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On Wed, Sep 27, 2017 at 8
t, then step 2) works!
To reproduce all this, and like with any problem reported on the build
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sure that you have the latest devel version of BiocStyle (whi
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...)
* or maybe dropping dimnames altogether, storing them only once
elsewhere (although a slot for that seems overkill)
There may be other possibilities that I haven't thought of yet, but
I thought I'd get the ball rolling.
Having well-defined dimnames sounds
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On 09/20/2017 09:49 PM, Laurent Gatto wrote:
On 21 September 2017 04:15, Hervé Pagès wrote:
If we want to move export() to BiocGenerics of course import()
would need to follow.
My rough estimate is that this move would possibly break between
20-30 packages or more. The BioC 3.6 release is
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This email message may contain legally privileged and/or...{{dropp
2017 22:22, Michael Lawrence wrote:
I was also about to suggest that we converge on export() but held back
because I was obviously biased. I also agree with making the target
explicit in the function name. It makes the intent of the code way
more obvious.
On Mon, Sep 18, 2017 at 3:15 PM, Hervé
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On 09/14/2017 02:23 PM, Laurent Gatto wrote:
On 14 September 2017 15:15, Hervé Pagès wrote:
Hi,
Note that right now the name of the Ontology getter matches the
name of the corresponding field in all our annotations:
> library(org.Hs.eg.db)
> org.Hs.egGO[["92610"
logy.org/amigo/term/GO:0005622
So I actually don't think that we should rename the Ontology getter,
sorry.
@Laurent: any chance you use something else in rols?
Thanks,
H.
On 09/12/2017 03:52 PM, Hervé Pagès wrote:
On 09/12/2017 01:58 PM, Vincent Carey wrote:
For this particular problem,
rts:. Furthermore,
I use them as BSgenome.Hsapiens.UCSC.hg38::Hsapiens in my code.
Kind regards,
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P.O. Box 19024
Seattle, WA 98109-1024
h
E-mail:
arently in the coercion
##from SummarizedExperiment to RangedSummarizedExperiment
rse <- as(se, "RangedSummarizedExperiment")
rowData(rse)
DataFrame with 200 rows and 0 columns
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g200 here?)
## Coercing to Expression makes me losing the rowData/fData
eset <- as(se, "ExpressionSet")
fData(eset)
data frame with 0 columns and 200 rows
## So where is the problem?
## Apparently in the coercion
##from SummarizedExperiment to RangedSummarizedExperiment
rse <- as(
rols
works again, similar to what happens for function.
Is this something that is worth raising on R-devel?
Best wishes,
Laurent
On 12 September 2017 16:35, Hervé Pagès wrote:
Hi Laurent,
The 2 Ontology,character methods defined in AnnotationDbi and
rols do very different things. The 1st
y", "character")
Error in getMethod("Ontology", "character") :
no method found for function 'Ontology' and signature character
getMethod("Ontology", "character", where = "package:rols")
Method Definition:
function (object)
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On 09/06/2017 03:51 PM, Michael Lawrence wrote:
On Wed, Sep 6, 2017 at 2:23 PM, Hervé Pagès wrote:
Hi,
Personally I like replaceSlots() better.
Not only because it's more readable but also the fact that you can use
initialize() to update an existing object is an undocumented feature
On 09/06/2017 03:53 PM, Hervé Pagès wrote:
One of the reasons it's not exported is because it started as something
kind of experimental and we didn't find a good home for it yet. I could
probably move it to S4Vectors where we already have some low-level
S4-related utils. Not the best h
cern. I cannot remember why I did not just
use direct assignment to slots, however. Perhaps I just found the
function and
decided using it would be better. It would be nice to export replaceSlots
if it does not contravene an important principle.
On Wed, Sep 6, 2017 at 5:23 PM, Hervé P
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nt responsible for the delivery of this message to the intended
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generic with the same signature
setGeneric("Ontology", function(object) standardGeneric("Ontology"))
Could it be moved to BiocGenerics, please?
Best wishes,
Laurent
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eers,
H.
Thanks!
Kind regards,
Roel Janssen
________
From: Hervé Pagès [hpa...@fredhutch.org]
Sent: Sunday, July 23, 2017 7:44 PM
To: Vincent Carey; Janssen-10, R.R.E.
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Change in BSgenome.Hsapiens.U
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lt;- updateObject(x, verbose=TRUE)
Let me know if you run into any issue with this.
Cheers,
H.
On 07/18/2017 03:00 PM, Robert Castelo wrote:
great, thanks Hervé!
robert.
On 18/07/2017 20:57, Hervé Pagès wrote:
Hi Robert,
I'm working on this.
Best,
H.
