similar to: example fails during R CMD CHECK but works interactively?

Thank you Dan but it isn't my tests that are failing (all of them pass without problem) but one of the examples from the inst/examples directory. I did try, however, to start R with the environmental variables as you suggest but it had no effect on my tests. Charles On Wed, May 13, 2015 at 1:51 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote: > > > ----- Original Message

Does anyone else have any thoughts about troubleshooting the R CMD check environment? Charles On Wed, May 13, 2015 at 1:57 PM, Charles Determan <cdetermanjr at gmail.com> wrote: > Thank you Dan but it isn't my tests that are failing (all of them pass > without problem) but one of the examples from the inst/examples directory. > I did try, however, to start R with the

Make the example print out Sys.getenv() and then manually inspect? Otherwise, you'll need to debug the code by adding print statements. Something clearly is not as you expect, so you need carefully empirically verify your assumptions about the inputs to and environment of the function. Hadley On Fri, May 15, 2015 at 7:05 AM, Charles Determan <cdetermanjr at gmail.com> wrote: > Does

----- Original Message ----- > From: "Charles Determan" <cdetermanjr at gmail.com> > To: r-devel at r-project.org > Sent: Wednesday, May 13, 2015 11:31:36 AM > Subject: [Rd] example fails during R CMD CHECK but works interactively? > > Greetings, > > I am collaborating with developing the bigmemory package and have run > in to > a strange problem

Dear all, bigKRLS, which has been on CRAN for a couple of years, had to be pulled recently due to what seems to be a sanitizer issue stemming from its use of bigmemory. bigKRLS works fine (we?ve used it ourselves on many different platforms and have had over 15,000 downloads without an end user reporting difficulties because of this issue). Unfortunately, we have been unable to reproduce the

R Developers, Could someone help explain what it means that R is single threaded? I am trying to understand what is actually going on inside R when users want to parallelize code. For example, using mclapply or foreach (with some backend) somehow allows users to benefit from multiple CPUs. Similarly there is the RcppParallel package for RMatrix/RVector objects. But none of these address the

This is strictly a curiosity question. I am aware the R doesn't possess a float data type. I also don't mean to request that such functionality be implemented as I'm sure it would require a large amount of work with potential back compatibility conflicts. But I wanted to know why R has never had a float data type available? Regards, Charles [[alternative HTML version deleted]]

Charles, 1. Perhaps this question is better directed at the R-help or R-pacakge-devel mailinglist. 2. It basically means that R itself can only evaluate one R expression at the time. The parallel package circumvents this by starting multiple R-sessions and dividing workload. Compiled code called by R (such as C++ code through RCpp or C-code through base R's interface) can execute

On 12 May 2016 at 13:11, Mark van der Loo wrote: | Charles, | | 1. Perhaps this question is better directed at the R-help or | R-pacakge-devel mailinglist. | | 2. It basically means that R itself can only evaluate one R expression at | the time. | | The parallel package circumvents this by starting multiple R-sessions and | dividing workload. | | Compiled code called by R (such as C++ code

Hello everybody, by the way, speaking about the r-cran-rcurl package in Ubuntu, the versions in trusty and vivid are linked by error to the "NSS" flavour of libcurl3 instead of the "OpenSSL flavour", which cause at least problems when using the CRAN devtools package. A bit more details are available in the Debian bug tracking system (https://bugs.debian.org/786473). I am not

I am trying to add the bigmemory packages but I get the following error message: In file included from bigmemory.cpp:14:0: ../inst/include/bigmemory/isna.hpp: In function 'bool neginf(double)': ../inst/include/bigmemory/isna.hpp:22:57: error: 'isinf' was not declared in this scope make: *** [bigmemory.o] Error 1 ERROR: compilation failed for package 'bigmemory' * removing

Hello All, I tried to intall the bigmemory package from a CRAN mirror site and received the following output while installing. Any idea what's going on and how to fix it? The system details are provided below. --------------------- begin error messages ----------------------- * installing *source* package 'bigmemory' ... checking for Sun Studio compiler...no checking for

My long-promised Rdsm package is now on CRAN. Some of you may recall that I made a prototype available on my own Web page last July. This is the official version, much evolved since I released the prototype. The CRAN description states: Provides a threads-like programming environment for R, usable both on a multicore machine and across a network of multiple machines. The package

Hi, I am trying to run the bigmemory example provided on the http://www.bigmemory.org/ The example runs on the "airline data" and generates summary of the csv files:- library(bigmemory) library(biganalytics) x <- read.big.matrix("2005.csv", type="integer", header=TRUE, backingfile="airline.bin", descriptorfile="airline.desc",

Hi, I'm playing around with the 'bigmemory' package, and I have finally managed to create some really big matrices. However, only now I realize that there may not be functions made for what I want to do with the matrices... I would like to perform a cluster analysis based on a big.matrix. Googling around I have found indications that a certain kmeans.big.matrix() function should

I work with problems that have rather large data requirements -- typically a bunch of multigig arrays. Given how generous R is with using memory, the only way for me to work with R has been to use bigmatrices from bigmemory package. One thing that is missing a bit is interoperability of bigmatrices with C++ and possibly java. What i mean by that is API that would allow read and write filebacked

Dear R-list I'm on my way to start a new project on a rather big panel, consisting of approximately 8 million observations in 30 waves of data and about 15 variables. I have a similar data set that is approximately 7 gigabytes in size. Until now I have done my data management in SAS, and Stata, mostly identifying spells, counting events in intervals, and a like, but I would like to

To answer your first question about read.big.matrix(), we don't know what your acc3.dat file is, but it doesn't appear to have been detected as a standard file (like a CSV file) or -- perhaps -- doesn't even exist (or doesn't exist in your current directory)? Next: > In addition, I am planning to do a multiple imputation with MICE package > using the data read by bigmemory

I recently learned about the bigmemory and foreach packages and am trying to use them to help me create a very large matrix. Without those packages, I can create the type of matrix that I want with 10 columns and 5e6 rows. I would like to be able to scale up to 5e9 rows, or more, if possible. I have created a simplified example of what I'm trying to do, below. The first part of the

Hi, With reference to the mail below, I have large datasets, coming from various different sources, which I can read into filebacked big.matrix using library bigmemory. I want to merge them all into one 'big.matrix' object. (Later, I want to run regression using library 'biglm'). I am unsuccessfully trying to do this from quite some time now. Can you please