Displaying 20 results from an estimated 10000 matches similar to: "What is preferable - a single large package or a few smaller packages?"
2018 Feb 13
4
Setting the path to Rtools for package compilation on Windows
Hi all,
I'm trying to set up the Windows Rtools toolset for building packages
with compiled code. I installed for Windows R-3.4.3 from CRAN and
installed Rtools-3.4 in a custom location M:\R\R-3.4.3 and
M:\R\Rtools-3.4
Following the instructions, in shell, I set
Path=M:\R\Rtools-3.4\bin;M:\R\Rtools-3.4\gcc-4.6.3\bin;M:\R\R-3.4.3\bin;...
(the ... are other paths irrelevant for R/Rtools).
2012 Oct 18
1
WGCNA: Combining block-wise dendrograms and modules into a single figure
Hello fellow R users,
I am currently learning to use R, so please forgive me if there is an
obvious explanation for the following problem. My goal is to perform WGCNA
on a dataset of 19776 genes, so I opted to follow the block-wise network
construction (Section 2c) in the WGCNA R Tutorial by Peter Langfelder and
Steve Horvath.
I ended up with 10 blocks and am able to plot the dendrograms and
2018 Apr 12
1
WGCNA package installation segmentation fault
Hi all,
a user contacted me about a segfault when installing WGCNA package
dowloaded from CRAN. I also see a segfault like that on certain
installs of R.
The package passes all CRAN checks, so presumably this has something
to do with the R installation or environment. The R versions here are
not the newest but I would guess that this is not an R version issue.
I'm attaching two
2017 Dec 17
2
OpenBLAS in everyday R?
It seems like many of the multi-threaded BLASes have some sort of
fundamental problem preventing use in the way Juan suggests:
- Dirk's vignette states that ATLAS "fixes the number of cores used at
compile-time and cannot vary this setting at run-time", so any
user-friendly implementation for R would have to compile ATLAS for 1-16
threads to allow the user to switch at run-time.
2018 Jan 09
2
OpenBLAS in everyday R?
Please pardon my ignorance, but doesn't OpenBLAS still not always play
nicely with multi-threaded OpenMP? (for example, don't race conditions
sometimes crop up)? If so, it might be nice to have the ability to
temporarily disable multi-threaded OpenMP (effectively:
omp_set_num_threads(1)) for the duration of operations using OpenBLAS.
Regards
Ben
> Julia using OpenBLAS is *very*
2017 Dec 17
1
OpenBLAS in everyday R?
Julia Programming Language uses also OpenBlas, and it is actively
maintained with bugs being fixed as I have checked it out:
http://www.openblas.net/Changelog.txt
So I still see it ok to be included as an options(...) feature (by default
off, just for safety), over other Blas libraries.
R could not use Intel MKL for legal reasons (I think), because as long that
R ships with GPL libraries,
2018 Jan 10
5
OpenBLAS in everyday R?
I didn't do the compile; is there a way to check whether that was used?
If not, I'll inquire with our sysadmin and report back.
In any case, my suggestion was motivated by the fact that some parts of
R use OpenMP while others do not, in the hope that the former could have
their OpenBLAS omelet without breaking the OpenMP eggs, so to speak.
On 01/09/2018 06:41 PM, Keith O'Hara
2018 Jan 11
2
OpenBLAS in everyday R?
Thanks Keith. We checked, and indeed libopenblas is not linked against
libomp nor libgomp. We suspect this is because we used conda to install
R and OpenBLAS. So I guess we should be barking up the conda tree instead?
By the way, I also noticed on my home machine (Ubuntu),
/usr/lib/libopenblas.so.0 is also not linked against those, for what
that's worth.
Regards,
Ben
On 01/10/2018 12:04
2011 Mar 27
3
comparing heatmaps
Dear all,
I've been trying to find how to compare tow different heatmaps but I'm having trouble getting the colors bar to be the same. I'm doing something like the following:
library(gplots)
dat<-cor(matrix(rnorm(100, m=10), nrow=10))
mat<-cor(matrix(rnorm(100), nrow=10))
dev.new()
heatmap.2(mat, Rowv=NA, Colv=NA, col=redgreen(75), symm=TRUE, trace="none",
2018 Feb 13
0
Setting the path to Rtools for package compilation on Windows
I can confirm the behaviour that you report.?
