On 12/04/2016 03:41 AM, Knoll, Max wrote:
Hi,
I'm stuck in the submission process and encounter the following error when
CHECK is performed (on oaxaca):
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF v
Hi Nan, Zach, Val,
On 12/05/2016 01:45 PM, Obenchain, Valerie wrote:
Hi,
We need to make several updates to the mac machines. These are the last
2 builders that still need to move from the Hutch to RPCI. Because they
are still at the Hutch, access to them is limited. We will get to these
update
This helps, Thank you so much!
From: Herv� Pag�s
Sent: Monday, December 5, 2016 9:16:15 PM
To: Dwivedi, Bhakti
Cc: bioc-devel
Subject: Re: [Bioc-devel] biconductor build error and warning
Hi Bhakti,
Please see my post from October here
https://stat.ethz.ch/p
Hi Bhakti,
Please see my post from October here
https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009997.html
for why Rmpfr (and thus HH) fails to install on oaxaca.
We're still hoping that the CRAN folks will start providing Mac
binary packages for r-devel soon.
In the meantime please
Hi,
We need to make several updates to the mac machines. These are the last
2 builders that still need to move from the Hutch to RPCI. Because they
are still at the Hutch, access to them is limited. We will get to these
updates as soon as we can.
Valerie
On 12/05/2016 01:27 PM, Dan Tenenbaum w
Hi Zach and Dan,
- thanks a lot for the information, that made things much clearer.
>From the build error message, it seems rcdk 3.3.8 only "partially" made to
the BioC builds, which means 3.3.8 is available on Linux and Windows, but
not Mac (still 3.3.6). Maybe I'll just wait for the Java update
Actually it looks like the version of java installed on morelia is 1.6. So it
appears that 1.7 (or higher) needs to be installed.
Dan
- Original Message -
> From: "Zach Charlop-Powers"
> To: "Nan Xiao"
> Cc: "bioc-devel"
> Sent: Monday, December 5, 2016 1:02:52 PM
> Subject: Re: [Bio
Hi Marcin,
I'm not sure I agree with that Stack Overflow answer. Sure,
ceiling(1:100/10) is a neat arithmetical trick to get what you want, but it
would be a lot more obvious to me at least to use rep(1:10, each=10). And
even better to use Partitioning objects when you have IRanges around. If
you
Hi Nan,
rCDK 3.3.6 requires Java8 and will throw error if the Java environment is
incorrect. BioC Build only has Java7 hence the error. The new version of
rCDK requires Java7. Once rcdk 3.3.8 makes it onto the BioC builds (its on
CRAN), these errors should clear up. Please keep me posted if the
Hi,
I was trying to get the gene mapping for one of the datasets in Affymetrix. I
found a dissimilarity between Affymetrix file and the database in hgu133plus2.
As per example, For the probeset "1553011_at", I have found a mapping to both
these ENTREZ ID's 6872 /// 138474 in the file downloaded
Hey guys,
- it seems this problem is also affecting the other two Bioc packages
depending on rcdk, i.e. RMassBank and rcellminer (release + devel). Any
ideas why?
Thanks,
-Nan
On Fri, Dec 2, 2016 at 2:29 PM, Nan Xiao wrote:
> Hi Bioc,
>
> - the Rcpi package depends on rcdk, and the rcdk packag
Hi Jurat,
Please read the Writing R Extensions manual if you have not already:
https://cran.r-project.org/doc/manuals/r-release/R-exts.html
It is quite comprehensive. A gentler introduction is:
https://bioconductor.org/developers/how-to/buildingPackagesForBioc/
As for your vignette, note that
Sorry about that. I pushed a fix to devel (2.9.14) and soon release. Btw,
it's not typically a good idea to use a real valued vector as a factor. In
this case, you could use %/% or better yet a partitioning, i.e., relist(ir,
PartitioningByEnd(seq(10, 100, 10))).
Michael
On Sun, Dec 4, 2016 at 8:
Dear Leonardo :
Thanks again for your helpful package to resolve my doubt. Through Dan's
kind instruction, previous problems are partially solved instead still
getting error with vignette compilation. I reproduced example bed files and
tried most simplest way to load these data to let vignette com
Hi,
I downloaded your package from github, removed the dependencies on
AnnotationHub and utils and was able to reproduce the problem for
read.csv() but not query().
I've reworked the suggested .onLoad() file in the ExperimentHubData
vignette. Hopefully this is a more straightforward implementatio
On 12/04/2016 11:34 PM, Keyvān Karami via Bioc-devel wrote:
Hi
My question is how i can get sequence some genes with "
BSgenome.Btaurus.UCSC.bosTau8"
i want to get sequence of a list of locations of genes
like:
chr25 3510245435102482
chr19 4403596944036049
chr18 10444115
Dear Dan :
Thank you very much. I applied your approach and it worked perfectly,
external data now are available for vignette code. I am sorry for my naive
question, didn't realize it become simple question to ask here. I'll make
sure to state my question valid, understandable. Thanks again for ki
Hi
My question is how i can get sequence some genes with "
BSgenome.Btaurus.UCSC.bosTau8"
i want to get sequence of a list of locations of genes
like:
chr25 3510245435102482
chr19 4403596944036049
chr18 1044411510444121
chr27 3724030037240538
chr23 274
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