[R-pkg-devel] warning: type of ‘zhpevx_’ does not match original declaration [-Wlto-type-mismatch]
Dear all, The problem: I struggle to solve a WARNING that is shown on the CRAN system but not on my side when I use "R-devel check --as-cran IndependenceTests". This seems to be related to the declaration of a LAPACK Fortran subroutine (zhpevx) that I call from C. I could not find any hint on Google allowing me to solve the issue. I read the following sections of the "Writing R Extensions" manual (but could not understand how to solve the problem): * 4.5 Using Link Time Optimization * 6.6 Calling C from Fortran and vice versa Maybe the solution is obvious, but not to me. The warning shown on CRAN is: checking whether package �IndependenceTests� can be installed ... [11s/11s] WARNING Found the following significant warnings: myzhpevx.cpp:13:23: warning: type of �zhpevx_� does not match original declaration [-Wlto-type-mismatch] Other feedback I received from the CRAN team: Professor Brian Ripley suggested the two pieces of advice below (which I believe to have followed): * For registering/interfacing Fortran calls, gfortran -c -fc-prototypes-external is the best way to extract a prototype (with gfortran >= 9.2). If this includes int_least32_t, see the comment below on Fortran-LOGICAL. hint). * Fortran subroutines correspond to C void functions What is the current state of my source code: I have a Fortran subroutine (defined in the file src/zhpevx.f at line 232): SUBROUTINE zhpevx( JOBZ, RANGE, UPLO, N, AP, VL, VU, IL, IU, $ abstol, m, w, z, ldz, work, rwork, iwork, $ ifail, info ) This subroutine is declared (in file myzhpevx.cpp at line 13) as follows: void F77_NAME(zhpevx)(char *jobz, char *range, char *uplo, const int *n, Rcomplex *ap, const double *vl, const double *vu, const int *il, const int *iu, const double *abstol, int *m, double *w, Rcomplex *z, const int *ldz, Rcomplex *work, double *rwork, int *iwork, int *ifail, int *info, FC_LEN_T jobz_len, FC_LEN_T range_len, FC_LEN_T uplo_len); Source package can be downloaded here: http://biostatisticien.eu/IndependenceTests_0.5.tar.gz My system: Linux Debian 10 Buster Last version of R-devel Many thanks in advance for your help. Best regards, Pierre Lafaye de Micheaux Associate Professor UNSW Sydney Co-op Academic Coordinator for Data Science & Decisions and Advanced Maths Tel.: (00.[+612]) 9385 7029 School of Mathematics and Statistics http://web.maths.unsw.edu.au/~lafaye/UNSW Sydney, NSW 2052, AUSTRALIA Beginning of all science is the surprise that things are what they are (Aristotle). C'est par l'exemple et la coh�rence qu'on arrive � convaincre (P. Rabhi). [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] NOTE from checking for detritus in the temp directory
Dear All, I got a NOTE from CRAN: ** checking for detritus in the temp directory ... NOTEFound the following files/directories: ‘calibre_4.99.6_tmp_lezpx205’ ‘calibre_4.99.6_tmp_mzjswhrh’ ‘calibre_4.99.6_tmp_zc8txrmi’ ‘calibre_4.99.6_tmp_zw0pp8wj’* DONEStatus: 1 NOTE* Here is the log file for the CRAN check. (At the bottom, you can find the above NOTE.) https://win-builder.r-project.org/incoming_pretest/rQCC_1.20.7_20200702_112950/Debian/00check.log When I checked my package, there was no detritus in the temp dir. I tested my package using the command below: > rhub::platforms() > rhub::check_for_cran(platforms = "debian-clang-devel") > rhub::check_for_cran(platforms = "debian-gcc-devel" ) > rhub::check_for_cran(platforms = "debian-gcc-devel-nold" ) > rhub::check_for_cran(platforms = "debian-gcc-patched" ) > rhub::check_for_cran(platforms = "debian-gcc-release" ) As shown below, it says "OK" https://artifacts.r-hub.io/rQCC_1.20.7.tar.gz-66c588542824483db19cdc9130c715c4/ Please help me if you know how to fix the detritus issue in the temp dir. Thanks, CP [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE from checking for detritus in the temp directory
