Re: [Bioc-devel] rsvg on mac

[Obenchain, Valerie]

Yes, when a new version appears on CRAN it is automatically picked up by the 
build machines.

Valerie


 On 05/14/2018 05:04 AM, Kevin Horan wrote:

Valerie,

Sorry, I think my memory of what the actual problem was was wrong. I have 
spoken to the rsvg author and he has now fixed the build of rsvg in CRAN for OS 
X. So will that then just get automatically put on your machines, or else, 
would it now be possible to manually put it on? Sorry for all the confusion, 
and thanks for you help.

ChemmineR is green now because I removed the functions requiring rsvg to 
get it through the release. They were new functions anyway.

Kevin

On 05/09/2018 03:25 PM, Obenchain, Valerie wrote:
Kevin,

I feel like we're not on the same page. We've had this discussion and both 
Herve and I tried to explain the situation:

  https://stat.ethz.ch/pipermail/bioc-devel/2018-February/012812.html

We do not build CRAN packages from source on the Windows and Mac build 
machines. If a CRAN binary is not available for one of your dependencies, e.g., 
rsvg, the best thing for you to do is contact the maintainer or post on the 
r-sig-mac mailing list:

  https://stat.ethz.ch/mailman/listinfo/r-sig-mac

However, ChemmineR is green on both release and devel build reports. I'm not 
sure why you are asking us (again) to install the rsvg system dependency on the 
Mac builders. Did I misunderstand what you wanted?

Valerie


On 05/09/2018 07:41 AM, Kevin Horan wrote:

Now that this past bioc release is done, and R 3.5 is stable, would it be 
possible to install the "rsvg" package on your build machines? Thanks.

Kevin

On 02/19/2018 02:01 PM, Alexey Sergushichev wrote:
Valerie, thanks. Will try to ask there.

However, after looking through the mailing list it looks like R-devel builds 
for OS X aren't trivial and aren't part of CRAN...

--
Alexey

On Mon, Feb 19, 2018 at 9:05 PM, Obenchain, Valerie 
> 
wrote:
Hi,

There has been some discussion of the devel Mac binaries on the R-SIG-Mac 
mailing list. That list would be the best place to ask this question.

https://stat.ethz.ch/pipermail/r-sig-mac/2018-January/thread.html

Valerie



On 02/19/2018 08:32 AM, Alexey Sergushichev wrote:
Valerie,

Are there any estimates on how often CRAN OS X builds happen? There are still 
no builds for rsvg and other packages...

Thanks,
Alexey

On Wed, Feb 7, 2018 at 8:09 PM, Obenchain, Valerie 
> 
wrote:
Hi Kevin,

CRAN binaries for El Capitan in devel aren't available. You can see this on the 
rsvg landing page:

https://cran.r-project.org/web/packages/rsvg/index.html

Nothing we can do until CRAN makes them available.

Valerie


On 02/07/2018 08:29 AM, Kevin Horan wrote:


The ChemmineR build is failing on the mac due to a new dependency not
being available, the package "rsvg". Would it be possible to install
that on the mac build machine? Thanks.

http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html


Kevin

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Re: [Bioc-devel] [Fwd: Problem showing a GRanges with a meta data column of data frame]

[Jialin Ma]

Hi Hervé,

Thanks a lot for addressing it!

Best regards,
Jialin


On Tue, 2018-05-15 at 09:02 -0700, Hervé Pagès wrote:
> Hi Jialin,
> 
> Thanks for the report. This should be fixed in BioC 3.7 (S4Vectors
> 0.18.2 and IRanges 2.14.10) and BioC devel (S4Vectors 0.19.3 and
> IRanges 2.15.11).
> 
> The updated packages will become available via biocLite() in the
> next 24h (if everything goes as expected).
> 
> Best,
> H.
> 
> On 05/14/2018 07:38 PM, Jialin Ma wrote:
> > Sorry, forgot to attach the session info:
> > 
> > sessionInfo()
> > R version 3.5.0 (2018-04-23)
> > Platform: x86_64-suse-linux-gnu (64-bit)
> > Running under: openSUSE Tumbleweed
> > 
> > Matrix products: default
> > BLAS: /usr/lib64/R/lib/libRblas.so
> > LAPACK: /usr/lib64/R/lib/libRlapack.so
> > 
> > locale:
> >   [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
> >   [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> >   [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> >   [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
> >   [9] LC_ADDRESS=C   LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> > 
> > attached base packages:
> > [1] parallel  stats4stats graphics  grDevices
> > utils datasets
> > [8] methods   base
> > 
> > other attached packages:
> > [1] GenomicRanges_1.32.2 GenomeInfoDb_1.16.0  IRanges_2.14.8
> > [4] S4Vectors_0.18.1 BiocGenerics_0.26.0  magrittr_1.5
> > 
> > loaded via a namespace (and not attached):
> > [1]
> > zlibbioc_1.26.0compiler_3.5.0 XVector_0.20.0
> > [4] tools_3.5.0GenomeInfoDbData_1.1.0 RCurl_1.95-
> > 4.10
> > [7] yaml_2.1.19bitops_1.0-6
> > 
> > 
> >  Forwarded Message 
> > From: Jialin Ma 
> > To: bioc-devel 
> > Subject: Problem showing a GRanges with a meta data column of data
> > frame
> > Date: Tue, 15 May 2018 10:17:35 +0800
> > Mailer: Evolution 3.24.4
> > 
> > > Hi all,
> > > 
> > > I recently upgraded R to 3.5 and use the new release of
> > > Bioconductor.
> > > The new version of S4Vectors seems to have problem showing a
> > > GRanges
> > > with a meta-data column of a data frame. One simplified example
> > > is:
> > > 
> > > gr <- GRanges('chr2', IRanges(1, 11))
> > > gr$df <- data.frame(a = 32)
> > > 
> > > rep(gr, 11) ## No error
> > > 
> > > rep(gr, 12) ## Error when printing
> > > # GRanges object with 12 ranges and 1 metadata column:
> > > # Error in .Call2("vector_OR_factor_extract_ranges", x, start,
> > > width,
> > > PACKAGE = "S4Vectors") :
> > > #   'end' must be <= 'length(x)'
> > > 
> > > Any help would be appreciated!
> > > 
> > > Best regards,
> > > Jialin
> > > 
> > > 
> > 
> > ___
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> > 
> 
> 

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Re: [Bioc-devel] Package download when using functions from affy and oligo

[Ben Bolstad]

One of the CEL files is truncated or otherwise corrupted. The 
appropriate place to really detect that is in the code that reads the 
CEL file data and appropriately warn or error to the user.


The bug below occurs because of a massive mismatch between the 
assumptions of the RMA background model (essentially the modal spike at 
0 intensity throws it completely off) and I think the only time I've see 
it occur in the past was also with corrupted data. Any which way a 
segfault is a less than desirable outcome.


Ben

On 2018-05-14 17:11, Martin Morgan wrote:

One of your cell files is funky


colSums(exprs(alldata) == 0)

GSM907854.CEL.gz GSM907866.CEL.gz GSM907857.CEL.gz GSM907863.CEL.gz
   000   686388
GSM907856.CEL.gz GSM907862.CEL.gz GSM907855.CEL.gz GSM907861.CEL.gz
   0000

and it's tickling a bug in preprocessCore

$ R -d gdb -f testOligo.R
...
0x7fffe190418a in max_density (z=0x7fffcc0008c0, rows=0, cols=1, 
column=0)

at rma_background4.c:128
128 rma_background4.c: No such file or dire

(gdb) dir /home/mtmorgan/b/git/preprocessCore/src/
Source directories searched: 
/home/mtmorgan/b/git/preprocessCore/src:$cdir:$cwd

(gdb) l
123
124   max_y = find_max(dens_y,16384);
125
126   i = 0;
127   do {
128 if (dens_y[i] == max_y)
129   break;
130 i++;
131
132   } while(1);
(gdb) p i
$1 = 1821306
(gdb) p max_y


Maybe one of the preprocessCore pros will chime in...

Martin

On 05/14/2018 09:15 AM, Joris Meys wrote:

Dear all,

sorry for the delayed response, due to some unfortunate events I had 
to

prioritize my family the past week.

You find an RStudio project in a zipped folder on this link :
https://jorismeys.stackstorage.com/s/3ik0vMwsvueuT5a

It contains a script called testOligo.R that can be sourced and nukes 
my R

session in the second step of the rma() function. It also contains the
faulty .gz files. If you need more information, don't hesitate to 
contact

me.

Regarding improving general maintainability, I'm willing to help out 
on
that. Problem is that I'm rather behind with my own work, so I'm short 
on
time for the moment. I'll fork affy tomorrow (need to give class now) 
and

let's start from there then?

Cheers
Joris



On Sat, May 5, 2018 at 5:17 PM, Vincent Carey 


wrote:


How about a google drive?  This problem of autodownloading should be
addressed directly.
These facilities are still important but their maintenance is clearly 
a

lower priority as the
technologies handled have diminished use in the field.  I think we 
should
be able to team up and remove autoinstallation elements of these 
packages,

and
perhaps improve general maintainability -- Joris, can you pick
one, make a github repo that we can collaborate on revising, and then
we can start?  It will involve a deprecation process.

On Sat, May 5, 2018 at 10:54 AM, Joris Meys  
wrote:



Thank you for the answer.

I was trying to create a reproducible example before I vented maybe 
a bit

too much in my previous mail.

I managed to get closer to the problem and it is related to data 
that was
corrupted at download. I can send you a reproducible example that 
bombs R,
but I will have to send the specific data files as well. How do I 
send

them
best?

Cheers
Joris

On Sat, 5 May 2018, 00:09 James W. MacDonald,  
wrote:


I think there are multiple complaints here, so I'll take them one 
at a

time.

On Fri, May 4, 2018 at 3:56 PM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:


Joris,

Sorry I don't have much to offer here. I've cc'd the authors of 
oligo

and

affy who may have some insight.

Valerie


On 05/02/2018 11:35 AM, Joris Meys wrote:

Dear,

I've noticed that using certain functions in affy and oligo (eg
oligo::read.celfiles and affy::bg.correct) start with downloading

another

package and end with either R crashing or a warning that -after
installation succeeded- the package is not available.



This is true for oligo, and perhaps a bit annoying. If you don't 
have

the
package installed already, it gets the package, installs it, and 
then

says

it's not available. This is an easy enough fix.


After which using

some functions of both packages still crash R.



I don't know what to do with that. What functions?




The warning I get when trying oligo::read.celfiles() on a single 
CEL

file
right after installing it about the pd.hugene.1.0.st.v1 package. 
The

even
more annoying thing is that on my machine it insists on building 
from

source, whereas on another Windows machine without Rtools, it

downloads a

binary.



That is an options setting that gets changed when you install 
Rtools.

The
'pkgType' option gets set to 'both' because you can now install 
both

kinds.

And in install.packages it ends up getting switched from 'both' to
'source'. I haven't dug any 

Re: [Bioc-devel] EXTERNAL: Re: Cannot update my development package to Bioconductor

[cstrato]

Dear Nitesh,

Thank you for pointing me to the website how to resolve the conflict.
I hope that now everything is ok.

For the records, here is what I did:

$ cd /Volumes/T3Data/CRAN/GIT/xps

$ git status
On branch master
Your branch is up-to-date with 'origin/master'.
Untracked files:
  (use "git add ..." to include in what will be committed)

.DS_Store
xps/

nothing added to commit but untracked files present (use "git add" to track)

$ git add DESCRIPTION
$ git commit -m "Fixed conflicts in version change"
[master 0d3ccd0] Fixed conflicts in version change
 1 file changed, 4 deletions(-)

$ git push origin master
Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
Counting objects: 3, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 324 bytes | 0 bytes/s, done.
Total 3 (delta 2), reused 0 (delta 0)
remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
To github.com:cstrato/xps.git
   4121457..0d3ccd0  master -> master

$ git push upstream master
Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
Counting objects: 3, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 324 bytes | 0 bytes/s, done.
Total 3 (delta 2), reused 0 (delta 0)
To git.bioconductor.org:packages/xps
   4121457..0d3ccd0  master -> master

# check in Firefox
https://github.com/cstrato/xps


Best regards,
Christian



On 05/15/18 14:50, Turaga, Nitesh wrote:

Hi

You have to fix the merge conflicts. Again, please take a look at the 
documentation on the website

The canonical documentation for git: 
http://bioconductor.org/developers/how-to/git/

The documentation relevant to your problem: 
http://bioconductor.org/developers/how-to/git/resolve-conflicts/

Best,

Nitesh


On May 15, 2018, at 8:43 AM, cstrato  wrote:

Dear Marcel,

Thank you for the clarification, now it seems to work.


However, there is a strange problem. Here is what I did:

$ cd /Volumes/T3Data/CRAN/GIT/xps

$ git remote -v
origin  g...@github.com:cstrato/xps.git (fetch)
origin  g...@github.com:cstrato/xps.git (push)
upstreamg...@git.bioconductor.org:packages/xps (fetch)
upstreamg...@git.bioconductor.org:packages/xps (push)

$ git checkout master
Already on 'master'
Your branch is up-to-date with 'origin/master'.

$ git pull upstream master
Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
remote: Counting objects: 6, done.
remote: Compressing objects: 100% (6/6), done.
remote: Total 6 (delta 4), reused 0 (delta 0)
Unpacking objects: 100% (6/6), done.
 From git.bioconductor.org:packages/xps
* branchmaster -> FETCH_HEAD
* [new branch]  master -> upstream/master
Auto-merging DESCRIPTION
CONFLICT (content): Merge conflict in DESCRIPTION
Automatic merge failed; fix conflicts and then commit the result.

$ git add -v DESCRIPTION
add 'DESCRIPTION'

$ git add -v NEWS

$ git commit -m "update for NEWS"
[master 4121457] update for NEWS

$ git push origin master
Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
Counting objects: 9, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (9/9), done.
Writing objects: 100% (9/9), 1.01 KiB | 0 bytes/s, done.
Total 9 (delta 6), reused 0 (delta 0)
remote: Resolving deltas: 100% (6/6), completed with 3 local objects.
To github.com:cstrato/xps.git
   cf326be..4121457  master -> master

$ git pull upstream master
Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
 From git.bioconductor.org:packages/xps
* branchmaster -> FETCH_HEAD
Already up-to-date.

$ git push upstream master
Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
Counting objects: 11, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (11/11), done.
Writing objects: 100% (11/11), 1.68 KiB | 0 bytes/s, done.
Total 11 (delta 8), reused 0 (delta 0)
To git.bioconductor.org:packages/xps
   aae14d1..4121457  master -> master


It seems that there was a conflict with DESCRIPTION,
so I did again 'git add DESCRIPTION'

Now everything seems to be ok, but when looking at the
DESCRIPTION file in e.g. https://github.com/cstrato/xps
the first lines of DESCRIPTION looks as follows:

Package: xps
<<< HEAD
Version: 1.41.2
===
Version: 1.41.0

aae14d1351c754876880f9b50af9da70f80034ce



Should I keep this DESCRIPTION file or delete the additional lines or update 
the DESCRIPTION file again?

Best regards,
Christian

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Re: [Bioc-devel] [Fwd: Problem showing a GRanges with a meta data column of data frame]

[Hervé Pagès]

Hi Jialin,

Thanks for the report. This should be fixed in BioC 3.7 (S4Vectors
0.18.2 and IRanges 2.14.10) and BioC devel (S4Vectors 0.19.3 and
IRanges 2.15.11).

The updated packages will become available via biocLite() in the
next 24h (if everything goes as expected).

Best,
H.

On 05/14/2018 07:38 PM, Jialin Ma wrote:

Sorry, forgot to attach the session info:

sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Tumbleweed

Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so

locale:
  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
  [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4stats graphics  grDevices
utils datasets
[8] methods   base

other attached packages:
[1] GenomicRanges_1.32.2 GenomeInfoDb_1.16.0  IRanges_2.14.8
[4] S4Vectors_0.18.1 BiocGenerics_0.26.0  magrittr_1.5

loaded via a namespace (and not attached):
[1]
zlibbioc_1.26.0compiler_3.5.0 XVector_0.20.0
[4] tools_3.5.0GenomeInfoDbData_1.1.0 RCurl_1.95-
4.10
[7] yaml_2.1.19bitops_1.0-6


 Forwarded Message 
From: Jialin Ma 
To: bioc-devel 
Subject: Problem showing a GRanges with a meta data column of data
frame
Date: Tue, 15 May 2018 10:17:35 +0800
Mailer: Evolution 3.24.4


Hi all,

I recently upgraded R to 3.5 and use the new release of Bioconductor.
The new version of S4Vectors seems to have problem showing a GRanges
with a meta-data column of a data frame. One simplified example is:

gr <- GRanges('chr2', IRanges(1, 11))
gr$df <- data.frame(a = 32)

rep(gr, 11) ## No error

rep(gr, 12) ## Error when printing
# GRanges object with 12 ranges and 1 metadata column:
# Error in .Call2("vector_OR_factor_extract_ranges", x, start, width,
PACKAGE = "S4Vectors") :
#   'end' must be <= 'length(x)'

Any help would be appreciated!

Best regards,
Jialin




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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [Bioc-devel] EXTERNAL: Re: Cannot update my development package to Bioconductor

[Turaga, Nitesh]

Hi 

You have to fix the merge conflicts. Again, please take a look at the 
documentation on the website

The canonical documentation for git: 
http://bioconductor.org/developers/how-to/git/

The documentation relevant to your problem: 
http://bioconductor.org/developers/how-to/git/resolve-conflicts/

Best,

Nitesh

> On May 15, 2018, at 8:43 AM, cstrato  wrote:
> 
> Dear Marcel,
> 
> Thank you for the clarification, now it seems to work.
> 
> 
> However, there is a strange problem. Here is what I did:
> 
> $ cd /Volumes/T3Data/CRAN/GIT/xps
> 
> $ git remote -v
> origin  g...@github.com:cstrato/xps.git (fetch)
> origin  g...@github.com:cstrato/xps.git (push)
> upstreamg...@git.bioconductor.org:packages/xps (fetch)
> upstreamg...@git.bioconductor.org:packages/xps (push)
> 
> $ git checkout master
> Already on 'master'
> Your branch is up-to-date with 'origin/master'.
> 
> $ git pull upstream master
> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
> remote: Counting objects: 6, done.
> remote: Compressing objects: 100% (6/6), done.
> remote: Total 6 (delta 4), reused 0 (delta 0)
> Unpacking objects: 100% (6/6), done.
> From git.bioconductor.org:packages/xps
> * branchmaster -> FETCH_HEAD
> * [new branch]  master -> upstream/master
> Auto-merging DESCRIPTION
> CONFLICT (content): Merge conflict in DESCRIPTION
> Automatic merge failed; fix conflicts and then commit the result.
> 
> $ git add -v DESCRIPTION
> add 'DESCRIPTION'
> 
> $ git add -v NEWS
> 
> $ git commit -m "update for NEWS"
> [master 4121457] update for NEWS
> 
> $ git push origin master
> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
> Counting objects: 9, done.
> Delta compression using up to 8 threads.
> Compressing objects: 100% (9/9), done.
> Writing objects: 100% (9/9), 1.01 KiB | 0 bytes/s, done.
> Total 9 (delta 6), reused 0 (delta 0)
> remote: Resolving deltas: 100% (6/6), completed with 3 local objects.
> To github.com:cstrato/xps.git
>   cf326be..4121457  master -> master
> 
> $ git pull upstream master
> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
> From git.bioconductor.org:packages/xps
> * branchmaster -> FETCH_HEAD
> Already up-to-date.
> 
> $ git push upstream master
> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
> Counting objects: 11, done.
> Delta compression using up to 8 threads.
> Compressing objects: 100% (11/11), done.
> Writing objects: 100% (11/11), 1.68 KiB | 0 bytes/s, done.
> Total 11 (delta 8), reused 0 (delta 0)
> To git.bioconductor.org:packages/xps
>   aae14d1..4121457  master -> master
> 
> 
> It seems that there was a conflict with DESCRIPTION,
> so I did again 'git add DESCRIPTION'
> 
> Now everything seems to be ok, but when looking at the
> DESCRIPTION file in e.g. https://github.com/cstrato/xps
> the first lines of DESCRIPTION looks as follows:
> 
> Package: xps
> <<< HEAD
> Version: 1.41.2
> ===
> Version: 1.41.0
> >>> aae14d1351c754876880f9b50af9da70f80034ce
> 
> 
> Should I keep this DESCRIPTION file or delete the additional lines or update 
> the DESCRIPTION file again?
> 
> Best regards,
> Christian
> 
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Re: [Bioc-devel] htSeqTools and giniCoverage error

[Shepherd, Lori]

But ... yes.  The package is scheduled to be removed unless it is fixed before 
the next release so it is not advisable in its current state to utilize its 
functionality.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Shepherd, Lori
Sent: Tuesday, May 15, 2018 8:30:32 AM
To: Nicolas Descostes
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] htSeqTools and giniCoverage error


You could always reach out to the maintainer to try and get them interested 
again.


Or reach out on the mailing list or support site to see if anyone else is 
interested in taking over maintaining the package.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Nicolas Descostes 
Sent: Tuesday, May 15, 2018 8:20:47 AM
To: Shepherd, Lori
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] htSeqTools and giniCoverage error

I guess I should make my package independent of it then, but that's going to 
ask some work. That's very unfortunate...

2018-05-15 7:24 GMT-04:00 Shepherd, Lori 
>:

What is your sessionInfo()? This was corrected in version 1.27.1 of the package 
so you could try updating to that version.



However,  htSeqTools is currently deprecated in Release Bioc 3.7 and currently 
scheduled to be removed in Bioc 3.8 as the maintainer has be inactive in 
maintaining the package and unresponsive to our requests to fix their package.



Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
> on 
behalf of Nicolas Descostes 
>
Sent: Sunday, May 13, 2018 1:35:05 PM
To: bioc-devel@r-project.org
Cc: oscar.re...@irbbarcelona.org
Subject: [Bioc-devel] htSeqTools and giniCoverage error

Dear all,

I am using htseqtools on the devel version and I get the following error
when using giniCoverage:

test <- lapply(endoExoBamlist, function(bam_files){
return(lapply(bam_files, function(bamfile){
ga <- if(paired)
granges(readGAligmentPairs(bamfile))
else granges(readGAlignments(bamfile))
}))
})
test2 <- lapply(test, GRangesList)
giniCoverage(sample=test2[[1]])

Simulating uniformily distributed data
Error: The RangesList() constructor is defunct. Please coerce to IRangesList
  instead e.g. do 'as(list(x1, x2), "IRangesList")' instead of
  'RangesList(x1, x2)'. Alternatively, you can use the IRangesList()
  constructor e.g. 'IRangesList(x1, x2, compress=FALSE)'. See
  '?IRangesList' for more information.
In addition: Warning messages:
1: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData
2: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData


Looking at the code it seems that the problem is coming from the line 212
of giniCoverage.R:

   RD<-RangedData(RangesList(rangesl))


Would it be possible to correct this? I am using version 1.27.0

Thanks a lot,

Nicolas

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Re: [Bioc-devel] htSeqTools and giniCoverage error

[Shepherd, Lori]

You could always reach out to the maintainer to try and get them interested 
again.


Or reach out on the mailing list or support site to see if anyone else is 
interested in taking over maintaining the package.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Nicolas Descostes 
Sent: Tuesday, May 15, 2018 8:20:47 AM
To: Shepherd, Lori
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] htSeqTools and giniCoverage error

I guess I should make my package independent of it then, but that's going to 
ask some work. That's very unfortunate...

2018-05-15 7:24 GMT-04:00 Shepherd, Lori 
>:

What is your sessionInfo()? This was corrected in version 1.27.1 of the package 
so you could try updating to that version.



However,  htSeqTools is currently deprecated in Release Bioc 3.7 and currently 
scheduled to be removed in Bioc 3.8 as the maintainer has be inactive in 
maintaining the package and unresponsive to our requests to fix their package.



Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
> on 
behalf of Nicolas Descostes 
>
Sent: Sunday, May 13, 2018 1:35:05 PM
To: bioc-devel@r-project.org
Cc: oscar.re...@irbbarcelona.org
Subject: [Bioc-devel] htSeqTools and giniCoverage error

Dear all,

I am using htseqtools on the devel version and I get the following error
when using giniCoverage:

test <- lapply(endoExoBamlist, function(bam_files){
return(lapply(bam_files, function(bamfile){
ga <- if(paired)
granges(readGAligmentPairs(bamfile))
else granges(readGAlignments(bamfile))
}))
})
test2 <- lapply(test, GRangesList)
giniCoverage(sample=test2[[1]])

Simulating uniformily distributed data
Error: The RangesList() constructor is defunct. Please coerce to IRangesList
  instead e.g. do 'as(list(x1, x2), "IRangesList")' instead of
  'RangesList(x1, x2)'. Alternatively, you can use the IRangesList()
  constructor e.g. 'IRangesList(x1, x2, compress=FALSE)'. See
  '?IRangesList' for more information.
In addition: Warning messages:
1: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData
2: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData


Looking at the code it seems that the problem is coming from the line 212
of giniCoverage.R:

   RD<-RangedData(RangesList(rangesl))


Would it be possible to correct this? I am using version 1.27.0

Thanks a lot,

Nicolas

[[alternative HTML version deleted]]

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responsible for the delivery of this message to the intended recipient(s), you 
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notify the sender immediately by e-mail and delete this email message from your 
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This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] EXTERNAL: Re: Cannot update my development package to Bioconductor

[cstrato]

Dear Marcel,

Thank you for the clarification, now it seems to work.


However, there is a strange problem. Here is what I did:

$ cd /Volumes/T3Data/CRAN/GIT/xps

$ git remote -v
origin  g...@github.com:cstrato/xps.git (fetch)
origin  g...@github.com:cstrato/xps.git (push)
upstreamg...@git.bioconductor.org:packages/xps (fetch)
upstreamg...@git.bioconductor.org:packages/xps (push)

$ git checkout master
Already on 'master'
Your branch is up-to-date with 'origin/master'.

$ git pull upstream master
Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
remote: Counting objects: 6, done.
remote: Compressing objects: 100% (6/6), done.
remote: Total 6 (delta 4), reused 0 (delta 0)
Unpacking objects: 100% (6/6), done.
From git.bioconductor.org:packages/xps
 * branchmaster -> FETCH_HEAD
 * [new branch]  master -> upstream/master
Auto-merging DESCRIPTION
CONFLICT (content): Merge conflict in DESCRIPTION
Automatic merge failed; fix conflicts and then commit the result.

