Hi Martin,
On 06/07/2017 03:54 AM, Martin Maechler wrote:
Martin Maechler <maech...@stat.math.ethz.ch>
on Tue, 6 Jun 2017 09:45:44 +0200 writes:
Hervé Pagès <hpa...@fredhutch.org>
on Fri, 2 Jun 2017 04:05:15 -0700 writes:
>> Hi, I have a long numeric vect
im(a2) <- c(2, 3)
Error in dim(a2) <- c(2, 3) : invalid first argument
On Mon, Jun 5, 2017 at 6:08 PM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wrote:
Hi,
It's nice to be able to define S4 classes with slots that correspond
'dimnames' applied to non-array
So it seems that the presence of a "dim" or "dimnames" slot prevents a
class from being extended. Is this expected? I couldn't find anything
in TFM about this. Sorry if I missed it.
Thanks,
H.
--
Hervé Pagès
Progr
() already does this so that wouldn't create a
precedent. Also and FWIW prod() avoids the problem by always returning
a double, whatever the type of the input is (except on a complex
vector).
I can provide a patch if this change sounds reasonable.
Cheers,
H.
--
Hervé Pagès
Program in Computational B
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2==5, print("Hey!!!") == "Hey!!!")
Stopifnot(2+2==4, print("Hey!!!") == "Hey!!!")
Stopifnot(T,T,T,T,T,T,T,T,T,T,T,T,T,T,T,T,F,T)
On 15 May 2017, at 15:37 , Martin Maechler <maech...@stat.math.ethz.ch> wrote:
I'm still curious about Hervé's idea on using sw
)
> Serguei.
Well, a good idea, but the 'warning' case is more complicated
(and the above incorrect): I do want the warning there, but
_not_ return the warning, but rather, the result of eval() :
So this needs even more sophistication, using withCallingHandlers(.)
and maybe that really get's too s
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
tary and privileged
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message.
On 5/11/17, 4:25 PM, "Hervé Pagès"
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Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
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Phone: (206) 667-5791
Fax:(206) 667-1319
On 05/03/2017 12:04 PM, Hervé Pagès wrote:
Not sure why the performance penalty of nonstandard evaluation would
be more of a concern here than for something like switch().
which is actually a primitive. So it seems that there is at least
another way to go than 'dots <- match.call(expand.d
17, at 02:50 , Hervé Pagès <hpa...@fredhutch.org> wrote:
Hi,
It's surprising that stopifnot() keeps evaluating its arguments after
it reaches the first one that is not TRUE:
> stopifnot(3 == 5, as.integer(2^32), a <- 12)
Error: 3 == 5 is not TRUE
In addition: Warning message:
all(B)) stop(...) }
Best,
H.
--
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
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Hervé Pagès
Program in Computational Biology
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at the end of the
paragraph for enableJIT.
Indeed. Sorry for missing that (I was playing with several versions
of R and probably looked at the enableJIT man page in the wrong R).
H.
Best,
luke
On Wed, 26 Apr 2017, Hervé Pagès wrote:
Hi,
I'm running into a case where byte-compilation changes
On 04/26/2017 01:51 PM, Duncan Murdoch wrote:
On 26/04/2017 4:36 PM, Hervé Pagès wrote:
Hi,
I'm running into a case where byte-compilation changes
the semantic of a function. This is with R 3.4.0:
foo <- function(x) { TRUE && x }
foo(c(a=FALSE))
# [1] FALSE # O
C_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.0
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Hervé Pagès
Program in Comp
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Program in Computational Biology
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Fred Hutchinson Cancer
.
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 <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wrote:
Hi Maia,
se.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=QzqBONt6vp_Oq6FB3KMJerSAAggLgiauNhROOSs0EzM=Qc0PP8DM7D6TVI78OCfBh9S_0CfQMWRvo-5yiuKfCkA=
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Program in Computational Biology
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Fred H
it seems to work in your
case.
On 04/23/17 02:32, Hervé Pagès wrote:
On 04/22/2017 02:57 PM, cstrato wrote:
Dear Herve,
Thank you for your efforts to get xps running.
I will make the changes in Makefile.arch, too, and update README and
rename it to install.
I am also surprised that the libs
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 04/20
. Every page I've read on this topic
strongly discourages doing this.
- Original Message -
From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "Dan Tenenbaum" <dtene...@fredhutch.org>
Cc: "bioc-devel" <bioc-d
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' might help xps on veracruz2 but that
^^
oops, no double negative intended
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; bioc-de
otype 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
____
從: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日
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 data
.
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 is missing
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Program in Computational Biology
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Fred Hutchinson Cancer Research
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 users.
I'm no expert
having to use
'-rpath'?
Thank you in advance.
Best regards,
Christian
On 04/19/17 22:51, Hervé Pagès wrote:
Hi Christian,
So I installed ROOT 5 from source on veracruz2. It's in
/usr/local/root.
However, Apple's SIP (System Integrity Protection, new and
enabled by default on El Capitan
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
QuasR
We only see this error on tokay2
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)
nks,
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 18:02, Hervé Pagès wrote:
On 03/24/2017 06:52 AM, cstrato wrote:
R/Bi
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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
<martin.mor...@roswellpark.org> wrote:
On 04/06/2017 05:33 AM, Aaron Lun wrote:
The tool is not p
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
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this message in error, please notify the sender immediately by e-mail and
delete this email mess
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E-mail: hpa...@fredhutch.org
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ovizBase
and
ggbio, but it did not work out that smoothly 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, He
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leshoot this, I have a vague memory
that this, or something related to this, has been discussed
previously, but I cannot locate it.