Most likely this is because you start a web browser in your examples or tests. Try to find where that happens, and don't run it that example or test case on CRAN. Gabor On Sat, Jul 4, 2020 at 1:46 PM Applied Statistics Laboratory wrote: > > Dear All, > > I got a NOTE from CRAN: > > > > > > > > ** checking for detritus in the temp directory ... NOTEFound the following > files/directories: ‘calibre_4.99.6_tmp_lezpx205’ > ‘calibre_4.99.6_tmp_mzjswhrh’ ‘calibre_4.99.6_tmp_zc8txrmi’ > ‘calibre_4.99.6_tmp_zw0pp8wj’* DONEStatus: 1 NOTE* > Here is the log file for the CRAN check. (At the bottom, you can find the > above NOTE.) > > https://win-builder.r-project.org/incoming_pretest/rQCC_1.20.7_20200702_112950/Debian/00check.log > > > > When I checked my package, there was no detritus in the temp dir. I tested > my package using the command below: > > > rhub::platforms() > > rhub::check_for_cran(platforms = "debian-clang-devel") > > rhub::check_for_cran(platforms = "debian-gcc-devel" ) > > rhub::check_for_cran(platforms = "debian-gcc-devel-nold" ) > > rhub::check_for_cran(platforms = "debian-gcc-patched" ) > > rhub::check_for_cran(platforms = "debian-gcc-release" ) > > As shown below, it says "OK" > > https://artifacts.r-hub.io/rQCC_1.20.7.tar.gz-66c588542824483db19cdc9130c715c4/ > > Please help me if you know how to fix the detritus issue in the temp dir. > > Thanks, > CP > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE from checking for detritus in the temp directory
Thanks Gábor, I removed all the URLs in the *.Rd files and resubmitted to CRAN. I got the same NOTE again as below: After removing the URLs in the *.Rd : https://win-builder.r-project.org/incoming_pretest/rQCC_1.20.7_20200704_161730/Debian/00check.log Just in case, the below is the NOTE before removing the ULRs in the Rd: https://win-builder.r-project.org/incoming_pretest/rQCC_1.20.7_20200702_112950/Debian/00check.log I have this trouble after adding vignettes. So my guess is that this NOTE may be from vignette. I checked the package using rhub::check_for_cran with all the platforms. They do not have this kind of issue. Only CRAN produces this NOTE. My vignette is written in *.Rnw (essentially the same as LaTeX format). When the vignette file is compiled, some aux files are generated. So, I think that CRAN may not delete aux files properly. Thanks, CP On Sat, Jul 4, 2020 at 9:48 PM Gábor Csárdi wrote: > Most likely this is because you start a web browser in your examples > or tests. Try to find where that happens, and don't run it that > example or test case on CRAN. > > Gabor > > On Sat, Jul 4, 2020 at 1:46 PM Applied Statistics Laboratory > wrote: > > > > Dear All, > > > > I got a NOTE from CRAN: > > > > > > > > > > > > > > > > ** checking for detritus in the temp directory ... NOTEFound the > following > > files/directories: ‘calibre_4.99.6_tmp_lezpx205’ > > ‘calibre_4.99.6_tmp_mzjswhrh’ ‘calibre_4.99.6_tmp_zc8txrmi’ > > ‘calibre_4.99.6_tmp_zw0pp8wj’* DONEStatus: 1 NOTE* > > Here is the log file for the CRAN check. (At the bottom, you can find the > > above NOTE.) > > > > > https://win-builder.r-project.org/incoming_pretest/rQCC_1.20.7_20200702_112950/Debian/00check.log > > > > > > > > When I checked my package, there was no detritus in the temp dir. I > tested > > my package using the command below: > > > > > rhub::platforms() > > > rhub::check_for_cran(platforms = "debian-clang-devel") > > > rhub::check_for_cran(platforms = "debian-gcc-devel" ) > > > rhub::check_for_cran(platforms = "debian-gcc-devel-nold" ) > > > rhub::check_for_cran(platforms = "debian-gcc-patched" ) > > > rhub::check_for_cran(platforms = "debian-gcc-release" ) > > > > As shown below, it says "OK" > > > > > https://artifacts.r-hub.io/rQCC_1.20.7.tar.gz-66c588542824483db19cdc9130c715c4/ > > > > Please help me if you know how to fix the detritus issue in the temp dir. > > > > Thanks, > > CP > > > > [[alternative HTML version deleted]] > > > > __ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > -- Applied Statistics Laboratory https://sites.google.com/view/appliedstatlab [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE from checking for detritus in the temp directory
URLs are fine, the problem is with opening external programs like a
web browser or a PDF viewer. I think you do that here:
https://github.com/AppliedStat/R/blob/8e4173da8917caf0f4f68d4056902075fb9013c2/rQCC/man/factors.cc.Rd#L118
https://github.com/AppliedStat/R/blob/8e4173da8917caf0f4f68d4056902075fb9013c2/rQCC/man/rcc.Rd#L297
Maybe at other places as well.
