Displaying 20 results from an estimated 600 matches similar to: "trouble with installing Biobase package"
2017 Nov 29
2
SAMseq errors
Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (20000 genes x 550 samples) with survival endpoint. It quickly give the following error:
> library(samr)Loading required package: imputeLoading required package: matrixStats
Attaching package: ?matrixStats?
The following objects are masked from ?package:Biobase?:
? ? anyMissing, rowMedians
Warning messages:1: package ?samr? was
2017 Nov 29
0
SAMseq errors
Sorry forgot to use plain text format, hope this time it works:
Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (20000 genes x 550 samples) with survival endpoint. It quickly give the following error:
> library(samr)
Loading required package: impute
Loading required package: matrixStats
Attaching package: ?matrixStats?
The following objects are masked from
2008 May 01
2
Error while making R package
Hi All,
I am trying to make R package using R 2.6.2
And I am getting following error.
When I give R CMD check t1\
---------- Making package t1 ------------
adding build stamp to DESCRIPTION
making DLL ...
making CGHseg_rewrite.d from CGHseg_rewrite.c
making rowMedians.d from rowMedians.c
making runavg.d from runavg.c
gcc-sjlj -std=gnu99 -Ic:/R/R-2.6.2/include -O3 -Wall -c
2007 May 14
1
Native implementation of rowMedians()
Hi,
I've got a version of rowMedians(x, na.rm=FALSE) for matrices that
handles missing values implemented in C. It has been optimized for
memory and speed. To avoid coercing integers to doubles, and hence
allocate an additional 200% memory, there is one C function for
integers and one for doubles.
The rowMedians() implementation is currently sitting in my non-CRAN
package R.native
2004 Oct 11
1
install failure Ruuid package on OS X
Dear All,
When installing the Ruuid package (from Bioconductor) from sources on my
MAC (OS X 10.3.5, R version 2.0.0) I get the following errors:
m00245:~ ivisser$ R CMD INSTALL -l /Users/ivisser/Library/R/library/
/Users/ivisser/Desktop/Ruuid
* Installing *source* package 'Ruuid' ...
loading cache ./config.cache
checking for glib-config... no
checking how to run the C preprocessor...
2006 Feb 13
1
MinGW and the ld bug
Hi.
I noticed that Brian Ripley found and corrected a bug in MinGW's
ld.exe, see http://www.murdoch-sutherland.com/Rtools/. Thanks for
this. I wonder if this is the same bug that cause my problems. I
have tiny toy package with C code that installs perfectly on R Version
2.2.1 beta (2005-12-18 r36792) [this version was mislabelled "beta"
the first few hours on CRAN when the stable
2006 Jun 12
1
Ruuid had non-zero exit status (PR#8965)
> source("http://www.bioconductor.org/biocLite.R")
> biocLite(c("Ruuid"))
Running getBioC version 0.1.6 with R version 2.3.1
Running biocinstall version 1.8.4 with R version 2.3.1
Your version of R requires version 1.8 of Bioconductor.
trying URL
'http://bioconductor.org/packages/1.8/bioc/src/contrib/Ruuid_1.10.0.tar.gz'
Content type 'application/x-gzip'
2018 Jan 19
1
IBM Power vs Markdown
Hi, folks.
I was wondering if any of you could point me in the right direction.
Using R 3.3.3 (and later), on an IBM Power LPAR, Red Hat 7 PPC64le, markdown build fails as below.
> install.packages("markdown")
trying URL 'https://cloud.r-project.org/src/contrib/markdown_0.8.tar.gz'
Content type 'unknown' length 80583 bytes (78 KB)
2014 Dec 06
1
R CMD check --as-cran and (a)spell checking
Does anyone know if it is possible to add a dictionary file of known
words that becomes part of the *built* package to tell 'R CMD check
--as-cran' not to report these words as misspelled. I want this
dictionary to come with the *.tar.gz such that it will be available
regardless where the package is checked. For instance, currently I
get:
* using log directory
2013 Apr 03
1
Select single probe-set with median expression from multiple probe-sets corresponding to same gene -AFFY
Hello All,
I need your help. I am analysing affymetrix data and have to select the
probe-set that has median expression among all the probe-sets for same
gene. This way I want to remove the redundancy by keeping the analysis
to single gene entry level. I am fully aware that it is not a nice thing
to do but I just have to do it.