On 07/14/2017 02:31 AM,
9.0 RCurl_1.95-4.8
[7] bitops_1.0-6
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thods. Is that OK?
Bests,
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P.O. Box 19024
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E-mail: hpa...@fredhutch.org
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On 05/11/2017 06:44 PM, Hervé Pagès wrote:
Hi Michael,
On 05/11/2017 03:27 PM, Michael Lawrence wrote:
There is a bug in S4Vectors, but thanks to an R 3.4 bug in the methods
package (recently fixed in devel), the bug is masked. So, we should
fix S4Vectors. The problem is that order,Rle has a
ged
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On 5/11/17, 4:25 PM, "Hervé Pagès" wrote:
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Prog
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in the report.
Hope this helps,
H.
On 04/23/2017 06:29 PM, Maia Smith wrote:
Thanks, Hervé. Very strange, when I checked that link earlier today, it
appeared to still have errors. All good now!
On Sun, Apr 23, 2017 at 4:49 PM, Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:
Hi
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hrIBBK0fqAFQNmW8a8vTIHbmcNOB7IVjsclAMGCjKLY&e=
There was an interesting reply:
Better don't use -j4 when using cmake, just when using make.
I am not sure whether this is still true, since it seems to work in your
case.
On 04/23/17 02:32, Hervé Pagès wrote:
On 04/22/2017 02:57 PM, cstrato
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Do you use the environment variable ROOTSYS?
Best regards,
Christian
On 04/22/17 22:36, Hervé Pagès wrote:
Hi Christian,
Tha
ot.cern.ch/building-root
so no ROOTSYS (the above document doesn't even mention that
variable).
H.
Best regards,
Christian
On 04/22/17 22:36, Hervé Pagès wrote:
Hi Christian,
Thanks for the update. Glad it works for you.
One small thing is that, if CMAKE_INSTALL_PREFIX is specif
il (I have realized this
when googling around).
On 04/21/17 00:29, Hervé Pagès wrote:
Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and
has been discouraged for years. xps is the only Bioconductor package
that relies on these variables for its configure/build process.
H.
On
. Every page I've read on this topic
strongly discourages doing this.
- Original Message -
From: "Hervé Pagès"
To: "cstrato" , "Dan Tenenbaum"
Cc: "bioc-devel"
Sent: Thursday, April 20, 2017 3:17:23 PM
Subject: Re: [Bioc-devel] xps build p
they should also be
able to install xps from source. So that defeats the purpose of
providing a binary in the first place.
Cheers,
H.
Best regards,
Christian
On 04/20/17 20:00, Hervé Pagès wrote:
On 04/20/2017 10:59 AM, Hervé Pagès wrote:
Hi Christian,
Disabling 'csrutil disable
now won't propagate unless
you bump the version to > 1.2.2.
H.
On 04/20/2017 02:52 PM, 王棣台 wrote:
it should be in my package since anamiR version 1.1.8
That is weird.
Ti-Tai
從: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 05:49
至: 王棣台; bi
enotype data of 'mirna' about breast cancer
pheno.mrna phenotype data of 'mrna' about breast cancer
So again, did you forget to commit it to svn, or did you add it to the
wrong place?
H.
Ti-Tai
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On 04/20/2017 02:45 PM, Hervé Pagès wrote:
On 04/20/2017 02:36 PM, 王棣台 wrote:
That missing object is a list format data generated by myself,
so I don't think it would be about Depends, Imports, or Suggests.
Except this one, other generated data can be found.
And where did you put this
t?
H.
Ti-Tai
____
從: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 05:16
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette
Why don't you give us the name of your package so we can look
at it? I suspect something
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Program in Computational Biolog
On 04/20/2017 10:59 AM, Hervé Pagès wrote:
Hi Christian,
Disabling 'csrutil disable' might help xps on veracruz2 but that
^^
oops, no double negative intended here. I meant, doing 'csrutil disable'
might help... etc
H.
won't help your end
_wJYbW0WYiZvSXAJJKaaPhzWA&m=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0&s=FL17xv1uuzR6UF59mgJstMQ-1seE1UeKDQVVXQgXnUo&e=
Do you think that either using the environment variable LD_RUN_PATH or
using 'install_name_tool' could solve the problem without having to use
'-rpath'
he vignette. What would you or other suggest to do
about that?
Any suggestions are appreciated,
Michael
On 17.04.2017 02:08, Hervé Pagès wrote:
FWIW here are all the packages that are victim of this
installed.packages bug in today's build report:
alpine
fCI
GenomicFeatures
Quas
Hi Michael,
On 04/17/2017 12:31 PM, Michael Love wrote:
alpine, which had this error as of Sunday, is now cleared (I didn't
make any changes to the code)
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process? Make sure
you test it on a machine where SIP is enabled.
