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

4 messages · Gmail2, Martin Morgan

Original
Gmail2
# 
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.


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...


Can you please help me with these two issues? Thank you very much!

Best regards,

Xiaobin
Martin Morgan
#
On 03/22/2016 08:34 AM, Gmail2 wrote:
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.
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
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1 day later
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
Martin Morgan
#
On 03/24/2016 05:08 AM, Gmail2 wrote:
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.
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
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