Re: [R] Install OpenCL
Dear Quirin, To be able to install OpenCL on ArchLinux, I needed to install opencl-headers first, because my system complained about CL/opencl.h ... Maybe there is something like that on Windows ... Best, Rasmus [1] https://archlinux.org/packages/extra/any/opencl-headers/ __ 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.
[R] Install OpenCL
Hi everyone,
the installation of OpenCL on windows with CUDA 11.7 failed. I can set
up tensorflow in python and communicate with the GPU, so I assume CUDA
is set up correctly. OpenCL headers are also available through the CUDA
toolkit.
However, the package installation of OpenCL in R fails. There is not
much documentation available. Can anyone help with that please?
> install.packages("OpenCL")
Installiere Paket nach ‘C:/Users/quiri/AppData/Local/R/win-library/4.2’
(da ‘lib’ nicht spezifiziert)
Paket, das nur als Quelltext vorliegt und eventuell Übersetzung von
C/C++/Fortran benötigt.: ‘OpenCL’
installiere Quellpaket ‘OpenCL’
trying URL 'https://cran.rstudio.com/src/contrib/OpenCL_0.2-2.tar.gz'
Content type 'application/x-gzip' length 20881 bytes (20 KB)
downloaded 20 KB
* installing *source* package 'OpenCL' ...
** Paket 'OpenCL' erfolgreich entpackt und MD5 Summen überprüft
** using staged installation
ERROR: OCL not set!
You will need a working OpenCL SDK with headers
and libraries for both i386 and x64
Set OCL to the root of the SDK
You can also set individial variables OCLINC,
OCL32LIB and OCL64LIB. If they are not set,
the default layout will be assumed.
ERROR: configuration failed for package 'OpenCL'
* removing 'C:/Users/quiri/AppData/Local/R/win-library/4.2/OpenCL'
Warning in install.packages :
Installation des Pakets ‘OpenCL’ hatte Exit-Status ungleich 0
Die heruntergeladenen Quellpakete sind in
‘C:\Users\quiri\AppData\Local\Temp\RtmpeepQng\downloaded_packages’
Best regards,
Quirin
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Re: [R] R_LIBS var needed to be set after upgrade to R 4.2.2
Dear Sir,
Many thanks for the reply.
Best,
Ashim
On Thu, Jun 2, 2022 at 12:56 PM Martin Maechler
wrote:
>
> > Ashim Kapoor
> > on Wed, 1 Jun 2022 14:30:58 +0530 writes:
>
> > Dear Sir,
> >> > I upgraded to R 4.2.2 on Debian 10 today.
> >>
> >> Well, I assume you mean R 4.2.0 .. at least that one exists.
>
> > My bad, yes I made a typo. I did mean R 4.2.0.
>
> >> > The R shell incantation worked fine and all libraries would load but,
> >> > I needed to point the R_LIBS variable to
> >> > /usr/local/lib/R/site-library/ in order for the R --vanilla <
> myfile.R
> >> > incantation to find the libraries.
> >>
> >> you mean other installed *packages*
> >>
> >> > May I ask, why was this ? I never needed to do this on any previous
> >> > upgrade to R.
> >>
> >> Well, for me, the R --vanilla form also only sees the
> >> 29 (14 "base" + 15 "Recommended") packages that come with R.
>
> > Has this ALWAYS been the case for you ? Even with prior versions of R ?
>
> Yes; I'm sorry this was unclear.
>
> >> Debian (& Ubuntu etc) have used a similar setup where the
> >> default {R-level} .libPaths() has contained three libraries,
> >> via
> >>
> >>
> R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}
> >>
> >> see
> >>
> >> https://cloud.r-project.org/bin/linux/debian/#pathways-to-r-packages
> >>
> >> also for much more.
> >> Note (also from the above CRAN page
> >> https://cloud.r-project.org/bin/linux/debian/
> >> [ Remember "menu" "Binaries" -> "Linux" -> "Debian" ]
> >>
> >> The good thing about the Debian (and derivatives) setup is that
> >> it also separates (as I do) the "packages that come with R" in
> >> one library (= /usr/lib/R/library) from packages that are
> >> installed differently.
