[Bioc-devel] Problem for Biostrings?

[Hervé Pagès]

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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