Re: [R-sig-Debian] read.csv fails in R console in Ubuntu terminal but works in RStudio after R 3.6.3 upgrade to R 4.0.2
On 15 July 2020 at 19:15, David Winsemius wrote: | (It does leave hanging the question of why `read.csv` is failing.) If I had to guess: due to the dark magic behind download.file() and the numerous different ways it could use (see the help page, it is truly impressive!) some of which involve `libcurl` (i.e. the C library from the curl project), some involve `curl` (the package for R), some involve `wget` (the binary), some involve internal code -- plus all that can cross with the SSL libraries use by curl and whatnot. Which is why my post suggested to separate the _download_ from the _file read_ aspect. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] read.csv fails in R console in Ubuntu terminal but works in RStudio after R 3.6.3 upgrade to R 4.0.2
On 7/15/20 1:35 PM, Dirk Eddelbuettel wrote:
On 15 July 2020 at 16:16, Sam H wrote:
| I am trying to download some data using read.csv and it works perfectly in
| RStudio and fails in the R console in the terminal in Ubuntu 18.04 after
| upgrading from R 3.6.3 to 4.0.2. Before upgrading this worked in the R
| console in the terminal also without any issues.
|
| Why would that be? How to fix this?
|
| Below please find R code output and sessionInfo().
|
| *Works in RStudio*
|
| >
read.csv("https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0=1=download;,
header=TRUE, as.is=TRUE, na="n/a")
Ok, let's stop right here. First off, for good debugging it helps to separate
- downloading a file via R from
- reading a file
- maybe varying the arguments you give there
In my case this got easier. I clicked on the link (in Ubuntu 20.04) and it
downloaded it. From there few problems. `read.csv()` just reads it:
In fact one can use the fread approach directly, rather than first using
your system or your browser to download the copy:
z <-
data.table::fread("https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0=1=download;,
header=TRUE)
Downloaded 486840 bytes...>
> str(z)
Classes ‘data.table’ and 'data.frame': 3631 obs. of 9 variables:
$ Symbol : chr "TXG" "YI" "PIH" "PIHPP" ...
$ Name : chr "10x Genomics, Inc." "111, Inc." "1347 Property
Insurance Holdings, Inc." "1347 Property Insurance Holdings, Inc." ...
$ LastSale : chr "90.93" "6.31" "4.528" "24.35" ...
$ MarketCap : chr "$8.94B" "$519.69M" "$27.48M" "n/a" ...
$ IPOyear : chr "2019" "2018" "2014" "n/a" ...
$ Sector : chr "Capital Goods" "Health Care" "Finance"
"Finance" ...
$ industry : chr "Biotechnology: Laboratory Analytical
Instruments" "Medical/Nursing Services" "Property-Casualty Insurers"
"Property-Casualty Insurers" ...
$ Summary Quote: chr "https://old.nasdaq.com/symbol/txg;
"https://old.nasdaq.com/symbol/yi; "https://old.nasdaq.com/symbol/pih;
"https://old.nasdaq.com/symbol/pihpp; ...
$ V9 : logi NA NA NA NA NA NA ...
- attr(*, ".internal.selfref")=
I had earlier experienced the hanging of the original example in Ubuntu
18.04 using R 3.6.1. I get teh same result in either a Terminal hosted R
session or an Rstudio R session.
(It does leave hanging the question of why `read.csv` is failing.)
--
David.