If you want to open the vignette from the example, maybe you can try
something like
if (interactive()) vignette("factors.cc", package="rQCC")
so it does not run in R CMD check.
Gabor
On Sun, Jul 5, 2020 at 12:51 AM Applied Statistics Laboratory
wrote:
>
> Thanks Gábor,
>
> I removed all the URLs in the *.Rd files and resubmitted to CRAN.
>
> I got the same NOTE again as below:
>
> After removing the URLs in the *.Rd :
> https://win-builder.r-project.org/incoming_pretest/rQCC_1.20.7_20200704_161730/Debian/00check.log
>
> Just in case, the below is the NOTE before removing the ULRs in the Rd:
> https://win-builder.r-project.org/incoming_pretest/rQCC_1.20.7_20200702_112950/Debian/00check.log
>
> I have this trouble after adding vignettes.
> So my guess is that this NOTE may be from vignette.
> I checked the package using rhub::check_for_cran with all the platforms.
> They do not have this kind of issue.
> Only CRAN produces this NOTE. My vignette is written in *.Rnw (essentially
> the same as LaTeX format).
> When the vignette file is compiled, some aux files are generated. So, I think
> that CRAN may not delete aux files properly.
>
> Thanks,
> CP
>
>
>
> On Sat, Jul 4, 2020 at 9:48 PM Gábor Csárdi wrote:
>>
>> Most likely this is because you start a web browser in your examples
>> or tests. Try to find where that happens, and don't run it that
>> example or test case on CRAN.
>>
>> Gabor
>>
>> On Sat, Jul 4, 2020 at 1:46 PM Applied Statistics Laboratory
>> wrote:
>> >
>> > Dear All,
>> >
>> > I got a NOTE from CRAN:
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > ** checking for detritus in the temp directory ... NOTEFound the following
>> > files/directories: ‘calibre_4.99.6_tmp_lezpx205’
>> > ‘calibre_4.99.6_tmp_mzjswhrh’ ‘calibre_4.99.6_tmp_zc8txrmi’
>> > ‘calibre_4.99.6_tmp_zw0pp8wj’* DONEStatus: 1 NOTE*
>> > Here is the log file for the CRAN check. (At the bottom, you can find the
>> > above NOTE.)
>> >
>> > https://win-builder.r-project.org/incoming_pretest/rQCC_1.20.7_20200702_112950/Debian/00check.log
>> >
>> >
>> >
>> > When I checked my package, there was no detritus in the temp dir. I tested
>> > my package using the command below:
>> >
>> > > rhub::platforms()
>> > > rhub::check_for_cran(platforms = "debian-clang-devel")
>> > > rhub::check_for_cran(platforms = "debian-gcc-devel" )
>> > > rhub::check_for_cran(platforms = "debian-gcc-devel-nold" )
>> > > rhub::check_for_cran(platforms = "debian-gcc-patched" )
>> > > rhub::check_for_cran(platforms = "debian-gcc-release" )
>> >
>> > As shown below, it says "OK"
>> >
>> > https://artifacts.r-hub.io/rQCC_1.20.7.tar.gz-66c588542824483db19cdc9130c715c4/
>> >
>> > Please help me if you know how to fix the detritus issue in the temp dir.
>> >
>> > Thanks,
>> > CP
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > __
>> > R-package-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
>
> --
> Applied Statistics Laboratory
>
> https://sites.google.com/view/appliedstatlab
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE from checking for detritus in the temp directory
Dear Gábor,
Thanks so much for your suggestions. Now my problems are solved.
