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2019 Apr 25
2
Questions/suggestions about new staged installation
...-e delete -e move path/to/R/library/
While in another terminal I install CRAN package abc with:
? R CMD INSTALL abc_2.1.tar.gz
All deps are already installed.
## With R 3.5
When installing abc the first time with R 3.5 inotifywait reports the
following events:
2019-04-24 16:57:42 -- /home/hpages/R/R-3.5.r75051/library/ CREATE,ISDIR
00LOCK-abc
2019-04-24 16:57:42 -- /home/hpages/R/R-3.5.r75051/library/ CREATE,ISDIR abc
2019-04-24 16:57:45 -- /home/hpages/R/R-3.5.r75051/library/ DELETE,ISDIR
00LOCK-
Then on subsequent times:
2019-04-24 16:58:14 -- /home/hpages/R/R-3.5.r75051/library/ CRE...
2011 Sep 23
2
cbind() crashes on raw vectors
Hi,
cbind() doesn't seem to like raw vectors:
> df <- cbind(a=integer(4000), b=raw(4000))
> df
*** glibc detected *** /home/hpages/R-2.13.1/bin/exec/R: malloc():
memory corruption: 0x0000000002d73ca0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x79d7a)[0x7f3592b91d7a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_malloc+0x6e)[0x7f3592b9431e]
/lib/libreadline.so.5(xmalloc+0x6)[0x7f3592620ab6]
/lib/libreadline.so...
2019 Apr 25
1
Questions/suggestions about new staged installation
...ith:
>>
>> ? ? R CMD INSTALL abc_2.1.tar.gz
>>
>> All deps are already installed.
>>
>> ## With R 3.5
>>
>> When installing abc the first time with R 3.5 inotifywait reports the
>> following events:
>>
>> 2019-04-24 16:57:42 -- /home/hpages/R/R-3.5.r75051/library/ CREATE,ISDIR
>> 00LOCK-abc
>> 2019-04-24 16:57:42 -- /home/hpages/R/R-3.5.r75051/library/
>> CREATE,ISDIR abc
>> 2019-04-24 16:57:45 -- /home/hpages/R/R-3.5.r75051/library/ DELETE,ISDIR
>> 00LOCK-
>>
>> Then on subsequent times:
>...
2019 Apr 25
0
Questions/suggestions about new staged installation
...nother terminal I install CRAN package abc with:
>
> ? R CMD INSTALL abc_2.1.tar.gz
>
> All deps are already installed.
>
> ## With R 3.5
>
> When installing abc the first time with R 3.5 inotifywait reports the
> following events:
>
> 2019-04-24 16:57:42 -- /home/hpages/R/R-3.5.r75051/library/ CREATE,ISDIR
> 00LOCK-abc
> 2019-04-24 16:57:42 -- /home/hpages/R/R-3.5.r75051/library/ CREATE,ISDIR abc
> 2019-04-24 16:57:45 -- /home/hpages/R/R-3.5.r75051/library/ DELETE,ISDIR
> 00LOCK-
>
> Then on subsequent times:
>
> 2019-04-24 16:58:14 -- /hom...
2019 Mar 22
2
selectMethod() can fail to find methods in situations of multiple dispatch
...d this sort of complexity, but "ANY" truncation has been happening since at least 2003.
> matchSignature(c("numeric", "ANY"), foo)
x
"numeric"
So I'm not sure we want to mess with it.
Michael
On Thu, Mar 21, 2019 at 8:14 PM Pages, Herve <hpages at fredhutch.org<mailto:hpages at fredhutch.org>> wrote:
Hi Michael,
Thanks for looking into this. I suspect that truncation of ANY suffixes from method signatures is also the culprit behind the sudden breakage of aliases of the form \alias{foo,numeric-method} when a method without the A...
2016 Mar 19
2
unary class union of an S3 class
On 03/19/2016 01:22 AM, Michael Lawrence wrote:
>
>
> On Sat, Mar 19, 2016 at 12:10 AM, Herv? Pag?s <hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>> wrote:
>
> On 03/18/2016 03:28 PM, Michael Lawrence wrote:
>
>
> On Fri, Mar 18, 2016 at 2:53 PM, Herv? Pag?s
> <hpages at fredhutch.org <mailto:hpages at fredhutch.org>
> <...
