Bill Dunlap
2021-Jul-22 18:18 UTC
[Rd] [R-pkg-devel] Tracking down inconsistent errors and notes across operating systems
A small example of the problem is
#define USE_RINTERNALS 1
#include <R.h>
#include <Rinternals.h>
#include <Rdefines.h>
static s_object* obj = NULL;
Prior to 2021-07-20, with svn 80639, this compiled but after, svn 80647,
that I get
$ gcc -I"/mnt/c/R/R-svn/trunk/src/include" -I. -I/usr/local/include
-fpic -g -O2 -flto -c s_object.c 2>&1
In file included from s_object.c:5:
/mnt/c/R/R-svn/trunk/src/include/Rdefines.h:168:33: error: unknown type
name ?SEXPREC?
168 | #define s_object SEXPREC
| ^~~~~~~
s_object.c:7:8: note: in expansion of macro ?s_object?
7 | static s_object* obj = NULL;
| ^~~~~~~~
On Thu, Jul 22, 2021 at 10:18 AM Bill Dunlap <williamwdunlap at gmail.com>
wrote:
> I think the problem with RPostgreSQL/sec/RS-DBI.c comes from some changes
> to Defn.h and Rinternals.h in RHOME/include that Luke made recently
> (2021-07-20, svn 80647). Since then the line
> #define s_object SEXPREC
> in Rdefines.h causes problems. Should it now be 'struct SEXPREC'?
>
> -Bill
>
>
> On Thu, Jul 22, 2021 at 7:04 AM I?aki Ucar <iucar at
fedoraproject.org>
> wrote:
>
>> Hi,
>>
>> On Thu, 22 Jul 2021 at 15:51, Hannah Owens <hannah.owens at
gmail.com>
>> wrote:
>> >
>> > Hi all,
>> > I am working on an update to a package I have on CRAN called
occCite. My
>> > latest release attempt didn?t pass incoming automated checks,
because
>> there
>> > is an outstanding error. Additionally, there are some weird notes
I
>> would
>> > like to get rid of, if anyone has suggestions.
>> >
>> > The killing error is in r-devel-linux-x86_64-debian-gcc, which is:
>> Packages
>> > required but not available: 'BIEN', 'taxize',
?RPostgreSQL'
>> >
>> > I don?t understand this, as it is the only system that throws this
>> error,
>> > and the packages mentioned are available via CRAN. Any
suggestions?
>>
>> This kind of message usually arises when there is some problem with
>> those packages on CRAN. Indeed,
>>
>> https://cran.r-project.org/web/checks/check_results_BIEN.html
>> https://cran.r-project.org/web/checks/check_results_taxize.html
>> https://cran.r-project.org/web/checks/check_results_RPostgreSQL.html
>>
>> the three of them have ERRORs in that platform. No issue on your end.
>> You reply pointing to that.
>>
>> > Additionally, there are multiple platforms
>> > (r-devel-linux-x86_64-fedora-clang;
r-devel-linux-x86_64-fedora-gcc;
>> > r-devel-windows-x86_64-gcc10-UCRT; r-patched-solaris-x86;
>> > r-release-macos-arm64; r-release-macos-x86_64;
r-oldrel-macos-x86_64)
>> where
>> > two notes pop up:
>> >
>> > NOTE 1: Namespace in Imports field not imported from: ?bit64? All
>> declared
>> > Imports should be used.
>> >
>> > The package does use bit64. Any tips on how to address this note?
>>
>> Are you sure? Your NAMESPACE file does not import(bit64) nor
>> importFrom(bit64,) anything.
>>
>> > NOTE 2: Found 6 marked UTF-8 strings.
>> >
>> > I presume this is thrown because of the small sample dataset I?ve
>> included
>> > in the package, but why is it not thrown for all the platforms?
>>
>> Not all the checks are necessarily done in all the platforms. You can
>> silence this NOTE by converting the offending strings in your datasets
>> to ASCII and resaving them.
