[Bioc-devel] Error in tokay2

[Romero, Juan Pablo]

Thanks to both Valerie and Hervé for all the comments with this problem.


Just to let you know, I encountered with this problem while developing the algorithm, initially. In both windows and mac, I wasn't able to run R CMD Check locally due to the same error. In both machines I did a new installation of R and all the packages again and that solved the problem for Mac but not for Windows.


Thanks Again!


Best,


Juan Pablo


> 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

>>>

________________________________
From: Hervé Pagès <hpages at fredhutch.org>
Sent: Monday, April 17, 2017 1:51:48 AM
To: Obenchain, Valerie; Romero, Juan Pablo; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Error in tokay2

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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>
>
> This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: hpages at fredhutch.org
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