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

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Sun Apr 7 22:33:58 CEST 2019

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:


Other Bioconductor packages that fail because they depend (directly or 
indirectly) on gdtools are: arrayQualityMetrics, CHETAH, ggcyto, and 

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:





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
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