[Bioc-devel] Problem for Biostrings?

[Hai Fang]

Thanks Herve for resolving it. Best, Hai

Sent from my iPhone

> On 30 Mar 2017, at 06:42, Hervé Pagès <hpages at fredhutch.org> wrote:
> 
> Hi Hai,
> 
> Looks you added CRAN ggforce recently (in February) to the Suggests
> field of Pi. ggforce depends on CRAN package udunits2, which itself
> requires system library libudunits2 in order to compile on Linux,
> which itself can be installed with
> 
>  sudo apt-get install libudunits2-dev
> 
> on Debian/Ubuntu.
> 
> We didn't have libudunits2-dev on malbec2 yet so I just installed it.
> The fact that we didn't have it indicates that Pi is the first
> Bioconductor package to (indirectly) require it.
> 
> If everything goes as expected, Pi should turn all green on Friday.
> 
> Cheers,
> H.
> 
> 
>> On 03/29/2017 09:08 PM, hfang.shanghai wrote:
>> Thanks for the clarification. Now everything is ok except the check in Linux (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Pi_malbec2-2Dchecksrc.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE&s=0Y-86XDQL67bMUlLmRJOg3cEWekH9GHDJNrc5ZEStPg&e= ). The package 'ggforce' is not preinstalled in Linux (others seem fine).
>> 
>> Best, Hai
>> 
>> Sent from my iPhone
>> 
>>> On 29 Mar 2017, at 17:17, Michael Lawrence <lawrence.michael at gene.com> wrote:
>>> 
>>> It's actually an error in rtracklayer.
>>> 
>>> On Wed, Mar 29, 2017 at 8:28 AM, Shepherd, Lori
>>> <Lori.Shepherd at roswellpark.org> wrote:
>>>> That is correct.  When the Biostrings package is corrected this ERROR in your package should resolve automatically.
>>>> 
>>>> 
>>>> Lori Shepherd
>>>> 
>>>> Bioconductor Core Team
>>>> 
>>>> Roswell Park Cancer Institute
>>>> 
>>>> Department of Biostatistics & Bioinformatics
>>>> 
>>>> Elm & Carlton Streets
>>>> 
>>>> Buffalo, New York 14263
>>>> 
>>>> ________________________________
>>>> From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Hai Fang <hfang at well.ox.ac.uk>
>>>> Sent: Wednesday, March 29, 2017 10:28:39 AM
>>>> To: bioc-devel at r-project.org
>>>> Subject: [Bioc-devel] Problem for Biostrings?
>>>> 
>>>> Hi,
>>>> 
>>>> I got the error ��object ��inverted�� is not exported by 'namespace:Biostrings�� at https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Pi_&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE&s=2bhT9aV6mJhSUF8Iq3BZHB_Y2EVt0wNFx6ZcylnnUaE&e= . It  seems due to the package ��Biostrings�� which failed to pass the check (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Biostrings_&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE&s=COIN8OGj-Nd6NzWJEoBq6sXBbJLSqHoZpwPKuGe8DH8&e= ). Is it right or something else?
>>>> 
>>>> Thanks,
>>>> 
>>>> Hai
>>>> 
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> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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> 
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