Re: [Rd] xps installation error on Mac OS X 10.11

2016-01-13 Thread cstrato 

Dear Jack,

First, please do not use r-help or r-devel to ask Bioconductor-related 
questions, Bioconductor has its own support site for BioC packages:

https://support.bioconductor.org/

Second, please note that ROOT_6.x cannot be used for xps.

In the README file I mention for Yosemite:
ftp://root.cern.ch/root/root_v5.34.30.macosx64-10.10-clang61.tar.gz
However, you can probably also use the newest version:
ftp://root.cern.ch/root/root_v5.34.34.macosx64-10.10-clang61.tar.gz

Before installing ROOT again please make sure to delete all versions of 
ROOT that you have already installed.


Best regards,
Christian




On 01/13/16 18:28, Zhu, Jack (NIH/NCI) [E] wrote:

  Dear Christian,

Sorry for bothering you, but it looks like I really need your help with
the xps installation on my Mac OS X 10.11 system.  I have been
struggling for a few days and tried all the options listed in your
README file:

http://bioconductor.org/packages/devel/bioc/readmes/xps/README

I also read all the online posts related to the xps installation.  But
still have problem.  By strictly following the instructions,  I
re-installed ROOT from both source and binary for Mac OS X 10.11 and
added ROOT environmental variables in my .bashrc (all the four lines).
  The ROOT itself seems working totally fine by different tests and the

$ echo $ROOTSYS
/Applications/root_v6.06.00

$ echo $LD_LIBRARY_PATH
/Applications/root_v6.06.00/lib
$ echo $DYLD_LIBRARY_PATH
/Applications/root_v6.06.00
$echo $PATH
/Applications/root_v6.06.00/bin:…

But I always get an error with LD_LIBRARY_PATH when I try to install the
xps package from the source:

---
$R CMD INSTALL -d -l /Users/zhujack/Library/R/3.3/library
xps_1.31.0.tar.gz

found ROOT version 6.06/00 in directory /Applications/root_v6.06.00

xps configuration error:

You must set the shell variable LD_LIBRARY_PATH to the
directory where ROOT resides and re-run R CMD INSTALL
e.g., (using Bourne shell syntax):

   export "LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH"
   R CMD INSTALL xps

Please consult the README file for more information

ERROR: configuration failed for package ‘xps’
* removing ‘/Users/zhujack/Library/R/3.3/library/xps’
* restoring previous ‘/Users/zhujack/Library/R/3.3/library/xps’

I also tried to add the following line to the /usr/local/bin/R:

LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/Applications/root_v6.06.00/lib"
export LD_LIBRARY_PATH


But I still get the same error.  Your help and insigts will be greatly
appreciared.

Jack

 > sessionInfo()
R Under development (unstable) (2016-01-11 r69918)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.2 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] BiocInstaller_1.21.2


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[Rd] subscripting a table changed behavior in R devel

2016-01-13 Thread Hervé Pagès 

Hi,

With R 3.2.3:

  > t <- table(sample(6, 50, replace=TRUE), sample(4, 50, replace=TRUE))
  > class(t[1:3, ])
  [1] "matrix"

With R devel:

  > t <- table(sample(6, 50, replace=TRUE), sample(4, 50, replace=TRUE))
  > class(t[1:3, ])
  [1] "table"

This breaks some Bioconductor packages that are calling as.data.frame()
on the result of this subscripting (as.data.frame.table and
as.data.frame.matrix behave very differently).

Could this change be mentioned in the NEWS file?

Thanks,
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
Fax:(206) 667-1319

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[Rd] as.data.frame and illegal row.names argument (bug in package:DoE.wrapper?)

2016-01-13 Thread William Dunlap via R-devel 
as.data.frame methods behave inconsistently when they are given a row.name
argument of the wrong length.  The matrix method silently ignores row.names
if it has the wrong length and the numeric, integer, and character methods
do not bother to check and thus make an illegal data.frame.

> as.data.frame(matrix(1:6,nrow=3), row.names=c("One","Two"))
  V1 V2
1  1  4
2  2  5
3  3  6
> as.data.frame(1:3, row.names=c("One","Two"))
1:3
One   1
Two   2
Warning message:
In format.data.frame(x, digits = digits, na.encode = FALSE) :
  corrupt data frame: columns will be truncated or padded with NAs
> as.data.frame(c("a","b","c"), row.names=c("One","Two"))
c("a", "b", "c")
Onea
Twob
Warning message:
In format.data.frame(x, digits = digits, na.encode = FALSE) :
  corrupt data frame: columns will be truncated or padded with NAs

(The warnings are from the printing, not the making, of the data.frames.)

I ran into this while using the DoE.wrapper package, which has what I think
is a typo,
giving "t" as the row.names for the output of mapply():
   cross.design.R:ro <- as.data.frame(mapply("touter",ro1, ro2,
"paste", sep="_"),"t")

I don't know all the reasons why people use as.data.frame instead of
data.frame.


Bill Dunlap
TIBCO Software
wdunlap tibco.com

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