>>
>> --
>> I?aki ?car
>>
>> ______________________________________________
>> R-package-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>
[[alternative HTML version deleted]]
iuke-tier@ey m@iii@g oii uiow@@edu
2021-Jul-22 19:22 UTC
[Rd] [External] Re: [R-pkg-devel] Tracking down inconsistent errors and notes across operating systems
Thanks; fix committed in r80654. Best, luke On Thu, 22 Jul 2021, Bill Dunlap wrote:> A small example of the problem is? > #define USE_RINTERNALS 1 > #include <R.h> > #include <Rinternals.h> > #include <Rdefines.h> > static s_object* obj = NULL; > > Prior to 2021-07-20, with svn 80639, this compiled but after, svn 80647, > that I get > > $ gcc -I"/mnt/c/R/R-svn/trunk/src/include" -I. ? -I/usr/local/include ? > -fpic ?-g -O2 -flto -c s_object.c 2>&1 > In file included from s_object.c:5: > /mnt/c/R/R-svn/trunk/src/include/Rdefines.h:168:33: error: unknown type name > ?SEXPREC? > ? 168 | #define s_object ? ? ? ? ? ? ? ?SEXPREC > ? ? ? | ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ^~~~~~~ > s_object.c:7:8: note: in expansion of macro ?s_object? > ? ? 7 | static s_object* obj = NULL; > ? ? ? | ? ? ? ?^~~~~~~~ > > > > On Thu, Jul 22, 2021 at 10:18 AM Bill Dunlap <williamwdunlap at gmail.com> > wrote: > I think the problem with RPostgreSQL/sec/RS-DBI.c comes from > some changes to Defn.h and Rinternals.h in RHOME/include that > Luke made recently (2021-07-20, svn 80647).? Since then the > line? ?#define s_object SEXPREC > in Rdefines.h causes problems.? Should it now be 'struct SEXPREC'? > > -Bill > > > On Thu, Jul 22, 2021 at 7:04 AM I?aki Ucar <iucar at fedoraproject.org> > wrote: > Hi, > > On Thu, 22 Jul 2021 at 15:51, Hannah Owens > <hannah.owens at gmail.com> wrote: > > > > Hi all, > > I am working on an update to a package I have on CRAN > called occCite. My > > latest release attempt didn?t pass incoming automated > checks, because there > > is an outstanding error. Additionally, there are some > weird notes I would > > like to get rid of, if anyone has suggestions. > > > > The killing error is in r-devel-linux-x86_64-debian-gcc, > which is: Packages > > required but not available: 'BIEN', 'taxize', > ?RPostgreSQL' > > > > I don?t understand this, as it is the only system that > throws this error, > > and the packages mentioned are available via CRAN. Any > suggestions? > > This kind of message usually arises when there is some > problem with > those packages on CRAN. Indeed, > > https://cran.r-project.org/web/checks/check_results_BIEN.html > https://cran.r-project.org/web/checks/check_results_taxize.html > https://cran.r-project.org/web/checks/check_results_RPostgreSQL.html > > the three of them have ERRORs in that platform. No issue > on your end. > You reply pointing to that. > > > Additionally, there are multiple platforms > > (r-devel-linux-x86_64-fedora-clang; > r-devel-linux-x86_64-fedora-gcc; > > r-devel-windows-x86_64-gcc10-UCRT; > r-patched-solaris-x86; > > r-release-macos-arm64; r-release-macos-x86_64; > r-oldrel-macos-x86_64) where > > two notes pop up: > > > > NOTE 1: Namespace in Imports field not imported from: > ?bit64? All declared > > Imports should be used. > > > > The package does use bit64. Any tips on how to address > this note? > > Are you sure? Your NAMESPACE file does not import(bit64) > nor > importFrom(bit64,) anything. > > > NOTE 2: Found 6 marked UTF-8 strings. > > > > I presume this is thrown because of the small sample > dataset I?ve included > > in the package, but why is it not thrown for all the > platforms? > > Not all the checks are necessarily done in all the > platforms. You can > silence this NOTE by converting the offending strings in > your datasets > to ASCII and resaving them. > > -- > I?aki ?car > > ______________________________________________ > R-package-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > >-- Luke Tierney Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics and Fax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: luke-tierney at uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu