Thanks Val that did the trick.
On Mon, May 2, 2016 at 4:40 PM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:
> Hi Vince,
>
> You need version >=1.13.9 of OrganismDbi. Unfortunately it's failing
> check because of the biomart problems so you'll have to get it from svn.
> Let me
On 05/02/2016 05:53 PM, Ou, Jianhong wrote:
Hi All,
I got some warnings when check. However, I could not see any details for that
warnings. How could I debug for these kind of warnings? Thank you.
Please see this thread
https://stat.ethz.ch/pipermail/bioc-devel/2016-May/009205.html
and
On 05/02/2016 12:37 PM, Ludwig Geistlinger wrote:
So yes, you should update the NAMESPACE file following the warning
message you see in your build report.
Hi Martin, I did not encounter such a note on importing from base packages
ever before - but ok, I followed your suggestion and added the
Hi All,
I got some warnings when check. However, I could not see any details for that
warnings. How could I debug for these kind of warnings? Thank you.
* using log directory �/home/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck�
* using R version 3.3.0 RC (2016-04-25 r70549)
* using
Hi Vince,
You need version >=1.13.9 of OrganismDbi. Unfortunately it's failing
check because of the biomart problems so you'll have to get it from svn.
Let me know if you still have problems after updating.
Val
On 05/02/2016 11:53 AM, Vincent Carey wrote:
> biocValid() says all is well ...
>
Well, you can tell your helpdesk that this is going to impact people's work as
the OS you are using will no longer be supported by R/Bioconductor starting
with the release this week.
Mavericks was released 3 years ago. It seems reasonable to support it now.
Dan
- Original Message -
>
Hi Dan,
Thank you for your answer. I hope I can update to Mavericks but our help
desk just ask me to hold on current OS.
Yours Sincerely,
Jianhong Ou
TEL: 508-856-5379
LRB 608
Bioinformatician of Bioinformatics core at
Department of Molecular, Cell and Cancer Biology
364 Plantation Street
Dear Herve,
After reinstalling BiocGenerics, there is no errors any more. Thank you
very much.
Yours Sincerely,
Jianhong Ou
TEL: 508-856-5379
LRB 608
Bioinformatician of Bioinformatics core at
Department of Molecular, Cell and Cancer Biology
364 Plantation Street Worcester,
MA 01605
On
Hi,
I got error when I update S4Vectors in R 3.3 RC r70564 today. I also tried
r70549, same error like this
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.21.6), R 3.3.0 RC (2016-04-28 r70564).
Old packages: 'S4Vectors'
Update all/some/none? [a/s/n]:
This question should probably go on the support site as it is not about package
development.
You should update to Mavericks or higher. Earlier versions of Mac OS X are no
longer officially supported by R or Bioconductor (that's why a binary is not
available).
Dan
- Original Message
biocValid() says all is well ...
> select(Homo.sapiens, keys="1001", keytype="ENTREZID", columns="SYMBOL")
*Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : *
* object '.testSelectArgs' not found*
> sessionInfo()
R version 3.3.0 beta (2016-04-01 r70412)
Platform:
> So yes, you should update the NAMESPACE file following the warning
> message you see in your build report.
Hi Martin, I did not encounter such a note on importing from base packages
ever before - but ok, I followed your suggestion and added the imports.
However all remaining NOTEs and WARNINGs
On 05/02/2016 11:11 AM, Ludwig Geistlinger wrote:
I encounter the same issue with EnrichmentBrowser - and apparently,
several other packages too, e.g. ensembldb, erma, ExiMiR ...
The warnings seem to be, at first glance, linked to messages e.g. for
masking:
I encounter the same issue with EnrichmentBrowser - and apparently,
several other packages too, e.g. ensembldb, erma, ExiMiR ...
The warnings seem to be, at first glance, linked to messages e.g. for
masking:
---
* checking S3
Thanks a lot! So I'll contact you after mid-May :)
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Hi Herve,
passing down additional arguments to the internal exonsBy, cdsBy,
fiveUTRsByTranscript and threeUTRsByTranscript would do it! That would be
great, thanks.
cheers, jo
> On 02 May 2016, at 07:38, Hervé Pagès wrote:
>
> Hi Johannes,
>
> We can make
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