2019 Mar 22
2
selectMethod() can fail to find methods in situations of multiple dispatch
...t's worth?
H.
On 3/19/19 10:12, Michael Lawrence wrote:
This is due to the intentional truncation of ANY suffixes from method signatures. I've hacked selectMethod() to be robust to that and will commit soon. Thanks for the report.
Michael
On Thu, Mar 14, 2019 at 9:32 AM Pages, Herve <hpages at fredhutch.org<mailto:hpages at fredhutch.org>> wrote:
Here is an example:
setGeneric("foo", function(x, y) standardGeneric("foo"))
setMethod("foo", c("numeric", "ANY"),
function(x, y) cat("I'm the foo#numeric#ANY metho...
2007 Aug 13
1
Compilation error with R-devel_2007-08-12.tar.gz snapshot
Hi,
I get a compilation error with last available R devel
snapshot (R-devel_2007-08-12.tar.gz, r42483):
==================== CONFIGURE ====================
hpages at wilson1:~/R-2.6.broken> ~/src/R-2.6.r42483/configure
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
[...]
R is now configured for x86_64-unknown-linux-gnu
Source directory: /home/hpages/src/R-2.6.r42483
Installation d...
2020 May 22
5
paste(character(0), collapse="", recycle0=FALSE) should be ""
...v2/url?u=http-3A__tibco.com&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Z1o-HO3_OqxOR9LaRguGvnG7X4vF_z1_q13I7zmjcfY&s=7ZT1IjmexPqsDBhrV3NspPTr8M8XiMweEwJWErgAlqw&e=>
>
>
> On Fri, May 22, 2020 at 9:12 AM Herv? Pag?s <hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>> wrote:
>
> I think that
>
> ? ? paste(c("a", "b"), NULL, c("c",? "d"),? sep = " ", collapse
> = ",",
> recycle0=TRUE)...
2020 May 24
0
paste(character(0), collapse="", recycle0=FALSE) should be ""
Herve (et al.),
On Fri, May 22, 2020 at 3:16 PM Herv? Pag?s <hpages at fredhutch.org> wrote:
> Gabe,
>
> It's the current behavior of paste() that is a major source of bugs:
>
> ## Add "rs" prefix to SNP ids and collapse them in a
> ## comma-separated string.
> collapse_snp_ids <- function(snp_ids)
> past...
2011 Dec 06
1
warning for inefficiently compressed datasets
...d("chr1-gzip.rda"))
user system elapsed
1.210 0.180 1.384
> system.time(load("chr1-bzip2.rda"))
user system elapsed
9.500 0.160 9.674
> system.time(load("chr1-xz.rda"))
user system elapsed
4.46 0.20 4.69
hpages at latitude:~/testing$ ls -lhtr chr1-*.rda
-rw-r--r-- 1 hpages hpages 61M 2011-12-06 12:13 chr1-gzip.rda
-rw-r--r-- 1 hpages hpages 55M 2011-12-06 12:15 chr1-bzip2.rda
-rw-r--r-- 1 hpages hpages 49M 2011-12-06 12:25 chr1-xz.rda
This is with R-2.14.0 on a 64-bit Ubuntu laptop with 8GB of RAM.
The...
2020 Mar 27
1
object.size vs lobstr::obj_size
On 3/27/20 15:19, Hadley Wickham wrote:
>
>
> On Fri, Mar 27, 2020 at 4:01 PM Herv? Pag?s <hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>> wrote:
>
>
>
> On 3/27/20 12:00, Hadley Wickham wrote:
> >
> >
> > On Fri, Mar 27, 2020 at 10:39 AM Herv? Pag?s
> <hpages at fredhutch.org <mailto:hpages at fredhutch.o...