edd@rob:~/Downloads$ Rscript -e 'data.table::fread("companylist.csv",
header=TRUE)'
Symbol Name LastSale MarketCap IPOyear
Sector industry
Summary Quote V9
1:TXG 10x Genomics, Inc.88.91$8.75B2019
Capital Goods Biotechnology: Laboratory Analytical Instruments
https://old.nasdaq.com/symbol/txg NA
2: YI 111, Inc. 6.64 $546.87M2018
Health Care Medical/Nursing Services
https://old.nasdaq.com/symbol/yi NA
3:PIH 1347 Property Insurance Holdings, Inc.4.528 $27.48M2014
Finance Property-Casualty Insurers
https://old.nasdaq.com/symbol/pih NA
4: PIHPP 1347 Property Insurance Holdings, Inc. 24.8631 n/a n/a
Finance Property-Casualty Insurers
https://old.nasdaq.com/symbol/pihpp NA
5: TURN 180 Degree Capital Corp. 1.67 $51.97M n/a
Finance Finance/Investors Services
https://old.nasdaq.com/symbol/turn NA
---
3622: ZS Zscaler, Inc. 122.43 $15.98B2018
Technology EDP Services
https://old.nasdaq.com/symbol/zs NA
3623: ZUMZZumiez Inc.25.55 $649.76M2005
Consumer Services Clothing/Shoe/Accessory Stores
https://old.nasdaq.com/symbol/zumz NA
3624: ZYNE Zynerba Pharmaceuticals, Inc. 3.41 $85.08M2015
Health CareMajor Pharmaceuticals
https://old.nasdaq.com/symbol/zyne NA
3625: ZYXIZynex, Inc.26.22 $870.31M n/a
Health Care Biotechnology: Electromedical & Electrotherapeutic Apparatus
https://old.nasdaq.com/symbol/zyxi NA
3626: ZNGA Zynga Inc. 9.82 $10.54B2011
Technology EDP Services
https://old.nasdaq.com/symbol/znga NA
edd@rob:~/Downloads$
For kicks, same with data.table:
edd@rob:~/Downloads$ Rscript -e 'str(read.csv("companylist.csv"))'
'data.frame': 3626 obs. of 9 variables:
$ Symbol : chr "TXG" "YI" "PIH" "PIHPP" ...
$ Name : chr "10x Genomics, Inc." "111, Inc." "1347
Re: [R-sig-Debian] R 4.0 for ARM processors
H. Perhaps I'm using the wrong terminology. My logic is: (1) I am running Ubuntu focal on the cluster. (2) Ubuntu focal is built on Debian bullseye but (3) Debian bullseye is not yet the stable release; it is the 'testing' release; hence (4) I will pull the r-base-core package from the 'testing' version of Debian. And, in fact, I found r-base-core for 4.0.2 in the bullseye distribution. Does that all make sense? My RPi cluster sits on the file cabinet next to my desk, all four boards. Yes, you could argue that it's merely a toy but it's bigger and cheaper than the AWS box that currently hosts my web site, RStudio server, and Shiny server! For the truly curious, you can view my RPi cluster here: https://photos.app.goo.gl/kALwoYCVxJ32VgxEA Thanks again, Dirk. Your contributions to Debian and Ubuntu are foundational for my computing platforms. Paul Teetor, Elgin, IL USA http://quantdevel.com/public On Wednesday, July 15, 2020, 11:52:03 AM CDT, Dirk Eddelbuettel wrote: On 15 July 2020 at 16:35, Paul Teetor wrote: | Thank you very much, Dirk. That nudge solved the problem, of course. I am embarrassed. I was so fixated on Ubuntu repositories that I neglected to check the Debian 'testing' world! | | Regarding the RPi: The RPi 4 uses the 'arm64' architecture, the full 64-bit one. I stopped using dedicated distros, such as Raspian, when Ubuntu went all-in on RPi support, which happened in their newest release focal (20). The dedicated distros often have an unhelpful attitude -- e.g., "you should use *this* package, not *that* package" -- that doesn't work for me. I am confused by these two paragraphs. Are you planning to use Debian 'testing' on you Raspberry Pi, or Ubuntu 'focal' aka 20.04? And out of curiousity, is that a hosted machine? Typically these are toy-sized and usually at home. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] R 4.0 for ARM processors
Thank you very much, Dirk. That nudge solved the problem, of course. I am embarrassed. I was so fixated on Ubuntu repositories that I neglected to check the Debian 'testing' world! Regarding the RPi: The RPi 4 uses the 'arm64' architecture, the full 64-bit one. I stopped using dedicated distros, such as Raspian, when Ubuntu went all-in on RPi support, which happened in their newest release focal (20). The dedicated distros often have an unhelpful attitude -- e.g., "you should use *this* package, not *that* package" -- that doesn't work for me. Paul Teetor, Elgin, IL USA http://quantdevel.com/public On Wednesday, July 15, 2020, 09:26:27 AM CDT, Dirk Eddelbuettel wrote: On 15 July 2020 at 14:03, Paul Teetor wrote: | Dear R-SIG-Debian