_FF_AS_CRAN_"
> [21] "_R_CHECK_FILE_TIMES_TOL_"
> [22] "_R_CHECK_FUTURE_FILE_TIMESTAMPS_LEEWAY_"
> [23] "_R_CHECK_MAINTAINER_ADDRESS_"
> [24] "_R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_"
> [25] "_R_CHECK_PACKAGE_DEPENDS_IGNORE_MISSING_ENHANCES_"
> [26] "_R_CHECK_PACKAGES_USED_CRAN_INCOMING_NOTES_"
> [27] "_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_"
> [28] "_R_CHECK_RD_CONTENTS_KEYWORDS_"
> [29] "_R_CHECK_SIZE_OF_TARBALL_"
> [30] "_R_CHECK_SRC_MINUS_W_SOMETIMES_UNINITIALIZED_"
> [31] "_R_CHECK_STANGLE_WARNINGS_"
> [32] "_R_CHECK_SUPPRESS_RANDR_MESSAGE_"
> [33] "_R_CHECK_UNLOAD_NAMESPACES_"
> [34] "_R_CHECK_URLS_USE_CURL_"
> [35] "_R_CHECK_VIGNETTE_TITLES_"
> [36] "_R_CHECK_VIGNETTES_SKIP_RUN_MAYBE_"
>
> Some of these (including _R_CHECK_CODOC_VARIABLES_IN_USAGES_) may be
> intended for internal use only; I'm not even certain the others are used
> in the checks. All I was looking for were patterns in the source using
>
>grep -r _R_CHECK_ *
>
> and within those lines I assumed ones with the pattern Sys.getenv("...")
> were actually environment variables being used, and ones in files in the
> doc directory were documented. The ones listed above appear to be used
> but not documented.
>
> Duncan Murdoch
>
> >
> > Best,
> > Miguel.
> >
> > --
> > Luis M. Rodriguez-R, Ph.D.
> > [ https://rodriguez-r.com
[R-pkg-devel] WinBuilder Debian: GnuTLS recv error
Hi,
I tried to use curl in examples and get the following error:
GnuTLS recv error (-110): The TLS connection was non-properly terminated.
Can I solve this without dontrun?
Below code of example and traceback:
> # detect encoding of the web pages content
> if (require("curl")) {
+ fetch_url <- function(u) curl_fetch_memory(u)$content
+ detect_raw_enc(fetch_url("https://www.corriere.it;))
+ detect_raw_enc(fetch_url("https://www.vk.com;))
+ detect_raw_enc(fetch_url("https://www.qq.com;))
+ detect_raw_enc(fetch_url("https://kakaku.com;))
+ detect_raw_enc(fetch_url("https://www.incruit.com/;))
+ }
Loading required package: curl
Error in curl_fetch_memory(u) :
GnuTLS recv error (-110): The TLS connection was non-properly terminated.
Calls: detect_raw_enc -> fetch_url -> curl_fetch_memory
Execution halted
--
Artem Klevtsov
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