>
> > My confusion is : Earlier R --vanilla incantation was working fine,
> > even without my intervening and
> > adding to R_LIBS. That is why I was confused.
>
> > My main query is : Is there anything special to R 4.2.0 which needs
> > R_LIBS to be setup seperately?
>
> to which Jeroen Ooms answered nicely -- thank you, Jeroen!
>
> > I was hit by this problem as well a few weeks ago. You may get a more
> > detailed answer in r-sig-debian or from Dirk directly, but from what I
> > understood, this is now expected behavior: indeed if you start R
> > --vanilla then /usr/local/lib is no longer included in the library path.
>
> > The reason is that R-core made a change in 4.2.0 to pre-set values for
> > R_LIBS_USER and R_LIBS_SITE in Renviron [1] which would take
> > precedence over the proper distro defaults (that include
> > /usr/local/lib) as configured by the r-base deb/rpm packages. To
> > mitigate the problem the r-base deb package moved the appropriate
> > R_LIBS_USER and R_LIBS_SITE definitions into Renviron.site, which
> > takes precedence over Renviron. However a side effect of this solution
> > is that Renviron.site is ignored in --vanilla mode. At least this is
> > my best understanding of the problem.
>
> > [1] https://cran.r-project.org/doc/manuals/r-release/NEWS.html
>
> Yes, as
>
> R --help | grep -A1 -e --vanilla | head -2
>
> has given
>
> --vanilla Combine --no-save, --no-restore, --no-site-file,
> --no-init-file and --no-environ
>
> (unchanged for many years).
>
>
> Being a Linux user of more than 25 years, I've not been much of a
> Debian-or-derivatives user in recent years (apart from setting up
> and maintaining Ubuntu LTS on my wife's computer) mainly because
> of lazyness as our IT staff helps me solve all problems with
> Fedora quickly, including lowelevel device-related ones,
> I think that Debian(+derivatives) has always been the exception
> among the Linux distros and for all the others, '--vanilla'
> really meant "vanilla" in a loose sense, i.e., "just base R".
>
> I agree that I had wanted a "vanilla+strawberry" version myself, really.
> which would be just not have the --no-site-file switch,
> so we could call it
>--vanilla+site
>
> {Others may hate "feature creep" and yet more output from
> 'R --help' ..}
>
> Martin
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Re: [R] Request for some help: Error when joining multiple csv files together
Hello, I'm seeing two obvious errors, those are not csv files and the columns spec is wrong, you have a spec of 6 columns but the posted data only has 4 and of different classes. If the data is in comma separated values (CSV) files the following worked without errors. library(readr) col_spec <- cols( d1 = col_double(), d2 = col_double(), d3 = col_double(), d4 = col_double() ) list.files(pattern = "*\\.csv$") |> lapply(read_csv, col_types = col_spec) |> dplyr::bind_rows() If the data is like in the question, try instead list.files(pattern = "*\\.csv$") |> lapply(read_delim, delim = " ", col_types = col_spec) |> dplyr::bind_rows() Hope this helps, Rui Barradas Às 00:17 de 02/06/2022, Bhaskar Mitra escreveu: Hello Everyone, I have a bunch of csv files, all with common headers (d1, d2, d3, d4). When I am trying to join the csv files together, with the following code (shown below), I am getting a warning when the files are joined. The values under columns d3 and d4 are not joined properly. The code and the error are given below. I would really appreciate some help in this regard. regards, bhaskar #---code df <- list.files(pattern = "*.csv") %>% lapply(read_csv) %>% bind_rows #---code Header of each file: d1 d2 d3 d4 3 4NA NA 4 5 NA 7 5 6 8 8 6 7 8 NA # #Warning when the codes run -- Column specification ─ cols( .default = col_double(), name = col_character(), d1 = col_datetime(format = ""), d2 = col_character(), d3 = col_logical(), d4 = col_logical() ) Warning: 48766 parsing failures. * row**col* * expected * *actual* *file* 3529 d3 1/0/T/F/TRUE/FALSE 100 'file1.csv' 3529 d41/0/T/F/TRUE/FALSE 100 'file1.csv' . .. .. [[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. __ 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.