folks, | | I seem to be chasing my tail, despite having a simple goal: | | - Install R 4.0.2 | - On Ubuntu 20.04 | - For an ARM processor (not Intel/AMD). | | Can someone please suggest a Debian/Ubuntu repository of the required packages (e.g., r-base-core) built for ARM? I can't seem to find one. | | (I can find the r-base-core package for R 3.6.3, but not R 4.0.2, built for ARM.) | | If there is no such Debian/Ubuntu repository, what would you recommend? Build R 4.0 for ARM from source? Use the cool 'rocker' images for R 4.0? Something else? | | Thank you so much for your advice. I must be misunderstanding something. I figured this would be a slam-dunk because (1) R 4.0 is the latest release, and (2) Ubuntu 20.04 is an LTS release, and (3) ARM is a supported architecture, or so I thought. | | Paul | | PS - Yes, the ARM processors in question are a Raspberry Pi cluster. Don't snicker. Hey, it's got 16 cores, 16 GB RAM total, and a | terabyte of space. And it's paid for, no monthly fee. When I look at the build pages for my packages, eg this one for r-base https://buildd.debian.org/status/package.php?p=r-base I see three (3) different arm labels: arm64, armel, armhf. I have no idea what the Pi uses, and never looked closely, but I am at least vaguely aware that there are apparently entire _dedicated_ distros and installers based on the Debian builds. Raspian is one name that comes to mind. Did you try that? Also, one second of Googling leads to: https://ubuntu.com/download/server/arm Good luck, keep us posted -- other architectures/platforms can be fun. Dirk (who just installed 20.04 on his daughters "retired / thought dead under a large cup of coffee spilled" macbook air) -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] read.csv fails in R console in Ubuntu terminal but works in RStudio after R 3.6.3 upgrade to R 4.0.2
On 15 July 2020 at 16:16, Sam H wrote:
| I am trying to download some data using read.csv and it works perfectly in
| RStudio and fails in the R console in the terminal in Ubuntu 18.04 after
| upgrading from R 3.6.3 to 4.0.2. Before upgrading this worked in the R
| console in the terminal also without any issues.
|
| Why would that be? How to fix this?
|
| Below please find R code output and sessionInfo().
|
| *Works in RStudio*
|
| >
read.csv("https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0=1=download;,
header=TRUE, as.is=TRUE, na="n/a")
Ok, let's stop right here. First off, for good debugging it helps to separate
- downloading a file via R from
- reading a file
- maybe varying the arguments you give there
In my case this got easier. I clicked on the link (in Ubuntu 20.04) and it
downloaded it. From there few problems. `read.csv()` just reads it:
edd@rob:~/Downloads$ Rscript -e 'data.table::fread("companylist.csv",
header=TRUE)'
Symbol Name LastSale MarketCap IPOyear
Sector industry
Summary Quote V9
1:TXG 10x Genomics, Inc.88.91$8.75B2019
Capital Goods Biotechnology: Laboratory Analytical Instruments
https://old.nasdaq.com/symbol/txg NA
2: YI 111, Inc. 6.64 $546.87M2018
Health Care Medical/Nursing Services
https://old.nasdaq.com/symbol/yi NA
3:PIH 1347 Property Insurance Holdings, Inc.4.528 $27.48M2014
Finance Property-Casualty Insurers
https://old.nasdaq.com/symbol/pih NA
4: PIHPP 1347 Property Insurance Holdings, Inc. 24.8631 n/a n/a
Finance Property-Casualty Insurers
https://old.nasdaq.com/symbol/pihpp NA
5: TURN 180 Degree Capital Corp. 1.67 $51.97M n/a
Finance Finance/Investors Services
https://old.nasdaq.com/symbol/turn NA
---
3622: ZS Zscaler, Inc. 122.43 $15.98B2018
Technology EDP Services
https://old.nasdaq.com/symbol/zs NA
3623: ZUMZZumiez Inc.25.55 $649.76M2005
Consumer Services Clothing/Shoe/Accessory Stores
https://old.nasdaq.com/symbol/zumz NA
3624: ZYNE Zynerba Pharmaceuticals, Inc. 3.41 $85.08M2015
Health CareMajor Pharmaceuticals
https://old.nasdaq.com/symbol/zyne NA
3625: ZYXIZynex, Inc.26.22 $870.31M n/a
Health Care Biotechnology: Electromedical & Electrotherapeutic Apparatus
https://old.nasdaq.com/symbol/zyxi NA
3626: ZNGA Zynga Inc. 9.82 $10.54B2011
Technology EDP Services
https://old.nasdaq.com/symbol/znga NA
edd@rob:~/Downloads$
For kicks, same with data.table:
edd@rob:~/Downloads$ Rscript -e 'str(read.csv("companylist.csv"))'
'data.frame': 3626 obs. of 9 variables:
$ Symbol : chr "TXG" "YI" "PIH" "PIHPP" ...
