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

[Gmail2]

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 <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)”.




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.


Best regards,

Xiaobin


> On 22 Mar 2016, at 13:55, Martin Morgan <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
>> 
>> 
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>> 
> 
> 
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