Re: [Bioc-devel] Error in tokay2

2017-04-15 Thread Obenchain, Valerie 
EventPointer 0.99.36 built clean today:

http://www.bioconductor.org/checkResults/devel/bioc-LATEST/

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://stat.ethz.ch/pipermail/bioc-devel/2017-April/010819.html
>
> 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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Re: [Bioc-devel] build on different version

2017-04-15 Thread Obenchain, Valerie 
Version 1.11.10 posted today:

http://www.bioconductor.org/checkResults/devel/bioc-LATEST/

For now I would not worry about the error on toluca2.

Valerie


On 04/14/2017 02:42 AM, Robert Castelo wrote:
> hi,
>
> on tuesday april 11th i checked in changes for VariantFiltering version 
> 1.11.10 and i've seen that today the build for tuesday gives errors on 
> version 1.11.9 with snapshot date from april 7th. i do my devel changes 
> in the github repo rcastelo/VariantFiltering and check them into SVN, 
> often with difficulties, but i always check that the SVN repo has the 
> latest version and builds and checks fine, currently that's the case 
> since i see it at 1.11.10.
>
> so, is there anything i can do on my side or is this just a matter of 
> waiting to the next build?
>
> thanks!
>
> robert.
>
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Re: [Bioc-devel] Error in BUILD report (anamiR)

2017-04-15 Thread Obenchain, Valerie 
It looks like this has been resolved on today's report:

http://www.bioconductor.org/checkResults/devel/bioc-LATEST/

Valerie


On 04/07/2017 02:21 PM, 王棣台 wrote:
> Hi all,
>
> I got en error when it tries to create vignette in BUILD:
> tokay2  Windows Server 2012 R2 Standard / x64
>
> Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics:
> could not run statement: Lost connection to MySQL server during query
>
> But for Linux or Mac, it all works.
> I have no idea how to solve this problem.
>
> Many thanks,
> Ti-Tai
>
>   [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5

2017-04-15 Thread Ramon Diaz-Uriarte 
Hi Hervé,



On Sat, 15-04-2017, at 05:36:35, Hervé Pagès  wrote:
> Hi Ramon,
>
> Good news: looks like a Cairo binary for R 3.4 showed up on CRAN
> yesterday:
>
>https://cran.r-project.org/bin/macosx/el-capitan/contrib/3.4/
>
> I installed it on veracruz2, and, according to the logs of the
> current builds, ADaCGH2 built and checked successfully on this

Great!

> machine :-) If everything goes well, this should be reflected
> in the next build report (Sat Apr 15).
>
> Thanks again for your patience,

Thank you and Martin for looking into this and letting me know.


Best,


R.

>
> Cheers,
> H.
>
>
> On 04/08/2017 06:34 AM, Ramon Diaz-Uriarte wrote:
>>
>> Dear Martin,
>>
>>
>> On Fri, 07-04-2017, at 12:55:55, Martin Morgan 
>>  wrote:
>>> On 04/07/2017 03:55 AM, Ramon Diaz-Uriarte wrote:

 Dear Martin and Valerie,


 I am not sure how to proceed here since the 14th is approaching and I still
 see this error (in both my package and at least one other package
 ---arrayQualityMetrics).


 I could comment out the plotting code for the vignette and examples when
 running on El Capitan. Is this a possible workaround that I should
>>>
>>> In general this is the wrong thing to do, since it enables shipping
>>> broken code with no possibility of future fixes. Be patient. Martin
>>
>> Thanks for your answer. I'll be patient :-)
>>
>> (Just to clarify: I understand that what I was proposing was an ugly
>> kludge; I think I have misunderstood the issue; apologies for the noise)
>>
>> Best,
>>
>> R.
>>
>>>
 implement? If this is reasonable, what is the recommended way to find out
 the code is running in El Capitan and not Mavericks? (For instance, can I
 tell from Sys.info()["sysname"]? --I do not have access to a Mac).


 Martin mentioned that the Cairo package requires a binary installation that
 is not yet available.  Should I continue to wait? There is not a lot of
 margin for changing the code, uploading to BioC, waiting for the build, and
 making sure it works.  What if it continues to fail on El Capitan by the
 14th?



 Best,


 R.




 On Mon, 03-04-2017, at 18:34:26, Martin Morgan 
  wrote:
> On 03/31/2017 04:19 AM, Ramon Diaz-Uriarte wrote:
>>
>> Dear All,
>>
>> A package I maintain, ADaCGH2, is failing to build in veracruz2 with a
>> segfault that seems to happen when plotting (in a call to plotting that
>> happens inside a mclapply)
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ADaCGH2_veracruz2-2Dbuildsrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=67SOhhQ_xN5IxOZP7n-Vuvtn1Da8u3G6YqpEVI4fTsw=yu6OVUP4gT1jkj9xheyXRvn5-tHhTOM1X3QgpWRr4DE=
>>
>>
>> these are some of the lines of the traceback:
>>
>> Traceback:
>>  1: dev.hold()
>>  2: plot.default(c(2925836, 5135683.5, 6415674.5, 7169722, 9715199, 
>> 13220514.5, 15307852, 41589471, 44534348, 47975338, 52729020, 54225865, 
>> 54970734, 55406435.5, 57169693.5, 57359284.5, 66362289.5, 69947314.5, 
>> 72243027.5, 75218239, 75268559.5, 75683700, 76272391, 76901797, 
>> 77282738, 83724180, 88707195.5, 89536816.5, 102463647.5, 104082964, 
>> 107610854, 108945724, 120577571, 122947762.5, 124680401, 129086592, 
>> 144839226, 148940008.5, 154240128.5, 155887373.5, 178034441.5, 
>> 184199138, 184552484), c(0.397, 0.002, -0.179, -0.1385, -0.095, -0.611, 
>> -0.165, -0.54, -0.358, 0.172, -0.2435, -0.044, -0.048, 0.078, -0.344, 
>> -0.139, -0.513, -0.681, -0.406, 0.083, -0.325, -0.186, -0.138, 0.393, 
>> -0.075, -0.655, 0.123, -0.346, -0.099, -0.3465, 0.463, -0.18, -0.101, 
>> -0.175, -0.101, 0.371, -0.642, -0.13, -0.33, -0.491, 0.138, -0.187, 
>> 0.21), ylab = "log ratio", xlab = quote("Chromosomal location"), col 
>> = c("orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange"), cex = 1, axes = FALSE, main = quote("Chr4@L.1"), pch = 20)
>>  3: plot(c(2925836, 5135683.5, 6415674.5, 7169722, 9715199, 13220514.5, 
>> 15307852, 41589471, 44534348, 47975338, 52729020, 54225865, 54970734, 
>> 55406435.5, 57169693.5, 57359284.5, 66362289.5, 69947314.5, 72243027.5, 
>> 75218239, 75268559.5, 75683700, 76272391, 76901797, 77282738, 83724180, 
>> 88707195.5, 89536816.5,