$ git add -v DESCRIPTION
add 'DESCRIPTION'

$ git add -v NEWS

$ git commit -m "update for NEWS"
[master 4121457] update for NEWS

$ git push origin master
Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
Counting objects: 9, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (9/9), done.
Writing objects: 100% (9/9), 1.01 KiB | 0 bytes/s, done.
Total 9 (delta 6), reused 0 (delta 0)
remote: Resolving deltas: 100% (6/6), completed with 3 local objects.
To github.com:cstrato/xps.git
   cf326be..4121457  master -> master

$ git pull upstream master
Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
From git.bioconductor.org:packages/xps
 * branchmaster -> FETCH_HEAD
Already up-to-date.

$ git push upstream master
Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
Counting objects: 11, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (11/11), done.
Writing objects: 100% (11/11), 1.68 KiB | 0 bytes/s, done.
Total 11 (delta 8), reused 0 (delta 0)
To git.bioconductor.org:packages/xps
   aae14d1..4121457  master -> master


It seems that there was a conflict with DESCRIPTION,
so I did again 'git add DESCRIPTION'

Now everything seems to be ok, but when looking at the
DESCRIPTION file in e.g. https://github.com/cstrato/xps
the first lines of DESCRIPTION looks as follows:

Package: xps
<<< HEAD
Version: 1.41.2
===
Version: 1.41.0
>>> aae14d1351c754876880f9b50af9da70f80034ce


Should I keep this DESCRIPTION file or delete the additional lines or 
update the DESCRIPTION file again?


Best regards,
Christian

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Re: [Bioc-devel] EXTERNAL: Re: Cannot update my development package to Bioconductor

[Turaga, Nitesh]

Hi Christian,

Marcel is correct. The documentation is given here, 
http://bioconductor.org/developers/how-to/git/pull-upstream-changes/.

Best,

Nitesh 

> On May 14, 2018, at 6:22 PM, Marcel Ramos  
> wrote:
> 
> Hi Christian,
> 
> It looks like you have to do
> 
> *git pull upstream master *
> 
> according to your `git remote -v`.
> 
> Regards,
> 
> Marcel
> 
> 
> On 05/14/2018 04:21 PM, cstrato wrote:
>> Dear Nitesh,
>> 
>> Thank you for your fast reply. Here is  what I tried now,
>> including using 'git pull':
>> 
>> $ cd /Volumes/T3Data/CRAN/GIT/xps
>> 
>> $ git checkout master
>> Already on 'master'
>> Your branch is up-to-date with 'origin/master'.
>> 
>> $ git pull
>> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
>> Already up-to-date.
>> 
>> $ git commit DESCRIPTION
>> On branch master
>> Your branch is up-to-date with 'origin/master'.
>> Untracked files:
>> .DS_Store
>> xps/
>> 
>> nothing added to commit but untracked files present
>> 
>> $ git push
>> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
>> Everything up-to-date
>> 
>> $ git push origin master
>> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
>> Everything up-to-date
>> 
>> $ git push upstream master
>> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
>> To git.bioconductor.org:packages/xps
>>  ! [rejected]master -> master (fetch first)
>> error: failed to push some refs to
>> 'g...@git.bioconductor.org:packages/xps'
>> hint: Updates were rejected because the remote contains work that you do
>> hint: not have locally. This is usually caused by another repository
>> pushing
>> hint: to the same ref. You may want to first integrate the remote changes
>> hint: (e.g., 'git pull ...') before pushing again.
>> hint: See the 'Note about fast-forwards' in 'git push --help' for
>> details.
>> 
>> 
>> Since I still get the same error I tried the following:
>> 
>> $ git merge upstream/master
>> merge: upstream/master - not something we can merge
>> 
>> $ git remote -v
>> origin  g...@github.com:cstrato/xps.git (fetch)
>> origin  g...@github.com:cstrato/xps.git (push)
>> upstreamg...@git.bioconductor.org:packages/xps (fetch)
>> upstreamg...@git.bioconductor.org:packages/xps (push)
>> 
>> $ git push -u origin master
>> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
>> Branch master set up to track remote branch master from origin.
>> Everything up-to-date
>> 
>> $ git push upstream master
>> Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
>> To git.bioconductor.org:packages/xps
>>  ! [rejected]master -> master (fetch first)
>> error: failed to push some refs to
>> 'g...@git.bioconductor.org:packages/xps'
>> hint: Updates were rejected because the remote contains work that you do
>> hint: not have locally. This is usually caused by another repository
>> pushing
>> hint: to the same ref. You may want to first integrate the remote changes
>> hint: (e.g., 'git pull ...') before pushing again.
>> hint: See the 'Note about fast-forwards' in 'git push --help' for
>> details.
>> 
>> 
>> Once again I get the same error.
>> 
>> - Do you know what might be the reason?
>> 
>> - Furthermore, why is it not possible to follow exactly the guidelines
>> in:
>> http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
>> 
>> Best regards,
>> Christian
>> 
>> 
>> On 05/14/18 20:50, Turaga, Nitesh wrote:
>>> Did you try to ‘git pull’ as mentioned in the error message?
>>> 
>>> Best,
>>> 
>>> Nitesh
>>> 
 On May 14, 2018, at 2:48 PM, cstrato  wrote:
 
 Dear GIT experts,
 
 On Saturday I wanted to update my development package to xps_1.41.1,
 however until now it was not updated in the 'Multiple platform
 build/check report' although I could confirm the changes with
 Firefox: https://github.com/cstrato/xps
 
 
 For this reason I tried today to update my development package to
 xps_1.41.2.
 