Re: [R] R_LIBS var needed to be set after upgrade to R 4.2.2
> Ashim Kapoor
> on Wed, 1 Jun 2022 14:30:58 +0530 writes:
> Dear Sir,
>> > I upgraded to R 4.2.2 on Debian 10 today.
>>
>> Well, I assume you mean R 4.2.0 .. at least that one exists.
> My bad, yes I made a typo. I did mean R 4.2.0.
>> > The R shell incantation worked fine and all libraries would load but,
>> > I needed to point the R_LIBS variable to
>> > /usr/local/lib/R/site-library/ in order for the R --vanilla < myfile.R
>> > incantation to find the libraries.
>>
>> you mean other installed *packages*
>>
>> > May I ask, why was this ? I never needed to do this on any previous
>> > upgrade to R.
>>
>> Well, for me, the R --vanilla form also only sees the
>> 29 (14 "base" + 15 "Recommended") packages that come with R.
> Has this ALWAYS been the case for you ? Even with prior versions of R ?
Yes; I'm sorry this was unclear.
>> Debian (& Ubuntu etc) have used a similar setup where the
>> default {R-level} .libPaths() has contained three libraries,
>> via
>>
>>
R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}
>>
>> see
>>
>> https://cloud.r-project.org/bin/linux/debian/#pathways-to-r-packages
>>
>> also for much more.
>> Note (also from the above CRAN page
>> https://cloud.r-project.org/bin/linux/debian/
>> [ Remember "menu" "Binaries" -> "Linux" -> "Debian" ]
>>
>> The good thing about the Debian (and derivatives) setup is that
>> it also separates (as I do) the "packages that come with R" in
>> one library (= /usr/lib/R/library) from packages that are
>> installed differently.
> My confusion is : Earlier R --vanilla incantation was working fine,
> even without my intervening and
> adding to R_LIBS. That is why I was confused.
> My main query is : Is there anything special to R 4.2.0 which needs
> R_LIBS to be setup seperately?
to which Jeroen Ooms answered nicely -- thank you, Jeroen!
> I was hit by this problem as well a few weeks ago. You may get a more
> detailed answer in r-sig-debian or from Dirk directly, but from what I
> understood, this is now expected behavior: indeed if you start R
> --vanilla then /usr/local/lib is no longer included in the library path.
> The reason is that R-core made a change in 4.2.0 to pre-set values for
> R_LIBS_USER and R_LIBS_SITE in Renviron [1] which would take
> precedence over the proper distro defaults (that include
> /usr/local/lib) as configured by the r-base deb/rpm packages. To
> mitigate the problem the r-base deb package moved the appropriate
> R_LIBS_USER and R_LIBS_SITE definitions into Renviron.site, which
> takes precedence over Renviron. However a side effect of this solution
> is that Renviron.site is ignored in --vanilla mode. At least this is
> my best understanding of the problem.
> [1] https://cran.r-project.org/doc/manuals/r-release/NEWS.html
Yes, as
R --help | grep -A1 -e --vanilla | head -2
has given
--vanilla Combine --no-save, --no-restore, --no-site-file,
--no-init-file and --no-environ
(unchanged for many years).
Being a Linux user of more than 25 years, I've not been much of a
Debian-or-derivatives user in recent years (apart from setting up
and maintaining Ubuntu LTS on my wife's computer) mainly because
of lazyness as our IT staff helps me solve all problems with
Fedora quickly, including lowelevel device-related ones,
I think that Debian(+derivatives) has always been the exception
among the Linux distros and for all the others, '--vanilla'
really meant "vanilla" in a loose sense, i.e., "just base R".
I agree that I had wanted a "vanilla+strawberry" version myself, really.
which would be just not have the --no-site-file switch,
so we could call it
--vanilla+site
{Others may hate "feature creep" and yet more output from
'R --help' ..}
Martin
__
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.
[R] rbind of multiple data frames by column name, when each data frames can contain different columns
Dear R-list users,
for each winter season from 2000 to 2022 I have a data frame collecting for
different weather stations snowpack height (Hs), snowfall in the last 24h (Hn)
and a validation flag.
