[Bioc-devel] package that will not build under Windows with Rtools35 (but works with Rtools40)

Ramon Diaz-Uriarte rd|@z02 @end|ng |rom gm@||@com
Wed Jun 12 15:24:12 CEST 2019

Hi Hervé,

Thank you for your reply; I understand the constraints and limitations. So
I'll look into the second solution you suggest (and will wait for Rtools40
to become the default toolchain).



On Wed, 12-June-2019, at 01:11:38, Pages, Herve <hpages using fredhutch.org> wrote:
> Hi Ramon,
> We try to not be adventurous with what we put on the build machines so
> we'd like to stick to whatever Rtools version is officially the current
> stable one.
> Also we don't have a mechanism for switching to a different package
> code base or branch on some platforms. This wouldn't be a good idea
> anyway because then Windows users trying to install the source package
> would get something different than what they get when installing the
> binary. This would maybe be acceptable if the source and binaries had
> different versions but I can't think of any versioning scheme that would
> both allow you to handle this and play nice with Bioconductor versioning
> scheme.
> So I'm afraid the 2 only solutions for now are:
>    1) Let the package fail on the Windows builder (we can mark it
>       as unsupported on Windows).
>    2) Use conditionals in your code (e.g. "if (platform is Windows)
>       then do this else do that") to make the new functionality available
>       on non Windows platforms. With this solution, Windows users
>       will be able to use everything in the package except this new
>       functionality.
> HTH,
> H.
> On 6/4/19 04:13, Ramon Diaz-Uriarte wrote:
>> Dear All,
>> (Follow up to
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2019-2DMay_015151.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_6xTfTTU7Nf_ytIv4RV3f0dN5rUUFrfwJu3b0_3lqsY&s=PtKX7VQrfC7KQbl6O-yXaEKys9IGQuUBSMVKtJ1EnO0&e= )
>> The newest version of a package we develop, OncoSimulR[1] cannot be built
>> with Rtools35, the current toolchain[2], because of a known problem where
>> compilation and linking fail[3].
>> However, we can build the package with Rtools40, and that produces a
>> binary zip file that works with current R-3.6.0, R-3.6.0 patched, and
>> R-devel.
>> Is there any way to make the new functionality available through BioC in
>> all the platforms? (I understand the answer is probably "no", since testing
>> under Windows would not be possible with the current Rtools35 toolchain).
>> Alternatively, is it possible to have some platforms use one code base or
>> branch in a repo, and another platform (Windows) use a different code
>> base/branch (i.e., use a code base without the new functionality so that it
>> can build and check OK with Rtools 35)?
>> Of course, any other suggestions welcome.
>> Thanks,
>> R.
>> [1]
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_release_bioc_html_OncoSimulR.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_6xTfTTU7Nf_ytIv4RV3f0dN5rUUFrfwJu3b0_3lqsY&s=MJq-nWf5OPsjWdfA_AO_5FQlFgHJDfSHzOpL3ldX4js&e=
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rdiaz02_OncoSimul_tree_freq-2Ddep-2Dfitness&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_6xTfTTU7Nf_ytIv4RV3f0dN5rUUFrfwJu3b0_3lqsY&s=uWPj2OmSHXduU9GTa2HuDAfSjT77Q643cHo7-dgLSw0&e=
>> [2] https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_bin_windows_Rtools_&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_6xTfTTU7Nf_ytIv4RV3f0dN5rUUFrfwJu3b0_3lqsY&s=AcfE1hiD6aC6pTBm2dLCoPLanwoDo0DabfZagD3k4jk&e=
>> [3] The "too many sections" error or the linker never finishing. E.g.,
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_p_mingw-2Dw64_discussion_723797_thread_c6b70624_&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_6xTfTTU7Nf_ytIv4RV3f0dN5rUUFrfwJu3b0_3lqsY&s=VyV58euSzIx7Bw678kuf3VQ-StYVUZT1r-gYuUA0qiU&e=
>> --
>> Ramon Diaz-Uriarte
>> Department of Biochemistry, Lab B-25
>> Facultad de Medicina
>> Universidad Autónoma de Madrid
>> Arzobispo Morcillo, 4
>> 28029 Madrid
>> Spain
>> Phone: +34-91-497-2412
>> Email: rdiaz02 using gmail.com
>>         ramon.diaz using iib.uam.es
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__ligarto.org_rdiaz&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_6xTfTTU7Nf_ytIv4RV3f0dN5rUUFrfwJu3b0_3lqsY&s=r6FEs_1DV66f_CPzlq__0vNjOtoYXaTZCdjSATihXmY&e=
>> _______________________________________________
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>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_6xTfTTU7Nf_ytIv4RV3f0dN5rUUFrfwJu3b0_3lqsY&s=5oVrYps_p71fghBetRc49b8su8Q5Ufdze9XyUlo8ZKI&e=

Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid

Phone: +34-91-497-2412

Email: rdiaz02 using gmail.com
       ramon.diaz using iib.uam.es


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