[Bioc-devel] Check report error on Windows platform

[Jiping Wang]

Hi Shuyu,

  Thanks so much for your comment.

  In my example codes, I didn’t include `proc.time()` anywhere. It seems NuPoP-Ex.R was automatically generated in R CMD check, and proc.time() was called in this procedure for some reason. I am not sure whether this is the reason to cause the error.

Best,
jiping

From: Zheng, Shuyu <shuyu.zheng using helsinki.fi>
Date: Wednesday, August 10, 2022 at 3:34 AM
To: Hervé Pagès <hpages.on.github using gmail.com>, Jiping Wang <jzwang using northwestern.edu>, bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Check report error on Windows platform
Hi Jiping,

The log on https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/NuPoP/palomino4-checksrc.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!VDw5z1b-SiC_KOmb4rLVIuDYOrcb5NMnIz6illT5E_O_GEcOLI3hL89RsEttBCW-T27M0dPUzFHRgTI1QJWwERzV3BYcTAc$<https://urldefense.com/v3/__https:/bioconductor.org/checkResults/devel/bioc-LATEST/NuPoP/palomino4-checksrc.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!VDw5z1b-SiC_KOmb4rLVIuDYOrcb5NMnIz6illT5E_O_GEcOLI3hL89RsEttBCW-T27M0dPUzFHRgTI1QJWwERzV3BYcTAc$>   shows the error is from examples in "NuPoP-Ex.R".  You called " base::assign(".ptime", proc.time(), pos = "CheckExEnv")" in this file. If you check the doc for function "proc.time()". There is a statement " Times of child processes are not available on Windows and will always be given as NA."

I guess this is the source of the error.

Best,
Shuyu


On 09/08/2022, 00:41, "Bioc-devel on behalf of Hervé Pagès" <bioc-devel-bounces using r-project.org on behalf of hpages.on.github using gmail.com> wrote:

    Hi jiping,

    I suspect R dies during the call to predNuPoP(). Could this be related
    to the recent changes you made to the master branch of the package, in
    particular to changes to the Fortran code? Note that the Fortran
    compiler of the Mac builder emits a warning about the size of the
    'trann4' array being unsafe:

    https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.16/bioc-LATEST/NuPoP/lconway-install.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!VDw5z1b-SiC_KOmb4rLVIuDYOrcb5NMnIz6illT5E_O_GEcOLI3hL89RsEttBCW-T27M0dPUzFHRgTI1QJWwERzVduRr4gs$<https://urldefense.com/v3/__https:/bioconductor.org/checkResults/3.16/bioc-LATEST/NuPoP/lconway-install.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!VDw5z1b-SiC_KOmb4rLVIuDYOrcb5NMnIz6illT5E_O_GEcOLI3hL89RsEttBCW-T27M0dPUzFHRgTI1QJWwERzVduRr4gs$>

    We don't see this warning on the Mac builder in release so may it's an
    issue that got introduced recently?

    https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.15/bioc-LATEST/NuPoP/merida1-install.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!VDw5z1b-SiC_KOmb4rLVIuDYOrcb5NMnIz6illT5E_O_GEcOLI3hL89RsEttBCW-T27M0dPUzFHRgTI1QJWwERzVBp6dfmU$<https://urldefense.com/v3/__https:/bioconductor.org/checkResults/3.15/bioc-LATEST/NuPoP/merida1-install.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!VDw5z1b-SiC_KOmb4rLVIuDYOrcb5NMnIz6illT5E_O_GEcOLI3hL89RsEttBCW-T27M0dPUzFHRgTI1QJWwERzVBp6dfmU$>

    On a different note, could you please remove the files in the
    NuPoP/inst/doc/ folder? These files don't belong to git (they get
    automatically generated and added to the package source tarball by 'R
    CMD build').

    Thanks,

    H.


    On 08/08/2022 07:24, Jiping Wang wrote:
    > Hi,
    >
    > Could anyone give some hints on the check errors of my package for windows system? It seems everything was fine for linux and macs. Please see checkResults page below. Thanks.
    >
    > Best,
    > jiping
    >
    > https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/NuPoP/palomino4-checksrc.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!VDw5z1b-SiC_KOmb4rLVIuDYOrcb5NMnIz6illT5E_O_GEcOLI3hL89RsEttBCW-T27M0dPUzFHRgTI1QJWwERzV3BYcTAc$<https://urldefense.com/v3/__https:/bioconductor.org/checkResults/devel/bioc-LATEST/NuPoP/palomino4-checksrc.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!VDw5z1b-SiC_KOmb4rLVIuDYOrcb5NMnIz6illT5E_O_GEcOLI3hL89RsEttBCW-T27M0dPUzFHRgTI1QJWwERzV3BYcTAc$>
    >
    >
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    --
    Hervé Pagès

    Bioconductor Core Team
    hpages.on.github using gmail.com

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