[Bioc-devel] some fixed bugs are not displayed properly in website

[Martin Morgan]

On 03/24/2016 05:08 AM, Gmail2 wrote:
> Dear Martin,
>
> Thanks for your helpful reply. I bumped the release version into 1.0.1
> and now it’s available in the website
> “http://bioconductor.org/packages/3.2/bioc/html/SICtools.html”. However,
> when I try to install it by command
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("SICtools")
>
>
> it got an error as “package SICtools is not available (for R version
> 3.1.0)”.

no need to include the screenshot, just the text output.

Note the 'Using Bioconductor version 3.0' line. The current release (the 
first release where SICtools was available) is 3.2 -- your Bioconductor 
(and R) are too old. Update R and update BiocInstaller via 
biocLite("BiocUpgrade") (or by remove.packages("BiocInstaller"); 
source("https://bioconductor.org/biocLite.R")).

As a developer you want to be using the 'devel' version of Bioconductor, 
which at the moment is available when using the R-3-3-branch version of R.

>
>
>
> As for your second concerning, we compiled a custom executable samtools,
> the output of which could improve indel detection and can’t be obtained
> by Rsamtools directly,… This is also the reason that the package can’t
> be used in Windows platform right now. We already have a plan to change
> this in future but not at this version.

To be sure we're talking about the same thing, I mean that you can use 
the samtools library created by Rsamtools in your own C code; you do not 
need to provide an implementation of any thing in

I see that there are minor differences in the source code in files 
shared by SICtools/src and Rsamtools/src/samtools, but I think these are 
either due to differences in samtools version (Rsamtools is slightly 
more recent; neither version is exactly 'current') or to additions to 
the Rsamtools version that have been made in response to bug reports.

I see also that there are additional files in SICtools not in Rsamtools; 
I guess these are your additions.

Why not link to the Rsamtools libraries in your own code, removing the 
duplicated code?

Martin

>
>
> Best regards,
>
> Xiaobin
>
>
>> On 22 Mar 2016, at 13:55, Martin Morgan <Martin.Morgan at roswellpark.org
>> <mailto:Martin.Morgan at roswellpark.org>> wrote:
>>
>>
>>
>> On 03/22/2016 08:34 AM, Gmail2 wrote:
>>> Dear Bioc-dev guys,
>>>
>>> I recently fixed some bugs in my package SICtools and commit the
>>> changes into Release_3_2. To my surprise, it seems that the source in
>>> the website
>>> (http://bioconductor.org/packages/3.2/bioc/html/SICtools.html
>>> <http://bioconductor.org/packages/3.2/bioc/html/SICtools.html>) was
>>> not updated at all.
>>>
>>> 1) On obvious discrepancy is that I replaced doMC with doParallel,
>>> however, in the Depends part, still doMC is displayed; and I checked
>>> the source, it’s still the old one.
>>
>> Remember that bug fixes only belong in release. Are all the changes
>> you've committed bug fixes?
>>
>> Did you remember to bump the version (to 1.0.1 in the release, 1.1.1
>> in devel)? If not the package is built but not pushed to the public
>> repository.
>>
>>
>>>
>>>
>>> 2) One more thing, when I try to install the package using
>>>
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("SICtools")
>>>
>>> I got an error message “Warning message: package ‘SICtools’ is not
>>> available”. Anyway, it should be installed even for the old version...
>>
>> What is your sessionInfo() ? As with any bug report it is helpful to
>> provide the full output of the command.
>>
>> It seems like your package is not supported on windows
>>
>> http://bioconductor.org/checkResults/3.2/bioc-LATEST/SICtools/zin1-buildsrc.html
>>
>> Too bad, why is that??
>>
>> And also it looks like you've got your own version of samtools in
>> there, which is also too bad --
>>
>> PLEASE REUSE Rsamtools or Rhtslib, both of which install across
>> platforms and have vignettes illustrating how the C code can be used
>> across packages.
>>
>> Martin
>>
>>>
>>>
>>> Can you please help me with these two issues? Thank you very much!
>>
>>
>>
>>>
>>> Best regards,
>>>
>>> Xiaobin
>>>
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
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