2020 May 22
2
paste(character(0), collapse="", recycle0=FALSE) should be ""
...e, processing collapse happens last so collapse=non-NULL
always leads to a single character string being returned, the same as
paste(collapse=""). See the altPaste function I posted yesterday.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Fri, May 22, 2020 at 9:12 AM Herv? Pag?s <hpages at fredhutch.org> wrote:
> I think that
>
> paste(c("a", "b"), NULL, c("c", "d"), sep = " ", collapse = ",",
> recycle0=TRUE)
>
> should just return an empty string and don't see why it needs to emit a
>...
2018 Jan 30
2
as.list method for by Objects
by() does not always return a list. In Gabe's example, it returns an
integer, thus it is coerced to a list. as.list() means that it should be a
VECSXP, not necessarily with "list" in the class attribute.
Michael
On Tue, Jan 30, 2018 at 2:41 PM, Herv? Pag?s <hpages at fredhutch.org> wrote:
> Hi Gabe,
>
> Interestingly the behavior of as.list() on by objects seem to
> depend on the object itself:
>
> > b1 <- by(1:2, 1:2, identity)
> > class(as.list(b1))
> [1] "list"
>
> > b2 <- by(warpbreaks[, 1:2], wa...
2019 Mar 14
2
selectMethod() can fail to find methods in situations of multiple dispatch
...uot;numeric" "logical"
defined "numeric" "ANY"
Thanks,
H.
--
Herv? Pag?s
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: hpages at fredhutch.org<mailto:hpages at fredhutch.org>
Phone: (206) 667-5791
Fax: (206) 667-1319
[[alternative HTML version deleted]]
2017 Nov 29
2
binary form of is() contradicts its unary form
...ote that object class is always `data.frame` here, check:
>
> > class(data.frame())
> [1] "data.frame"
> > is(data.frame(), "data.frame")
> [1] TRUE
>
> Best,
> Mehmet
>
>
>
>
>
> On 29 Nov 2017 19:13, "Herv? Pag?s" <hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>> wrote:
>
> Hi,
>
> The unary forms of is() and extends() report that data.frame
> extends list, oldClass, and vector:
>
> > is(data.frame())
> [1] "data.frame" "list&...
2018 Jan 30
2
as.list method for by Objects
...I'm not sure we can expect consistency across methods beyond
that, nor is it feasible at this point to match the semantics of the
methods package. It deals in "class space" while as.list() deals in
"typeof() space".
Michael
On Tue, Jan 30, 2018 at 3:47 PM, Herv? Pag?s <hpages at fredhutch.org> wrote:
> On 01/30/2018 02:50 PM, Michael Lawrence wrote:
>
>> by() does not always return a list. In Gabe's example, it returns an
>> integer, thus it is coerced to a list. as.list() means that it should be a
>> VECSXP, not necessarily with "li...
2006 Feb 01
1
Rd files with unknown sections
Hi,
With recent versions of R-devel, "R CMD check" complains about
some "Rd files with unknown sections".
hpages at gladstone:~> R CMD check multtest_1.9.4.tar.gz
...
...
* checking Rd files ... WARNING
Rd files with unknown sections:
/home/hpages/multtest.Rcheck/00_pkg_src/multtest/man/boot.resample.Rd:
notes
/home/hpages/multtest.Rcheck/00_pkg_src/multtest/man/MTP.Rd: notes
See chapter 'Wri...
2020 Mar 27
2
object.size vs lobstr::obj_size
On 3/27/20 12:00, Hadley Wickham wrote:
>
>
> On Fri, Mar 27, 2020 at 10:39 AM Herv? Pag?s <hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>> wrote:
>
> Hi Tomas,
>
> On 3/27/20 07:01, Tomas Kalibera wrote:
> > they provide an over-approximation
>
> They can also provide an "under-approximation" (to say the least) e.g....
2018 Jan 30
0
as.list method for by Objects
...lready does
this on a data.frame so why did someone bother adding an
as.list.data.frame method that does strict coercion?
2) The S4 coercion system based on as() does strict coercion by
default.
H.
>
> Michael
>
> On Tue, Jan 30, 2018 at 2:41 PM, Herv? Pag?s <hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>> wrote:
>
> Hi Gabe,
>
> Interestingly the behavior of as.list() on by objects seem to
> depend on the object itself:
>
> > b1 <- by(1:2, 1:2, identity)
> > class(as.list(b1))...