[Bioc-devel] "vdiffr" package load fail on celaya2

Tue Apr 9 17:35:00 CEST 2019

Hey Herve,

Yes this explains everything. Now I understand the building systems and
availability better.
It was not clear to me before that different versions of the package could
have different availability.

Many thanks for your clear answer,

Jurrian

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On Tue, Apr 9, 2019 at 4:41 PM Pages, Herve <hpages using fredhutch.org> wrote:

> Hi Jurrian,
>
> Let's keep this conversation on the list.
> On 4/9/19 01:43, Jurrian de Kanter wrote:
>
> Hello Herve,
>
> Thank you for your quick reaction!
> Good to know that it has been an issue before and that I can ignore it.
> Will my package still be included in bioconductor 3.9 though?
> I expect that nobody is going to check the errors manually before the
> release,
> so that would mean automatic exclustion due to this error, or do I
> misunderstand.
>
> The current situation only affects the availability of the CHETAH **Mac
> binary**. As you can see on the package landing page here
>
>   https://master.bioconductor.org/packages/CHETAH
> <https://master.bioconductor.org/packages/3.9/bioc/html/CHETAH.html>
>
> the source package and Windows binary are already available in BioC 3.9
> and so are not affected.
>
> When the gdtools Mac binary becomes available for R 3.6 on CRAN, here is
> what should happen (in this order):
>
>   1) Our build system will pick it up and install it on the Mac builders
>
>   2) CHETAH will be able to pass CHECK on the Mac builders
>
>   3) The CHETAH Mac binary will be allowed to propagate and so will show
> up on the package landing page next to the source package and Windows
> binary, and will become available via BiocManager::install() to BioC 3.9
> users.
>
> So we're just hoping that the gdtools Mac binary will become available
> soon.
>
> If it doesn't become available in time for the release, then Mac users
> won't be able to install CHETAH (unless they know how to install packages
> from source). But that will be a temporary situation only, until the
> gdtools Mac binary becomes available.
>
> Hope this helps,
>
> H.
>
>
>
> Thank you for your time,
>
> Jurrian de Kanter
>
>
>
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> On Sun, Apr 7, 2019 at 10:34 PM Pages, Herve <hpages using fredhutch.org> wrote:
>
>> Hi Jurrian,
>>
>> Many Mac binary packages for R 3.6 are still not available on CRAN.
>> gdtools (which CHETAH indirectly depends on, via the vdiffr package) is
>> one of them:
>>
>> https://cran.r-project.org/package=gdtools
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_package-3Dgdtools&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=2y3uBzesEzjNWMJIdx58GP6F6XQRp5SWkF_1byBDAPU&s=6YYnMJ5lB0bmEgLdngHNyPDuTtsec6TVYeL_NPGGX6I&e=>
>>
>> Other Bioconductor packages that fail because they depend (directly or
>> indirectly) on gdtools are: arrayQualityMetrics, CHETAH, ggcyto, and
>> SpatialCPie.
>>
>> Unfortunately, until the gdtools Mac binary becomes available for R 3.6,
>> these 4 Bioconductor packages cannot reliably be tested on our Mac
>> builders. So please ignore the error for now.
>>
>> Finally note that the non-availability of the Mac binary packages for R
>> 3.6 on CRAN has been plaguing our Mac builds for months. See for example:
>>
>> https://stat.ethz.ch/pipermail/bioc-devel/2018-December/014443.html
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2018-2DDecember_014443.html&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=2y3uBzesEzjNWMJIdx58GP6F6XQRp5SWkF_1byBDAPU&s=2DJbf3gJmUF6rYMftnIspDOpSIk-9q8toYe5rsnrtN4&e=>
>>
>> https://stat.ethz.ch/pipermail/bioc-devel/2019-March/014727.html
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2019-2DMarch_014727.html&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=2y3uBzesEzjNWMJIdx58GP6F6XQRp5SWkF_1byBDAPU&s=Fo6N3PaENO4Y1MtMm-JO0uR5WKM00XqB3ZybAyUXrvY&e=>
>>
>> Cheers,
>>
>> H.
>>
>>
>> On 4/7/19 09:55, Jurrian de Kanter wrote:
>> > Dear bioc-developers,
>> >
>> > I hope I am in the right place here. I did not know where else to ask
>> > my question.
>> > I am new to bioconductor. My package "CHETAH", has just been accepted
>> > two weeks ago.
>> > During the review process, my package failed on the Mac machines
>> > checks, because the package
>> > "vdiffr" that I use to check my plotting functions, fails to load on
>> > these machines. (error at the end of this mail)
>> >
>> > My reviewer recognized that this was not something that I could fix,
>> > and accepted my package.
>> > Now, this error also occurred in the build of the development branch,
>> > but the release schedule states that a package has to check
>> > without errors before the release of 3.9.
>> >
>> > My question is the following: what can I do or whom should I contact
>> > to fix this? I would like to keep my plotting checks, but if this
>> > doesn't change, I will get rid of those checks.
>> >
>> > Thanks in advance for any anwser,
>> >
>> > Jurrian de Kanter
>> >
>> > The error:
>> >
>> > Error: package or namespace load failed for 'vdiffr' in dyn.load(file,
>> > DLLpath = DLLpath, ...):
>> >     unable to load shared object
>> >
>> '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so':
>> >
>> dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so,
>> > 6): Symbol not found: _FT_Done_Face
>> >      Referenced from:
>> >
>> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so
>> >      Expected in: flat namespace
>> >     in
>> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so
>> >    Execution halted
>> >
>> >
>> > <
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com_email-2Dsignature-3Futm-5Fmedium-3Demail-26utm-5Fsource-3Dlink-26utm-5Fcampaign-3Dsig-2Demail-26utm-5Fcontent-3Dwebmail&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=raKu6m0UnhoHL1tY8ZD_HhuNaKhISyXcwy0muODEZRE&s=wPQlHgePRGFH_21mqlTCMISZ9xdgV6sPOAof1oWlrl4&e=
>> >
>> > Virusvrij.
>> > www.avg.com
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>> > <
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>> > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>> >
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>> >
>> > _______________________________________________
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>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages using fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>>
>
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> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages using fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>

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