$ Name : chr "10x Genomics, Inc." "111, Inc." "1347 Property
Insurance Holdings, Inc." "1347 Property Insurance Holdings, Inc." ...
$ LastSale : chr "88.91" "6.64" "4.528" "24.8631" ...
$ MarketCap: chr "$8.75B" "$546.87M" "$27.48M" "n/a" ...
$ IPOyear : chr "2019" "2018" "2014" "n/a" ...
$ Sector : chr "Capital Goods" "Health Care" "Finance" "Finance" ...
$ industry : chr "Biotechnology: Laboratory Analytical Instruments"
"Medical/Nursing Services" "Property-Casualty Insurers" "Property-Casualty
Insurers" ...
$ Summary.Quote: chr "https://old.nasdaq.com/symbol/txg;
"https://old.nasdaq.com/symbol/yi; "https://old.nasdaq.com/symbol/pih;
"https://old.nasdaq.com/symbol/pihpp; ...
$ X: logi NA NA NA NA NA NA ...
edd@rob:~/Downloads$
So in short, if you have a problem, it is not likely coming from the Ubuntu
binary for R 4.0.2 which I am running here.
Maybe start by downloading the file? You could have firewall or other
issues. We can't tell. And we can't reproduce the issue.
Good luck, Dirk
--
https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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[R-sig-Debian] read.csv fails in R console in Ubuntu terminal but works in RStudio after R 3.6.3 upgrade to R 4.0.2
Hi,
I am trying to download some data using read.csv and it works perfectly in
RStudio and fails in the R console in the terminal in Ubuntu 18.04 after
upgrading from R 3.6.3 to 4.0.2. Before upgrading this worked in the R
console in the terminal also without any issues.
Why would that be? How to fix this?
Below please find R code output and sessionInfo().
*Works in RStudio*
> read.csv("https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0=1=download;,
> header=TRUE, as.is=TRUE, na="n/a")
SymbolName
LastSale MarketCap IPOyear
1 TXG 10x Genomics, Inc.
87.4400 $8.6B2019
2 YI 111, Inc.
6.4800 $533.69M2018
3 PIH 1347 Property Insurance Holdings, Inc.
4.5350 $27.52M2014
sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.0.2 tools_4.0.2
*Fails in R console in terminal*
>
read.csv("https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0=1=download;,
header=TRUE, as.is=TRUE, na="n/a")
Error in file(file, "rt") :
cannot open the connection to
'https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0=1=download'
In addition: Warning message:
In file(file, "rt") :
URL
'https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0=1=download':
status was 'Failure when receiving data from the peer'
> traceback()
3: file(file, "rt")
2: read.table(file = file, header = header, sep = sep, quote = quote,
dec = dec, fill = fill, comment.char = comment.char, ...)
1:
read.csv("https://old.nasdaq.com/screening/companies-by-name.aspx?letter=0=1=download;,
header = TRUE, as.is = TRUE, na = "n/a")
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.0.2
>
I also asked this question here
https://stackoverflow.com/questions/62898008/why-read-csv-fails-in-r-console-in-ubuntu-terminal-but-works-in-rstudio-after-r
.
Since there was no answer on stackoverflow I sent this question also to
R-Help where I was advised to better ask this question on r-sig-debian.
