[Bioc-devel] Error in tokay2

[Hervé Pagès]

but not GenomicFeatures, which is another victim of this
install.packages bug:

 
https://bioconductor.org/checkResults/3.5/bioc-LATEST/GenomicFeatures/tokay2-checksrc.html

AFAICS we've been seeing this problem on tokay2 (Windows) almost every
day for the last few weeks. I guess it started after we updated R to a
more recent R 3.4 on this machine. So I suspect a change in R somehow
triggered this.

H.

On 04/15/2017 08:02 PM, Obenchain, Valerie wrote:
> EventPointer 0.99.36 built clean today:
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioconductor.org_checkResults_devel_bioc-2DLATEST_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=auvr-W1IWGGZ6bEm2_E4MMb1dYZxyOJiJEHxw8ffrPk&s=ZxAUJxS48UK2FAs1mcQeAC2XXy0-eiv9SW4OyyOUZDs&e=
>
> Valerie
>
>
>
> On 04/14/2017 09:16 AM, Obenchain, Valerie wrote:
>> Hi Juan Pablo,
>>
>> We think this is a problem related to installed.packages(), see
>> discussion here:
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2017-2DApril_010819.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=auvr-W1IWGGZ6bEm2_E4MMb1dYZxyOJiJEHxw8ffrPk&s=bSGL5D0ea0jkhT_HDTBTWVccTXfXi-E7uYm4ZCy4VuY&e=
>>
>> You can ignore this for now. Thanks for keeping an eye on the build report.
>>
>> Valerie
>>
>>
>>
>>
>> On 04/14/2017 12:41 AM, Romero, Juan Pablo wrote:
>>> Hello all,
>>>
>>>
>>> I know that today is the deadline for passing R CMD build and R CMD check without errors and warnings, and my package EventPointer has been working perfectly for the last weeks.
>>>
>>>
>>> Today the build report in tokay2 shows an error in one of the examples:
>>>
>>>
>>> ** running examples for arch 'x64' ... ERROR
>>>
>>>
>>> Make the TxDb object ... Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
>>>   missing value where TRUE/FALSE needed
>>>
>>>
>>> The error is coming from the function makeTxDbFromGFF and the error does not come from functions from
>>>
>>> my package.
>>>
>>>
>>> Is anybody having a similar error?
>>>
>>>
>>> I will appreciate any help on this to avoid problems related with adding the package to the new release.
>>>
>>>
>>> Thanks!
>>>
>>>
>>> Best regards,
>>>
>>>
>>> Juan Pablo
>>>
>>>
>>> 	[[alternative HTML version deleted]]
>>>
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>>
>>
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-- 
Hervé Pagès

Program in Computational Biology
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