Suppose I have these three following data frames
df1 <- data.frame(data_POSIX=seq(as.POSIXct("2000-12-01", format="%Y-%m-%d",
tz="Etc/GMT-1"), as.POSIXct("2000-12-05", format="%Y-%m-%d", tz="Etc/GMT-1"),
by="1 days"), Station1_Hs = c(30, 40, 50, NA, 55), Station1_Hn = c(10, 20, 10,
NA, 5), Station1_flag = c(0, 0, 0, NA, 0), Station2_Hs = c(20, 20, 30, 30, 0),
Station2_Hn = c(0, 0, 10, 0, 5), Station2_flag = c(0, 0, 0, 1, 0))
df2 <- data.frame(data_POSIX=seq(as.POSIXct("2001-12-01", format="%Y-%m-%d",
tz="Etc/GMT-1"), as.POSIXct("2001-12-05", format="%Y-%m-%d", tz="Etc/GMT-1"),
by="1 days"), Station1_Hs = c(50, 60, 70, NA, NA), Station1_Hn = c(20, 20, 20,
NA, NA), Station1_flag = c(0, 0, 0, NA, NA), Station3_Hs = c(20, 20, 30, 30,
0), Station3_Hn = c(0, 0, 10, 0, 5), Station3_flag = c(0, 0, 0, 1, 0))
df3 <- data.frame(data_POSIX=seq(as.POSIXct("2002-12-01", format="%Y-%m-%d",
tz="Etc/GMT-1"), as.POSIXct("2002-12-05", format="%Y-%m-%d", tz="Etc/GMT-1"),
by="1 days"), Station2_Hs = c(50, 60, 70, NA, NA), Station2_Hn = c(20, 20, 20,
NA, NA), Station2_flag = c(0, 0, 0, NA, NA), Station3_Hs = c(20, 20, 30, 30,
0), Station3_Hn = c(0, 0, 10, 0, 5), Station3_flag = c(0, 0, 0, 1, 0))
As you can see, each data frame can have different stations loaded.
I would need to call rbind matching data frames by column name (i.e. by station
name), keeping in mind that the number of stations loaded in each data frame
may differ. The result should be
data_POSIX Station1_Hs Station1_Hn Station1_flag Station2_Hs Station2_Hn
Station2_flag Station3_Hs Station3_Hn Station3_flag
2000-12-01 30 10 0 20 0 0 NA NA NA
2000-12-02 40 20 0 20 0 0 NA NA NA
2000-12-03 50 10 0 30 10 0 NA NA NA
2000-12-04 NA NA NA 30 0 0 NA NA NA
2000-12-05 55 5 0 0 5 0 NA NA NA
2001-12-01 50 20 0 NA NA NA 20 0 0
2001-12-02 60 20 0 NA NA NA 20 0 0
2001-12-03 70 20 0 NA NA NA 30 10 0
2001-12-04 NA NA NA NA NA NA 30 0 1
2001-12-05 NA NA NA NA NA NA 0 5 0
2002-12-01 NA NA NA 50 20 0 20 0 0
2002-12-02 NA NA NA 60 20 0 20 0 0
2002-12-03 NA NA NA 70 20 0 30 10 0
2002-12-04 NA NA NA NA NA NA 30 0 1
2002-12-05 NA NA NA NA NA NA 0 5 0
I tried this code
df_list <- list(df1, df2, df3)
allNms <- unique(unlist(lapply(df_list, names)))
do.call(rbind, c(lapply(df_list, function(x) data.frame(c(x,
sapply(setdiff(allNms, names(x)), function(y) NA, make.row.names=FALSE))
but I get this error:
Error in (function (..., row.names = NULL, check.rows = FALSE, check.names =
TRUE, :
arguments imply differing number of rows
Could someone please help me?
Thank you for your attention
Stefano
(oo)
--oOO--( )--OOo--
Stefano Sofia PhD
Civil Protection - Marche Region - Italy
Meteo Section
Snow Section
Via del Colle Ameno 5
60126 Torrette di Ancona, Ancona (AN)
Uff: +39 071 806 7743
E-mail: stefano.so...@regione.marche.it
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