Best regards,
Sam
[[alternative HTML version deleted]]
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Re: [R-sig-Debian] R 4.0 for ARM processors
On 15 July 2020 at 19:44, Paul Teetor wrote: | H. Perhaps I'm using the wrong terminology. My logic is: (1) I am running Ubuntu focal on the cluster. I am with you so far. | (2) Ubuntu focal is built on Debian bullseye but Not really. Ubuntu does their own thing, and their own snapshots. There is no relationship to Debian _stable_ releases. They take sources from Debian unstable and then do their thing. Which sometimes is minor variation, often no change, but sometimes a lot more (i.e. snaps, different boot stuff, different window manager, fonts, branding, software store, alliances with third parties, paid-for patent technology (they always included mp3 players). In short, I think you started from the wrong gate here. | (3) Debian bullseye is not yet the stable release; it is the 'testing' release; hence (4) I will pull the r-base-core package from the 'testing' version of Debian. And, in fact, I found r-base-core for 4.0.2 in the bullseye distribution. Does that all make sense? Given (2) you more or less land in a bad spot with (3) and (4). | My RPi cluster sits on the file cabinet next to my desk, all four boards. Yes, you could argue that it's merely a toy but it's bigger and cheaper than the AWS box that currently hosts my web site, RStudio server, and Shiny server! Got it. Missed the cluster part earlier and then confused myself looking for arm64 16core machines. There aren't any :) | For the truly curious, you can view my RPi cluster here: https://photos.app.goo.gl/kALwoYCVxJ32VgxEA Neat :) Very geek chic! | Thanks again, Dirk. Your contributions to Debian and Ubuntu are foundational for my computing platforms. You're too kind. Cheers, Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] Openblas?
Here is the reproducible example (very educational ...):
--
$ wget http://ehar.se/data/reex_0.1.1.tar.gz
$ R CMD INSTALL reex_0.1.1.tar.gz
{with "status = 1: blas/libblas.so.3, and lapack..}
$ R
> library("reex")
> system.time(res <- coxfunk(beta = 1, X = X, rs = rs, what = 2))
# user system elapsed
# 0.093 0.000 0.093
> q()
{Change to "status 2; openmp/libblas.so.3", and lapack..}
$ R
> library(reex)
> system.time(res <- coxfunk(beta = 1, X = X, rs = rs, what = 2))
# user system elapsed
# 72.050 1.006 6.123
>
> system.time(res <- coxfunk(beta = 1, X = X, rs = rs, what = 1))
# user system elapsed
# 0.088 0.000 0.088
---
Comment:
## what = 1 calculates loglik and score, what = 2 in addition hessian
## "Extra" code when what = 2:
if (*what >= 2){ /* Second derivatives: */
F77_CALL(dsyr)(, p, (wsc + i),
(x + (*p) * i), ,
sumd2score, p FCONE);
}
and
if (*what >= 2){
alpha = -alpha;
F77_CALL(daxpy)(, , sumd2score, ,
d2loglik, );
alpha = -alpha / sumscore;
F77_CALL(dsyr)(, p, , sumdscore, ,
d2loglik, p FCONE);
}
Full C and R code in package.
Göran
On 2020-07-15 16:32, Dirk Eddelbuettel wrote:
On 15 July 2020 at 16:13, Göran Broström wrote:
| On 2020-07-15 14:36, Dirk Eddelbuettel wrote:
| >
| > Göran,
| >
| > This is not an easy email to reply to because it _contains nothing
| > reproducible_.
|
| Thanks Dirk,
|
| Sorry about that, but my real question was (see below): "Is the problem
| that openblas uses C versions of blas?" That is, do I need to change
|
| F77_CALL(name)(...);
|
| to
|
| cblas_name(...);
|
| everywhere? And if so, is this really a good idea with old code?
I don't think so. At the end of the day it comes from "higher up" (say,
crossprod()) and is just passed down.
Remember, at the end it's all assembler :)
| I'll try to extract a reproducible example from the package (eha) where
| I run it.