Best wishes,
CP
On Sun, Jul 5, 2020 at 9:52 AM Gábor Csárdi wrote:
> URLs are fine, the problem is with opening external programs like a
> web browser or a PDF viewer. I think you do that here:
>
>
> https://github.com/AppliedStat/R/blob/8e4173da8917caf0f4f68d4056902075fb9013c2/rQCC/man/factors.cc.Rd#L118
>
> https://github.com/AppliedStat/R/blob/8e4173da8917caf0f4f68d4056902075fb9013c2/rQCC/man/rcc.Rd#L297
>
> Maybe at other places as well.
>
> If you want to open the vignette from the example, maybe you can try
> something like
>
> if (interactive()) vignette("factors.cc", package="rQCC")
>
> so it does not run in R CMD check.
>
> Gabor
>
> On Sun, Jul 5, 2020 at 12:51 AM Applied Statistics Laboratory
> wrote:
> >
> > Thanks Gábor,
> >
> > I removed all the URLs in the *.Rd files and resubmitted to CRAN.
> >
> > I got the same NOTE again as below:
> >
> > After removing the URLs in the *.Rd :
> >
> https://win-builder.r-project.org/incoming_pretest/rQCC_1.20.7_20200704_161730/Debian/00check.log
> >
> > Just in case, the below is the NOTE before removing the ULRs in the Rd:
> >
> https://win-builder.r-project.org/incoming_pretest/rQCC_1.20.7_20200702_112950/Debian/00check.log
> >
> > I have this trouble after adding vignettes.
> > So my guess is that this NOTE may be from vignette.
> > I checked the package using rhub::check_for_cran with all the
> platforms. They do not have this kind of issue.
> > Only CRAN produces this NOTE. My vignette is written in *.Rnw
> (essentially the same as LaTeX format).
> > When the vignette file is compiled, some aux files are generated. So, I
> think that CRAN may not delete aux files properly.
> >
> > Thanks,
> > CP
> >
> >
> >
> > On Sat, Jul 4, 2020 at 9:48 PM Gábor Csárdi
> wrote:
> >>
> >> Most likely this is because you start a web browser in your examples
> >> or tests. Try to find where that happens, and don't run it that
> >> example or test case on CRAN.
> >>
> >> Gabor
> >>
> >> On Sat, Jul 4, 2020 at 1:46 PM Applied Statistics Laboratory
> >> wrote:
> >> >
> >> > Dear All,
> >> >
> >> > I got a NOTE from CRAN:
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > ** checking for detritus in the temp directory ... NOTEFound the
> following
> >> > files/directories: ‘calibre_4.99.6_tmp_lezpx205’
> >> > ‘calibre_4.99.6_tmp_mzjswhrh’ ‘calibre_4.99.6_tmp_zc8txrmi’
> >> > ‘calibre_4.99.6_tmp_zw0pp8wj’* DONEStatus: 1 NOTE*
> >> > Here is the log file for the CRAN check. (At the bottom, you can find
> the
> >> > above NOTE.)
> >> >
> >> >
> https://win-builder.r-project.org/incoming_pretest/rQCC_1.20.7_20200702_112950/Debian/00check.log
> >> >
> >> >
> >> >
> >> > When I checked my package, there was no detritus in the temp dir. I
> tested
> >> > my package using the command below:
> >> >
> >> > > rhub::platforms()
> >> > > rhub::check_for_cran(platforms = "debian-clang-devel")
> >> > > rhub::check_for_cran(platforms = "debian-gcc-devel" )
> >> > > rhub::check_for_cran(platforms = "debian-gcc-devel-nold" )
> >> > > rhub::check_for_cran(platforms = "debian-gcc-patched" )
> >> > > rhub::check_for_cran(platforms = "debian-gcc-release" )
> >> >
> >> > As shown below, it says "OK"
> >> >
> >> >
> https://artifacts.r-hub.io/rQCC_1.20.7.tar.gz-66c588542824483db19cdc9130c715c4/
> >> >
> >> > Please help me if you know how to fix the detritus issue in the temp
> dir.
> >> >
> >> > Thanks,
> >> > CP
> >> >
> >> > [[alternative HTML version deleted]]
> >> >
> >> > __
> >> > R-package-devel@r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
> >
> >
> > --
> > Applied Statistics Laboratory
> >
> > https://sites.google.com/view/appliedstatlab
>
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
