Re: [R] Unable to load GRanges
Looks like you do not have permissions to write to that directory, but
it's not clear that this is a major problem. The updating of boot and
foreign is not something that regular non BioC users would have usually
needed. Did you recently update your R installation? Library locations
sometimes get changed when you do that. If so, what happens when you
execute:
update.packages(checkBuilt=TRUE)
--
David.
On 8/17/19 7:56 AM, Tewelde Tesfaye wrote:
Dear Sir/Madam
Greetings
Error message [
install.packages("BiocManager")
Installing package into
‘C:/Users/default.DESKTOP-DE6RR7L/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL '
https://cloud.r-project.org/bin/windows/contrib/3.6/BiocManager_1.30.4.zip'
Content type 'application/zip' length 292998 bytes (286 KB)
downloaded 286 KB
package ‘BiocManager’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\default.DESKTOP-DE6RR7L\AppData\Local\Temp\RtmpKSLUUH\downloaded_packages
BiocManager::install("GenomicRanges")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
Installing package(s) 'GenomicRanges'
trying URL '
https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/GenomicRanges_1.36.0.zip
'
Content type 'application/zip' length 2135144 bytes (2.0 MB)
downloaded 2.0 MB
package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\default.DESKTOP-DE6RR7L\AppData\Local\Temp\RtmpKSLUUH\downloaded_packages
installation path not writeable, unable to update packages: boot, foreign,
nlme ]
[[alternative HTML version deleted]]
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Re: [R] Unable to load GRanges
This mailing list is the wrong place to ask a BioC question. I do recommend
asking a question when you finally do arrive at the correct forum ... the below
information seems to suggest that something you did or something odd about your
account privileges lead to that output but you haven't indicated what you did.
https://www.bioconductor.org/help/support/
https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html
On August 17, 2019 7:56:35 AM PDT, Tewelde Tesfaye wrote:
>Dear Sir/Madam
>Greetings
>Error message [
>install.packages("BiocManager")
>Installing package into
>‘C:/Users/default.DESKTOP-DE6RR7L/Documents/R/win-library/3.6’
>(as ‘lib’ is unspecified)
>--- Please select a CRAN mirror for use in this session ---
>trying URL '
>https://cloud.r-project.org/bin/windows/contrib/3.6/BiocManager_1.30.4.zip'
>Content type 'application/zip' length 292998 bytes (286 KB)
>downloaded 286 KB
>
>package ‘BiocManager’ successfully unpacked and MD5 sums checked
>
>The downloaded binary packages are in
>
>C:\Users\default.DESKTOP-DE6RR7L\AppData\Local\Temp\RtmpKSLUUH\downloaded_packages
>> BiocManager::install("GenomicRanges")
>Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
>Installing package(s) 'GenomicRanges'
>trying URL '
>https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/GenomicRanges_1.36.0.zip
>'
>Content type 'application/zip' length 2135144 bytes (2.0 MB)
>downloaded 2.0 MB
>
>package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
>
>The downloaded binary packages are in
>
>C:\Users\default.DESKTOP-DE6RR7L\AppData\Local\Temp\RtmpKSLUUH\downloaded_packages
>installation path not writeable, unable to update packages: boot,
>foreign,
>nlme ]
>
> [[alternative HTML version deleted]]
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
--
Sent from my phone. Please excuse my brevity.