+1
Dirk
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[R-sig-Debian] R 4.0 for ARM processors
Dear R-SIG-Debian folks, I seem to be chasing my tail, despite having a simple goal: - Install R 4.0.2 - On Ubuntu 20.04 - For an ARM processor (not Intel/AMD). Can someone please suggest a Debian/Ubuntu repository of the required packages (e.g., r-base-core) built for ARM? I can't seem to find one. (I can find the r-base-core package for R 3.6.3, but not R 4.0.2, built for ARM.) If there is no such Debian/Ubuntu repository, what would you recommend? Build R 4.0 for ARM from source? Use the cool 'rocker' images for R 4.0? Something else? Thank you so much for your advice. I must be misunderstanding something. I figured this would be a slam-dunk because (1) R 4.0 is the latest release, and (2) Ubuntu 20.04 is an LTS release, and (3) ARM is a supported architecture, or so I thought. Paul PS - Yes, the ARM processors in question are a Raspberry Pi cluster. Don't snicker. Hey, it's got 16 cores, 16 GB RAM total, and a terabyte of space. And it's paid for, no monthly fee. Paul Teetor, Elgin, IL USA ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] R 4.0 for ARM processors
On 15 July 2020 at 16:35, Paul Teetor wrote: | Thank you very much, Dirk. That nudge solved the problem, of course. I am embarrassed. I was so fixated on Ubuntu repositories that I neglected to check the Debian 'testing' world! | | Regarding the RPi: The RPi 4 uses the 'arm64' architecture, the full 64-bit one. I stopped using dedicated distros, such as Raspian, when Ubuntu went all-in on RPi support, which happened in their newest release focal (20). The dedicated distros often have an unhelpful attitude -- e.g., "you should use *this* package, not *that* package" -- that doesn't work for me. I am confused by these two paragraphs. Are you planning to use Debian 'testing' on you Raspberry Pi, or Ubuntu 'focal' aka 20.04? And out of curiousity, is that a hosted machine? Typically these are toy-sized and usually at home. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] Openblas?
On 15 July 2020 at 16:13, Göran Broström wrote: | On 2020-07-15 14:36, Dirk Eddelbuettel wrote: | > | > Göran, | > | > This is not an easy email to reply to because it _contains nothing | > reproducible_. | | Thanks Dirk, | | Sorry about that, but my real question was (see below): "Is the problem | that openblas uses C versions of blas?" That is, do I need to change | | F77_CALL(name)(...); | | to | | cblas_name(...); | | everywhere? And if so, is this really a good idea with old code? I don't think so. At the end of the day it comes from "higher up" (say, crossprod()) and is just passed down. Remember, at the end it's all assembler :) | I'll try to extract a reproducible example from the package (eha) where | I run it. +1 Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] R 4.0 for ARM processors
On 15 July 2020 at 14:03, Paul Teetor wrote: | Dear R-SIG-Debian folks, | | I seem to be chasing my tail, despite having a simple goal: | | - Install R 4.0.2 | - On Ubuntu 20.04 | - For an ARM processor (not Intel/AMD). | | Can someone please suggest a Debian/Ubuntu repository of the required packages (e.g., r-base-core) built for ARM? I can't seem to find one. | | (I can find the r-base-core package for R 3.6.3, but not R 4.0.2, built for ARM.) | | If there is no such Debian/Ubuntu repository, what would you recommend? Build R 4.0 for ARM from source? Use the cool 'rocker' images for R 4.0? Something else? | | Thank you so much for your advice. I must be misunderstanding something. I figured this would be a slam-dunk because (1) R 4.0 is the latest release, and (2) Ubuntu 20.04 is an LTS release, and (3) ARM is a supported architecture, or so I thought. | | Paul | | PS - Yes, the ARM processors in question are a Raspberry Pi cluster. Don't snicker. Hey, it's got 16 cores, 16 GB RAM total, and a | terabyte of space. And it's paid for, no monthly fee. When I look at the build pages for my packages, eg this one for r-base https://buildd.debian.org/status/package.php?p=r-base I see three (3) different arm labels: arm64, armel, armhf. I have no idea what the Pi uses, and never looked closely, but I am at least vaguely aware that there are apparently entire _dedicated_ distros and installers based on the Debian builds. Raspian is one name that comes to mind. Did you try that? Also, one second of Googling leads to: https://ubuntu.com/download/server/arm Good luck, keep us posted -- other architectures/platforms can be fun. Dirk (who just installed 20.04 on his daughters "retired / thought dead under a large cup of coffee spilled" macbook air) -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] Openblas?