Is the above a bug in R, a FAQ, a build error, overzealous compiler
optimization, and / or ...?
Thanks,
Henrik
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I get to work.
On Mon, Mar 27, 2017 at 3:59 AM, Martin Morgan
<martin.mor...@roswellpark.org> 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 <andrzej.o...@gmail.com>
on Wed, 22 Mar 2017 10:29:57 +0100 wri
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On 03/29/2017 11:04 AM, Hervé Pagès wrote:
Hi Tim,
On 03/29/2017 08:24 AM, Tim Keitt wrote:
I have a use case where I would like to create an SEXP around an existing
buffer that is managed by R, thus avoiding a copy operation.
What to you mean exactly by "an existing buffer managed
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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
.
Best regards,
Christian
On 03/24/17 01:10, Dan Tenenbaum wrote:
- Original Message -
From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "bioc-devel" <bioc-devel@r-project.org>
Sent: Thursday, March 23, 2017
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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 folks
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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="
1.17 2017-02-12 Bioconductor
withr 1.0.22016-06-20 CRAN (R 3.4.0)
XML3.98-1.5 2016-11-10 CRAN (R 3.4.0)
xtable 1.8-22016-02-05 CRAN (R 3.4.0)
XVector 0.15.2 2017-02-02 Bioconductor
zlibbioc 1.21.0 2016-10-23 Bioconductor
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oc"
installme
[1] "Biostrings" "IRanges""XVector"
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bump (Updated a link on the package vignette) caused
this problem.
Thank you.
Juan Pablo
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On 01/11/2017 02:33 AM, Alex Ivan Howard wrote:
There is nothing to sum
over, so it shouldn't actually be able to return a concrete numeric value?
How much did you spend at the grocery store if you didn't buy anything?
H.
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] compiler_3.4.0 GenomicFeatures_1.27.6 XML_3.98-1.5
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Hi Raymond,
This should be fixed now in GenomeInfoDb 1.10.3 (release) and 1.11.8
(devel). Both packages should become available via biocLite() in the
next 24 hours or so.
Thanks again for reporting the issue and for your patience.
Cheers,
H.
On 02/01/2017 12:32 PM, Hervé Pagès wrote:
Hi
m your computer. Thank you.
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XVector0.14.0 2016-10-18 Bioconductor
zlibbioc 1.20.0 2016-10-18 Bioconductor
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On 01/13/2017 12:36 PM, Hervé Pagès wrote:
Hi,
No ifelse() statement needed. Just use invertStrand() on your
GAlignments object to invert its strand.
strandMode is specific to paired-end reads and the supported modes
reflect what other software do with paired-end reads (e.g. TopHat,
Rsubread
Matrix_1.2-7.1 BiocParallel_1.8.1
[7] tools_3.3.2
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(). So it doesn't really
address the 1st problem and introduces a new one. Sounds like using
a plural form instead of the "list" prefix would be less confusing
e.g. 'vars', 'varnames', 'objnames' or something like that.
H.
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many packages use pandoc/pandoc-citeproc for their vignettes.
So again, I'm not sure what's going on, sorry. Likely a problem on
our side. I suggest you ignore this build error on oaxaca for now.
Cheers,
H.
Thank you.
On Thu, Dec 8, 2016 at 1:07 AM, Hervé Pagès <hpa...@fredhutch.org
<mai
ort:
http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161207152203.html
<http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161207152203.html>
On Wed, Dec 7, 2016 at 7:42 PM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wrote:
Hi Stian,
ct.org mailing list
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02:21 PM, Hervé Pagès wrote:
Hi Antonio,
Yes the stats for November look low compared to the previous months.
Looks like we'll hardly hit the 3 distinct IPs for the whole
Bioconductor software repository. Could be genuine though. I'll check
what's going on.
Thanks for bringing this to our
On 12/05/2016 01:05 AM, peter dalgaard wrote:
On 02 Dec 2016, at 23:13 , Hervé Pagès <hpa...@fredhutch.org> wrote:
More generally one might reasonably expect 'unlist(x)' to be equivalent
to 'do.call(c, x)' on a list 'x' where all the list elements are atomic
vectors:
Well, both are g
his message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
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uding any attachments) is for...{{dropped:22}}
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factors:
x <- list(factor("Z"), factor(c("a", "Z", "b")))
unlist(x)
# [1] Z a Z b
# Levels: Z a b
do.call(c, x)
# [1] 1 1 3 2
then it's the other way around. Also note that the fact that the first
2 numbers in the result of 'do.call(c,
installed when you install the
package, but the inst directory itself goes away.
If in your package source you have the following structure:
inst/extdata/
inst/foo.txt
In the installed package you end up with:
extdata/
foo.txt
HTH
Dan
- Original Message -
From: "Jurat Shay
st or extdata folder in that repository.
Maybe it has not yet been added/committed/pushed to git?
Note that everything _under_ inst gets installed when you install the
package, but the inst directory itself goes away.
If in your package source you have the following structure:
inst/extdata/
ins
l data must be located
in inst/, so I manually created this folder inst/extdata and paste my
data, but vignette compilation still failed. According to convention of R
package, my package structure will be:
myPackage
`- inst
`- extdata
`- data1.bed
`- data2.bed
`- R
`- ...
`- NAMESPACE
`- DESCRIPTI
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or other packages
that depend on ggplot2/ggproto.
Best,
R.
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