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

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Tue Apr 9 16:41:17 CEST 2019 

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<mailto: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
>
>
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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<mailto: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<mailto:hpages using fredhutch.org>
Phone:  (206) 667-5791
Fax:    (206) 667-1319


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