Usually I put Rtools in c:\programs\Rtools and modify the path
accordingly. Recently (don't recall for how long) I have encountered
the same problems as you have and I have resorted to moving Rtools to
c:\Rtools
I have no idea as how to proceed; perhaps it could be worth trying an
older version of Rtools (though that may cause other problems).
2011 Jul 06
2
wgcna
Hi,
I'm running a tutorial ("Meta-analyses of data from two (or more) microarray data sets"), which use wgcna package. I have an error in the function modulePreservation (it is below).
I'm using R2.13
Can you help me? Do you know, what is happens?
Thanks
Raquel
multiExpr = list(A = list(data=t(badea)),B = list(data=t(mayo)))
# two independent datasets (dim = 13447 x 36)
mp =
2017 Dec 16
4
OpenBLAS in everyday R?
Hi R-devel list,
OpenBLAS is readily available for unix-likes:
https://cloud.r-project.org/web/packages/gcbd/vignettes/gcbd.pdf
However, my questions are:
1) Would R-devel consider using OpenBLAS for the main distribution of R for
all platforms including Windows?
2) If so, would R-devel set the default multi-thread level to the number of
(real) cores on a machine?
My sense is there're a
2018 Oct 02
3
maximum matrix size
I am now getting the occasional complaint about survival routines that are not able to
handle big data.?? I looked in the manuals to try and update my understanding of max
vector size, max matrix, max data set, etc; but it is either not there or I missed it (the
latter more likely).?? Is it still .Machine$integer.max for everything??? Will that
change??? Found where?
I am going to need to go
2011 Mar 23
2
Estimating correlation in multiple measures data
Dear R-helpers,
This may sound simple to you, but I'm a beginner in this, so please be
forgiving.
I have a following problem: two analytes were measured in patient's
blood on 4 occasions: ProteinA and ProteinB. How to correctly evaluate
correlation between ProteinA and ProteinB?
I tried:
x <- data.frame(Patient.ID=rep(1:10, each=4), Visit=rep(c(1:4),10),
ProteinA=rnorm(m=10,
2017 Dec 17
0
OpenBLAS in everyday R?
On Sat, Dec 16, 2017 at 7:41 PM, Kenny Bell <kmbell56 at gmail.com> wrote:
> It seems like many of the multi-threaded BLASes have some sort of
> fundamental problem preventing use in the way Juan suggests:
>
> - Dirk's vignette states that ATLAS "fixes the number of cores used at
> compile-time and cannot vary this setting at run-time", so any
> user-friendly
2003 Mar 16
1
single rsync of large directory structure versus several smaller rsync's
Hello,
I am working on a backup script using rsync and have a question.
Rather than doing a single rsync of /home/ I have set my script up
to loop over /etc/passwd and do a seperate rsync of each user home dir
(/home/user1, /home/user2) etc.
In the end, I should have the exact same backup either way. However I feel
safest doing it as multiple rsyncs (one for each user). I am doing this
2017 Jul 09
0
Error in WGCNA package
First, please read WGCNA FAQ at
https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html
regarding using RNA-seq and other count data.
Second, if you insist on using WGCNA on raw count data (which I don't
recommend), use something like
storage.mode(datExpr) = "double"
and try again.
Peter
On Sun, Jul 9, 2017 at 2:29 AM, Ankush Sharma <ankush.sak at
2010 Sep 01
8
how to replace NA with a specific score that is dependant on another indicator variable
Hi everyone,
I’m looking for a clever bit of code to replace NA’s with a specific score
depending on an indicator variable.
I can see how to do it using lots of if statements but I’m sure there most
be a neater, better way of doing it.
Any ideas at all will be much appreciated, I’m dreading coding up all those
if statements!!!!!
My problem is as follows:
I have a data set with
2017 Jul 09
1
Error in WGCNA package
Dear all ,
I would like to reconstruct coexpression networks from proteomic count data
having integer values. Some internal function doesn't like to work well
with integers. How can this error be rectified?
> adjacency = adjacency(datExpr, power = softPower, type = "signed");
Error in cor(datExpr, use = "p") :
REAL() can only be applied to a 'numeric', not a
2018 Jan 09
0
OpenBLAS in everyday R?
Do those issues still arise when OpenBLAS is compiled with USE_OPENMP=1 ?
Keith
> On Jan 9, 2018, at 6:03 PM, Benjamin Tyner <btyner at gmail.com> wrote:
>
> Please pardon my ignorance, but doesn't OpenBLAS still not always play nicely with multi-threaded OpenMP? (for example, don't race conditions sometimes crop up)? If so, it might be nice to have the ability to