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[R] Unable to load GRanges
Dear Sir/Madam
Greetings
Error message [
install.packages("BiocManager")
Installing package into
‘C:/Users/default.DESKTOP-DE6RR7L/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL '
https://cloud.r-project.org/bin/windows/contrib/3.6/BiocManager_1.30.4.zip'
Content type 'application/zip' length 292998 bytes (286 KB)
downloaded 286 KB
package ‘BiocManager’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\default.DESKTOP-DE6RR7L\AppData\Local\Temp\RtmpKSLUUH\downloaded_packages
> BiocManager::install("GenomicRanges")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
Installing package(s) 'GenomicRanges'
trying URL '
https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/GenomicRanges_1.36.0.zip
'
Content type 'application/zip' length 2135144 bytes (2.0 MB)
downloaded 2.0 MB
package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\default.DESKTOP-DE6RR7L\AppData\Local\Temp\RtmpKSLUUH\downloaded_packages
installation path not writeable, unable to update packages: boot, foreign,
nlme ]
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] GMP help - converting rosetta RSA-code to R
Please post in plain text. You assume significant risk that we will
receive a corrupt version of your code if you fail to do this.
As far as I can see, the gmp package does not currently support a raw
interface to create bigz values. Here is my workaround:
plaintext <- "Rossetta Code"
stringtoasciihex <- function( s ) {
vs <- strsplit( s, "", fixed = TRUE )[[ 1 ]]
asc <- sapply( vs, function( C ) as.character( charToRaw( C ) ) )
paste( c( "0x", asc ), collapse="" )
}
gmp::as.bigz( stringtoasciihex( plaintext ) )
###
On Sat, 17 Aug 2019, Martin M?ller Skarbiniks Pedersen wrote:
Hi,
I am trying to make a R version a RosettaCode task involving big number.
More precise, I am trying to convert the c-solution
http://rosettacode.org/wiki/RSA_code#C
to R.
These two lines in C gives me problems:
const char *plaintext = "Rossetta Code";
mpz_import(pt, strlen(plaintext), 1, 1, 0, 0, plaintext);
I have tried:
library(gmp)
plaintext <- "Rossetta Code"
as.bigz(charToRaw(plaintext))
and
library(gmp)
plaintext <- "Rossetta Code
as.big(split(plaintext,""))
Thanks for any help/suggestions
Regards
Martin M. S. Pedersen
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---
Jeff NewmillerThe . . Go Live...
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Re: [R] gmp coredump - where to report?
I has trying to convert some raw values into a big number with the
library gmp.
However the library makes R crash. Two questions:
1. Should I report the problem and if yes, where can I report the problem?
You can report the problem by calling bug.report(package="gmp") and filling
in the details.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Fri, Aug 16, 2019 at 4:10 PM Martin Møller Skarbiniks Pedersen <
traxpla...@gmail.com> wrote:
> Hi,
>
> I has trying to convert some raw values into a big number with the
> library gmp.
> However the library makes R crash. Two questions:
>
> 1. Should I report the problem and if yes, where can I report the problem?
> 2. Is the source code for the R version of GMP somewhere on eg. github, so
> I can
> post an issue?
>
> Regards
> Martin
>
> Here is the code that generate the core-dump:
>
> $ head -3 ~/R/x86_64-pc-linux-gnu-library/3.6/gmp/DESCRIPTION
> Package: gmp
> Version: 0.5-13.5
> Date: 2019-02-21
>
> $ R --version | head -3
> R version 3.6.1 (2019-07-05) -- "Action of the Toes"
> Copyright (C) 2019 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> $ R --vanilla
>
> > library(gmp)
> > as.bigz(charToRaw("a"))
>
> *** caught segfault ***
> address 0x560e78e1dd4c, cause 'memory not mapped'
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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[R] GMP help - converting rosetta RSA-code to R
Hi, I am trying to make a R version a RosettaCode task involving big number. More precise, I am trying to convert the c-solution http://rosettacode.org/wiki/RSA_code#C to R. These two lines in C gives me problems: const char *plaintext = "Rossetta Code"; mpz_import(pt, strlen(plaintext), 1, 1, 0, 0, plaintext); I have tried: library(gmp) plaintext <- "Rossetta Code" as.bigz(charToRaw(plaintext)) and library(gmp) plaintext <- "Rossetta Code as.big(split(plaintext,"")) Thanks for any help/suggestions Regards Martin M. S. Pedersen [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