On 2020-07-15 14:36, Dirk Eddelbuettel wrote: Göran, This is not an easy email to reply to because it _contains nothing reproducible_. Thanks Dirk, Sorry about that, but my real question was (see below): "Is the problem that openblas uses C versions of blas?" That is, do I need to change F77_CALL(name)(...); to cblas_name(...); everywhere? And if so, is this really a good idea with old code? I'll try to extract a reproducible example from the package (eha) where I run it. Göran On 15 July 2020 at 13:24, Göran Broström wrote: | Hello, | | I thought that I should try openblas when building a CRAN package | containing lots of old (twentieth century) C-code with frequent calls to | blas and lapack routines. I have the following options on my Ubuntu | 20.04 machine: | | SelectionPath Priority Status | | * 0openblas-pthread/libblas.so.3 100 auto mode |1blas/libblas.so.3 10 manual mode |2openblas-openmp/libblas.so.395 manual mode |3openblas-pthread/libblas.so.3 100 manual mode | | I tried all four alternatives by timing one particular function call and | got quite surprising (to me) results: | | Selectionuser system elapsed | 0 3.2791.839 1.900 | 1 0.8990.052 0.953 | 2 158.9483.661 20.915 | 3 3.2771.894 1.908 | | Comments on that? How could I comment? I do not know what code you ran. | To me it seems clear that openblas (0, 2, 3) has | nothing to offer me, as my C code stands now. Is the problem that | openblas uses C versions of blas? I am using the Fortran version via | | F77_CALL(name) | | I tried adding | | PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS) | PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) This is missing LAPACK and BLAS so ... | | to src/Makevars, but then I got | | ...undefined symbol: dsytri_ ... so get a _linker error_ about missing symbols. | when compiling. You meant linking, not compiling. Dirk ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] Openblas?
Göran, This is not an easy email to reply to because it _contains nothing reproducible_. On 15 July 2020 at 13:24, Göran Broström wrote: | Hello, | | I thought that I should try openblas when building a CRAN package | containing lots of old (twentieth century) C-code with frequent calls to | blas and lapack routines. I have the following options on my Ubuntu | 20.04 machine: | | SelectionPath Priority Status | | * 0openblas-pthread/libblas.so.3 100 auto mode |1blas/libblas.so.3 10 manual mode |2openblas-openmp/libblas.so.395 manual mode |3openblas-pthread/libblas.so.3 100 manual mode | | I tried all four alternatives by timing one particular function call and | got quite surprising (to me) results: | | Selectionuser system elapsed | 0 3.2791.839 1.900 | 1 0.8990.052 0.953 | 2 158.9483.661 20.915 | 3 3.2771.894 1.908 | | Comments on that? How could I comment? I do not know what code you ran. | To me it seems clear that openblas (0, 2, 3) has | nothing to offer me, as my C code stands now. Is the problem that | openblas uses C versions of blas? I am using the Fortran version via | | F77_CALL(name) | | I tried adding | | PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS) | PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) This is missing LAPACK and BLAS so ... | | to src/Makevars, but then I got | | ...undefined symbol: dsytri_ ... so get a _linker error_ about missing symbols. | when compiling. You meant linking, not compiling. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
[R-sig-Debian] Openblas?
Hello, I thought that I should try openblas when building a CRAN package containing lots of old (twentieth century) C-code with frequent calls to blas and lapack routines. I have the following options on my Ubuntu 20.04 machine: SelectionPath Priority Status * 0openblas-pthread/libblas.so.3 100 auto mode 1blas/libblas.so.3 10 manual mode 2openblas-openmp/libblas.so.395 manual mode 3openblas-pthread/libblas.so.3 100 manual mode I tried all four alternatives by timing one particular function call and got quite surprising (to me) results: Selectionuser system elapsed 0 3.2791.839 1.900 1 0.8990.052 0.953 2 158.9483.661 20.915 3 3.2771.894 1.908 Comments on that? To me it seems clear that openblas (0, 2, 3) has nothing to offer me, as my C code stands now. Is the problem that openblas uses C versions of blas? I am using the Fortran version via F77_CALL(name) I tried adding PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS) PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) to src/Makevars, but then I got ...undefined symbol: dsytri_ when compiling. Göran ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
