Displaying 20 results from an estimated 300 matches similar to: "Windows download.file sometimes pauses / truncates large files"
2010 Sep 13
4
Problem with WARNING...headers with CRLF line endings
Dear all,
When running R CMD check on Windows XP to test my package I get the
following warning message:
"* checking line endings in C/C++/Fortran sources/headers ... WARNING
Found the following sources/headers with CR or CRLF line endings:
src/xpsDict.h"
The problem is that this file is created by the compiler AUTOMATICALLY
during the compilation process, and since the file is
2011 Feb 03
1
bug in codetools/R CMD check?
Hi Mr Tierney,
I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+)
e.g.:
http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html
----------------
* checking R code for possible problems ... NOTE
Warning: non-unique value when setting 'row.names': ?new?
Error in
2011 Apr 11
1
R CMD build --resave-data
Hi,
More about the new --resave-data option
As mentioned previously here
https://stat.ethz.ch/pipermail/r-devel/2011-April/060511.html
'R CMD build' and 'R CMD INSTALL' handle this new option
inconsistently. The former does --resave-data="gzip" by default.
The latter doesn't seem to support the --resave-data= syntax:
the --resave-data flag must either be
2010 Jul 12
0
Strange issues with new R-based 'R CMD build' and 'R CMD check' scripts on Windows
Hi,
Kind of related to the new R-based 'R CMD build' script being
sometimes confused on Windows (as reported here a couple of weeks
ago https://stat.ethz.ch/pipermail/r-devel/2010-June/057759.html),
I also started to observe that the new R-based 'R CMD check' script
gets also confused sometimes on Windows in a random way.
It seems that sometimes (maybe 1% of the times) running
2011 Oct 19
0
warnings issued at installation time not reported by 'R CMD check'
Hi,
Warnings issued at installation time are not reported by 'R CMD check'.
Some of them are really important and telling something very useful
to the developer. See for example this warning:
http://bioconductor.org/checkResults/2.9/bioc-LATEST/globaltest/wilson2-checksrc.html
Actually, there is no formal warning reported by 'R CMD check' for
this package but if you scroll
2006 Sep 22
1
Possible bug in base::namespaceImportFrom?
Hi,
namespaceImportFrom in base/R/namespace.R has the following:
fdef <- methods:::getGeneric(genName, impenv)
The definition of getGeneric is in methods/R/RMethodUtils.R starts
with:
getGeneric <-
## return the definition of the function named f as a generic.
##
## If there is no definition, throws an error or returns
## NULL according to the value of
2012 Oct 27
0
Remote access to R/Bioconductor on EBI's 64-bit Linux Cluster
Hi Rusers
Here is a place for testing R on Cloud.
http://www.ebi.ac.uk/Tools/rcloud/ <http://www.ebi.ac.uk/Tools/rcloud/>
Start the workbench by downloading the package for your operating system
(Macintosh or Windows), or via Java Web Start, and you will get access to an
instance of R running on one of EBI's powerful machines. You can install
additional packages, upload your own
2005 Feb 16
4
festival text for weather report
http://www.srh.noaa.gov/fwd/productviewnation.php?pil=OKXZFPOKX&version=
0
can anyone suggest how I could set up asterisk@home to read out allowed
the following text when I dial extension 850?
815 PM EST WED FEB 16 2005
.OVERNIGHT...MOSTLY CLEAR. LOWS 30 TO 35. NORTHWEST WINDS 15 TO 20
MPH WITH GUSTS UP TO 30 MPH...DIMINISHING TO 10 TO 15 MPH LATE.
.THURSDAY...PARTLY CLOUDY. COOLER
2008 Jun 12
3
Problem with rowMeans()
Hi all,
I have a matrix called 'data', which looks like:
> data[1:4,1:4]
Probe_ID Gene_Symbol M1601 M1602
1 A_23_P105862 13CDNA73 -1.6 0.16
2 A_23_P76435 15E1.2 0.18 0.59
3 A_24_P402115 15E1.2 1.63 -0.62
4 A_32_P227764 15E1.2 -0.76 -0.42
> dim(data)
[1]
2023 Nov 03
2
'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0
Hi list,
Here is an example:
??? hpages at XPS15:~$ R CMD INSTALL CoreGx
??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library?
??? * installing *source* package ?CoreGx? ...