 I did follow exactly the guidelines of:
 http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
 
 
 Here are the results:
 
 $ cd /Volumes/T3Data/CRAN/GIT/xps
 
 $ git remote -v
 origin  g...@github.com:cstrato/xps.git (fetch)
 origin  g...@github.com:cstrato/xps.git (push)
 upstreamg...@git.bioconductor.org:packages/xps (fetch)
 upstreamg...@git.bioconductor.org:packages/xps (push)
 
 $ git checkout master
 Already on 'master'
 Your branch is up-to-date with 'origin/master'.
 
 $ git add -v DESCRIPTION
 add 'DESCRIPTION'
 
 $ git add -v NEWS
 add 'NEWS'
 
 $ git commit -m "update for NEWS"
 [master cf326be] update for NEWS
 2 files changed, 6 insertions(+), 1 deletion(-)
 
 $ git push origin master
 Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
 Counting objects: 4, done.
 Delta compression using up to 8 threads.
 

Re: [Bioc-devel] htSeqTools and giniCoverage error

[Nicolas Descostes]

I guess I should make my package independent of it then, but that's going
to ask some work. That's very unfortunate...

2018-05-15 7:24 GMT-04:00 Shepherd, Lori :

> What is your sessionInfo()? This was corrected in version 1.27.1 of the
> package so you could try updating to that version.
>
>
>
> However,  htSeqTools is currently deprecated in Release Bioc 3.7 and
> currently scheduled to be removed in Bioc 3.8 as the maintainer has be
> inactive in maintaining the package and unresponsive to our requests to fix
> their package.
>
>
>
> Cheers,
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of
> Nicolas Descostes 
> *Sent:* Sunday, May 13, 2018 1:35:05 PM
> *To:* bioc-devel@r-project.org
> *Cc:* oscar.re...@irbbarcelona.org
> *Subject:* [Bioc-devel] htSeqTools and giniCoverage error
>
> Dear all,
>
> I am using htseqtools on the devel version and I get the following error
> when using giniCoverage:
>
> test <- lapply(endoExoBamlist, function(bam_files){
> return(lapply(bam_files, function(bamfile){
> ga <- if(paired)
> granges(readGAligmentPairs(
> bamfile))
> else granges(readGAlignments(bamfile))
> }))
> })
> test2 <- lapply(test, GRangesList)
> giniCoverage(sample=test2[[1]])
>
> Simulating uniformily distributed data
> Error: The RangesList() constructor is defunct. Please coerce to
> IRangesList
>   instead e.g. do 'as(list(x1, x2), "IRangesList")' instead of
>   'RangesList(x1, x2)'. Alternatively, you can use the IRangesList()
>   constructor e.g. 'IRangesList(x1, x2, compress=FALSE)'. See
>   '?IRangesList' for more information.
> In addition: Warning messages:
> 1: The "lapply" method for RangedData objects is deprecated and won't be
>   replaced. Please migrate your code to use GRanges or GRangesList
>   objects instead. RangedData objects will be deprecated soon (their use
>   has been discouraged since BioC 2.12, that is, since 2014). See
>   IMPORTANT NOTE in ?RangedData
> 2: The "lapply" method for RangedData objects is deprecated and won't be
>   replaced. Please migrate your code to use GRanges or GRangesList
>   objects instead. RangedData objects will be deprecated soon (their use
>   has been discouraged since BioC 2.12, that is, since 2014). See
>   IMPORTANT NOTE in ?RangedData
>
>
> Looking at the code it seems that the problem is coming from the line 212
> of giniCoverage.R:
>
>RD<-RangedData(RangesList(rangesl))
>
>
> Would it be possible to correct this? I am using version 1.27.0
>
> Thanks a lot,
>
> Nicolas
>
> [[alternative HTML version deleted]]
>
> ___
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>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.

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Re: [Bioc-devel] htSeqTools and giniCoverage error

[Shepherd, Lori]

What is your sessionInfo()? This was corrected in version 1.27.1 of the package 
so you could try updating to that version.



However,  htSeqTools is currently deprecated in Release Bioc 3.7 and currently 
scheduled to be removed in Bioc 3.8 as the maintainer has be inactive in 
maintaining the package and unresponsive to our requests to fix their package.



Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Nicolas 
Descostes 
Sent: Sunday, May 13, 2018 1:35:05 PM
To: bioc-devel@r-project.org
Cc: oscar.re...@irbbarcelona.org
Subject: [Bioc-devel] htSeqTools and giniCoverage error

Dear all,

I am using htseqtools on the devel version and I get the following error
when using giniCoverage:

test <- lapply(endoExoBamlist, function(bam_files){
return(lapply(bam_files, function(bamfile){
ga <- if(paired)
granges(readGAligmentPairs(bamfile))
else granges(readGAlignments(bamfile))
}))
})
test2 <- lapply(test, GRangesList)
giniCoverage(sample=test2[[1]])