To do so, I came across 'findLargest' function of
2008 Jan 07
2
Efficient way to substract all entries in two vectors from each other
Hi all,
I'm to inexperienced to come up with the matrix solution elusively appearing
on the horizon for the following problem and would appreciate if you could
give me a nudge ...
I have two vectors a, and b and need to find the closest match for each
value of a in b.
How to do that efficiently?
Thanks, Joh
2012 Jun 27
1
rJava Error
Hi,
I'm receiving an error when I am trying to install rJava. I have posted the
error below.
RHive_0.0-6.tar.gz rJava_0.9-3.tar.gz RJDBC_0.2-0.tar.gz
Rserve_0.6-8.tar.gz
[root at localhost Package]# R CMD INSTALL rJava_0.9-3.tar.gz
* installing to library ?/usr/local/lib64/R/library?
* installing *source* package ?rJava? ...
** package ?rJava? successfully unpacked and MD5 sums checked
2007 Aug 13
3
hasNA() / anyNA()?
Hi,
is there a hasNA() / an anyNA() function in R? Of course,
hasNA <- function(x) {
any(is.na(x));
}
would do, but that would scan all elements in 'x' and then do the
test. I'm looking for a more efficient implementation that returns
TRUE at the first NA, e.g.
hasNA <- function(x) {
for (kk in seq(along=x)) {
if (is.na(x[kk]))
return(TRUE);
}
FALSE;
}
2008 Aug 12
3
aligned memory allocation in C
Hi,
I'm currently R porting SF Mersenne Twister algorithm of Matsumoto and
Saito. To get the full power of their code, I want to use their
fonction fill_array32 which need aligned memory. That is to say I need
to use the C function memalign on windows, posix_memalign on linux and
classic malloc on Mac OS. In 'writing R extenstion', they recommand to
use R_alloc function to
2008 Aug 12
3
aligned memory allocation in C
Hi,
I'm currently R porting SF Mersenne Twister algorithm of Matsumoto and
Saito. To get the full power of their code, I want to use their
fonction fill_array32 which need aligned memory. That is to say I need
to use the C function memalign on windows, posix_memalign on linux and
classic malloc on Mac OS. In 'writing R extenstion', they recommand to
use R_alloc function to
2013 Mar 09
5
question on why Rigroup package moved to Archive on CRAN
Hi,
Who should I ask about my package Rigroup_0.83 being moved to Archive status on CRAN and no longer available via install.package? I have no problems with the move if this was simply because of low demand. However, if there was a build issue with the newest releases that caused problems, I would be happy to address it. I'll just ask my students to install it from my own locally hosted
2008 Sep 05
1
Problem installing Biobase on Solaris
Hi everyone
This is my first post to the list. I had experience installing and using
Bioconductor on Linux and Windows systems but I am encountering problems
installing Biobase on Solaris running on Sparc. The package compilation
works fine, with only a warning
warning: implicit declaration of function `__builtin_isnan'
the help files are generated but in the end it fails with an error
2006 Sep 05
1
Reserve and biobase
Hi
I am using Rserve for R2.3.1.
every time after I load Biobase library, a new Graphics window frame pops up. Could any onw know how can avoid it.
Best
Saeede
class testReserve {
public static void main(String[] args) {
RServeConnection rsCon = null;
Rconnection c = null;
Process proc = null;
try {
Runtime rt = Runtime.getRuntime();
proc
2006 Mar 15
1
installation problem with Biobase
Hello,
I wanted to install MergeMaid package in v 2.2.1. I could install it but couldn't use without its dependant, Biobase. at biobase installation, I got the following error message
In method for function "split": expanding the signature
to include omitted arguments in definition: drop = "missing"
Error in .MakeSignature(new("signature"), def, signature) :
2014 Sep 30
2
Shallow copies
I have a question about shallow copies in R. Since R 3.1.0, subsetting
a dataframe with respect to its columns no longer result in deep
copies. This is an amazing change in my opinion. Now, subsetting a
data.frame by rows (or subsetting a matrix by columns or rows) still
does deep copies. In particular, it is my understanding that running a
command on a very large subset of rows (say