??? ** using staged installation
??? ** R
??? ** data
??? *** moving datasets to lazyload DB
??? ** inst
??? ** byte-compile and prepare package for lazy loading
??? Error : in method for
2010 Jun 21
1
No output/no source tarball produced by 'R CMD build' on Windows (but ret code is 0)
Hi,
After updating R-2.12 on the Bioconductor build system about 1 week ago
(we update R every 4-6 weeks for our devel builds), we've started to see
something never seen before on Windows: for some BioC packages,
'R CMD build' would produce no output at all (0 byte) and, of course,
no source tarball. Even though, the code returned by the command is 0!
See an example of this is here:
2019 Nov 15
2
S3 methods in packages. Change in R 4.0.0?
Hello,
since Bioconductor devel branch 3.11 started, which is operating with
R-devel 4.0.0 (for e.g. 2019-11-03 r77362 on OS X 10.11.6 El Capitan),
my package CFAssay 1.21.0 is not built on none of all three Systems,
Linux, Windos and Mac. The error message refers to xy.coords which is
called by R function plot.default. I found out that it has to do with
the S3 object system. In my package I
2023 Nov 04
1
'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0
>>>>> Herv? Pag?s
>>>>> on Fri, 3 Nov 2023 15:10:40 -0700 writes:
> Hi list,
> Here is an example:
> ??? hpages at XPS15:~$ R CMD INSTALL CoreGx ??? * installing
> ??? hpages at XPS15:~$ R CMD INSTALL CoreGx
> ??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library?
2014 Jun 23
1
operation on ‘numsels’ may be undefined
Dear all,
Since many years the following C++ code does compile on ALL Bioconductor
servers (Linux, Windows, Mac) without any warnings:
Int_t numsels = 0; //number of selected entries
...
for (Int_t i=0; i<size; i++) {
numsels = (arrMask[i] == 1) ? ++numsels : numsels;
}//for_i
Even on the recently added release server 'zin2' Linux (Ubuntu 12.04.4
LTS) the
2012 Feb 09
1
scan() doesn't like '1.#IND'
Hi,
Since C++ code compiled with g++ 4.6.3 on Windows (the version included
in latest Rtools) now can produce things like '1.#IND' when writing
doubles to a file (using the << operator), I wonder whether scan()
shouldn't support those things. Right now (with recent R devel and
latest Rtools) we get errors like:
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
2018 Feb 07
1
release build of ChemmineR failing
The release version of ChemmineR is failing on windows. It seems to be a
build script issue though, possibly something on your side. The package
was building fine a few weeks ago and I have not modified it. Can you
please have a look? Thanks.
"C:/Users/BIOCBU?1/BBS-3?1.6-B/R/bin/Rscript" -e "library(rmarkdown); library(BiocStyle); rmarkdown::render('ChemmineR.Rmd')"
2010 Jun 10
1
R-based version of R CMD build broken on Windows
Hi,
The R-based version of R CMD build doesn't work for me on Windows:
E:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\Biobase
* checking for file 'meat\Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
Warning in shell(sprintf("%s > %s
2003 Jul 12
1
AGI script sample using bash shell script
Hi,
A quick and dirty (aka Rapid Application Developement) AGI script
implement using bash shell. No need to invoke a 10MB perl engine to
process simple asterisk agi scripts.
I found it to be very useful in learning the AGI interface. For example,
I learn that AGI won't execute the next command until you read the
results from STDIN.
Enjoy,
Sunny Woo
Solution Consultant
Avantnix
2013 Mar 03
1
Missing PROTECT in mkPRIMSXP ?
The Bioconductor build for a package DirichletMultinomial on
R Under development (unstable) (2013-02-26 r62077) -- "Unsuffered Consequences"
at
http://bioconductor.org/checkResults/devel/bioc-LATEST/DirichletMultinomial/george2-buildsrc.html
shows
* creating vignettes ... ERROR
...
Error: processing vignette ?DirichletMultinomial.Rnw? failed with diagnostics:
chunk 21 (label
2017 Apr 19
2
Default R-3.4.0 RC CXXFLAGS without -O2 on x86_64-linux-gnu with g++-5.4.0 causes WARNING from stl_list.h
Hi r-devel,
a recent install of R-3.4.0 RC (2017-04-13 r72510)?
on Linux (Ubuntu 16.04.1 LTS) x86_64-linux-gnu?
with?g++ (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609
(see?http://bioconductor.org/checkResults/devel/bioc-LATEST/malbec2-NodeInfo.html?for more)?
results in CXXFLAGS not containing "-O2" as optimisation flag,
there is only " -Wall", while?CFLAGS are happy with