Simulating uniformily distributed data
Error: The RangesList() constructor is defunct. Please coerce to IRangesList
  instead e.g. do 'as(list(x1, x2), "IRangesList")' instead of
  'RangesList(x1, x2)'. Alternatively, you can use the IRangesList()
  constructor e.g. 'IRangesList(x1, x2, compress=FALSE)'. See
  '?IRangesList' for more information.
In addition: Warning messages:
1: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData
2: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData


Looking at the code it seems that the problem is coming from the line 212
of giniCoverage.R:

   RD<-RangedData(RangesList(rangesl))


Would it be possible to correct this? I am using version 1.27.0

Thanks a lot,

Nicolas

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this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] Package size note

[Kasper Daniel Hansen]

Kenneth,

You should _always_ run R CMD check (and R CMD BiocCheck) on the tarball
generated by R CMD build.  The build step essentially cleans the code.  If
your vignette takes a bit to generate (the vignette gets generated with R
CMD build), just do R CMD build --no-build-vignettes

Best,
Kasper

On Tue, May 15, 2018 at 9:41 AM, Kenneth Condon 
wrote:

> Hi Lori,
>
>
> Thanks for the reply. The actual tar.gz built by R CMD build is only 3Mb so
> maybe I should ignore the note and submit? The note may actually be
> referring to large .git objects in the git history - not sure.
>
> Regards,
> Kenneth
>
> On Mon, May 14, 2018 at 12:15 PM, Shepherd, Lori <
> lori.sheph...@roswellpark.org> wrote:
>
> >
> > Please review the package guidelines -
> >
> >
> > http://bioconductor.org/developers/package-guidelines/
> >
> >
> > Generally, Bioconductor will insist that the R CMD built package tar.gz
> be
> > less than 4MB for software packages (There are some exceptions for data
> > experiment or annotation packages).
> >
> >
> > If this is a software packages,  there are a few options
> >
> >
> > With large data files:
> >
> > 1.  Reduce the size of the data.  A full data set is often not needed to
> > display the functionality and utility of a package.  A reduced smaller
> > subset of data is recommended
> >
> > 2.  See if there is already existing data available in one of the data
> > experiment packages or experimenthub that can be used instead of
> providing
> > new data.
> >
> > 3. separate out the data files into a separate associate data
> > experiment package or use the experimenthub to store data.
> >
> >
> >
> > Are you generating or providing a lot of static image files for the
> > vignette?  There might also be some opportunity to reduce the size but
> have
> > images generated automatically if this is the case.
> >
> >
> >
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Cancer Institute
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> > --
> > *From:* Bioc-devel  on behalf of
> > Kenneth Condon 
> > *Sent:* Saturday, May 12, 2018 6:23:02 PM
> > *To:* bioc-devel
> > *Subject:* [Bioc-devel] Package size note
> >
> > Hi all,
> >
> > I almost have a clean R CMD check.
> >
> > R CMD check results0 errors | 0 warnings | 1 note checking installed
> > package size ... NOTE
> >   installed size is  6.1Mb
> >   sub-directories of 1Mb or more:
> > data   3.0Mb
> > doc2.9Mb
> >
> >
> > Firstly, do I need to get this below 5Mb?
> >
> > Secondly, I don't have a sub-directory called 'doc' - what is this?
> >
> > Regards,
> > Kenneth
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> > This email message may contain legally privileged and/or confidential
> > information. If you are not the intended recipient(s), or the employee or
> > agent responsible for the delivery of this message to the intended
> > recipient(s), you are hereby notified that any disclosure, copying,
> > distribution, or use of this email message is prohibited. If you have
> > received this message in error, please notify the sender immediately by
> > e-mail and delete this email message from your computer. Thank you.
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
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>

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Re: [Bioc-devel] Package size note

[Kenneth Condon]

Hi Lori,


Thanks for the reply. The actual tar.gz built by R CMD build is only 3Mb so
maybe I should ignore the note and submit? The note may actually be
referring to large .git objects in the git history - not sure.

Regards,
Kenneth

On Mon, May 14, 2018 at 12:15 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

>
> Please review the package guidelines -
>
>
> http://bioconductor.org/developers/package-guidelines/
>
>
> Generally, Bioconductor will insist that the R CMD built package tar.gz be
> less than 4MB for software packages (There are some exceptions for data
> experiment or annotation packages).
>
>
> If this is a software packages,  there are a few options
>
>
> With large data files:
>
> 1.  Reduce the size of the data.  A full data set is often not needed to
> display the functionality and utility of a package.  A reduced smaller
> subset of data is recommended
>
> 2.  See if there is already existing data available in one of the data
> experiment packages or experimenthub that can be used instead of providing
> new data.
>
> 3. separate out the data files into a separate associate data
> experiment package or use the experimenthub to store data.
>
>
>
> Are you generating or providing a lot of static image files for the
> vignette?  There might also be some opportunity to reduce the size but have
> images generated automatically if this is the case.
>
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of
> Kenneth Condon 
> *Sent:* Saturday, May 12, 2018 6:23:02 PM
> *To:* bioc-devel
> *Subject:* [Bioc-devel] Package size note
>
> Hi all,
>
> I almost have a clean R CMD check.
>
> R CMD check results0 errors | 0 warnings | 1 note checking installed
> package size ... NOTE
>   installed size is  6.1Mb
>   sub-directories of 1Mb or more:
> data   3.0Mb
> doc2.9Mb
>
>
> Firstly, do I need to get this below 5Mb?
>
> Secondly, I don't have a sub-directory called 'doc' - what is this?
>
> Regards,
> Kenneth
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.

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