Thanks,
H.
On 03/24/2017 12:14 PM, cstrato wrote:
On 03/24/17 19:55, Hervé Pagès wrote:
On 03/24/2017 11:37 AM, cstrato wrote:
On 03/24/17 19:23, Hervé Pagès wrote:
On 03/24/2017 11:10 AM, cstrato wrote:
On 03/24/17 1
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Program in Computational Biology
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Fred Hutchinso
On 04/08/2017 06:50 AM, Martin Morgan wrote:
On 04/08/2017 08:16 AM, Aaron Lun wrote:
On 07/04/17 20:46, luke-tier...@uiowa.edu wrote:
On Fri, 7 Apr 2017, Hervé Pagès wrote:
On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote:
On Fri, 7 Apr 2017, Hervé Pagès wrote:
On 04/06/2017 03
On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote:
On Fri, 7 Apr 2017, Hervé Pagès wrote:
On 04/06/2017 03:29 AM, Michael Lawrence wrote:
On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan
wrote:
On 04/06/2017 05:33 AM, Aaron Lun wrote:
The tool is not perfect, so assess each report
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fr
ly that I hoped. For the other
packages that depend on ensembldb there's no problem or only small
changes
required (did contact the developers).
Fingers crossed that Michael can patch biovizBase and ggbio soon.
cheers, jo
On 4 Apr 2017, at 21:34, Hervé Pagès
mailto:hpa...@fredhutch.org>> wr
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the same DNAStringSets but had a different
environment address?
Regards,
Maarten
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ar 27, 2017 at 3:59 AM, Martin Morgan
wrote:
On 03/22/2017 01:12 PM, Hervé Pagès wrote:
Hi Martin,
On 03/22/2017 03:17 AM, Martin Maechler wrote:
Andrzej Oleś
on Wed, 22 Mar 2017 10:29:57 +0100 writes:
> Just for the record, on R-3.3.2 Herve's code fails with the
fo
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Program in Computat
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On 03/24/2017 11:37 AM, cstrato wrote:
On 03/24/17 19:23, Hervé Pagès wrote:
On 03/24/2017 11:10 AM, cstrato wrote:
On 03/24/17 18:02, Hervé Pagès wrote:
On 03/24/2017 06:52 AM, cstrato wrote:
R/Bioc is still building on Mavericks,
Not for R devel (3.4). The R folks have switched to El
On 03/24/2017 11:10 AM, cstrato wrote:
On 03/24/17 18:02, Hervé Pagès wrote:
On 03/24/2017 06:52 AM, cstrato wrote:
R/Bioc is still building on Mavericks,
Not for R devel (3.4). The R folks have switched to El Capitan a few
days ago:
You are right, I did not check R devel.
https
Cheers,
H.
Best regards,
Christian
On 03/24/17 01:10, Dan Tenenbaum wrote:
- Original Message -
From: "Hervé Pagès"
To: "cstrato" , "bioc-devel"
Sent: Thursday, March 23, 2017 12:14:38 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2
32 PM, Hervé Pagès wrote:
Hi Juan Pablo,
Thanks for adding unit tests to your package. We really encourage
developers to do this. I'm sorry that this is not reflected on
EventPointer's landing page.
I investigated this a bit (I'm not familiar with how the coverage
badges are gene
s?
Best,
Alexey
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one.)
Same reason as for the choice of compilers: that's what the R folks
decided to use for producing the Mac binaries of R and CRAN packages.
We're just following their lead on that.
Cheers,
H.
Best regards,
Christian
On 03/23/17 17:47, Hervé Pagès wrote:
Hi Christian,
The CRAN
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Hervé Pagès
Program in Computational
On 03/21/2017 05:28 PM, Martin Morgan wrote:
On 03/21/2017 08:21 PM, Hervé Pagès wrote:
Hi Leonardo,
Thanks for hunting down and isolating that bug! I tried to simplify
your code even more and was able to get a segfault with just:
setClass("A", representation(stuff="
ere I can trigger the bug.
Martin
> Cheers,
> Andrzej
> On Wed, Mar 22, 2017 at 1:28 AM, Martin Morgan <
> martin.mor...@roswellpark.org> wrote:
>> On 03/21/2017 08:21 PM, Hervé Pagès wrote:
>>
>>> Hi Leonardo,
>&
17-02-14 cran (@0.13.15)
scales 0.4.12016-11-09 CRAN (R 3.4.0)
stringi1.1.22016-10-01 CRAN (R 3.4.0)
stringr1.2.02017-02-18 CRAN (R 3.4.0)
SummarizedExperiment 1.5.7 2017-02-23 Bioconductor
survival 2.41-2 2017-03-
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