Re: [R-pkg-devel] Whack-a-mole base::assign(".ptime", proc.time(), pos = "CheckExEnv")

2019-04-30 Thread Mark Hogue
Thank you very much Peter. Your advice helped me find the error. I had not
previously known where to find the package's -Ex.R file, and I didn't even
realize that this was a timeout error. (The -Ex.R file was in my working
directory, not the package directory.) One function did have some long
examples, but that function was never mentioned in the error, so it was
very confusing.

Cheers,

Mark

On Tue, Apr 30, 2019 at 4:44 AM peter dalgaard  wrote:

> That line is a generic part of the timing (it records current time so that
> at the end you can do what amounts to "Time used:" proc.time() - .ptime).
>
> It is not likely to contain the actual error -- notice that the message
> just gives you a best guess of the error location and that may fail. You
> probably need to have a look at the actual radsafer-Ex.R file and its
> output to find the true culprit.
>
> If you have catastrophic failures, yes, you see them only one at a time.
>
> -pd
>
> > On 30 Apr 2019, at 03:16 , Mark Hogue  wrote:
> >
> > (The subject title is in reference to the arcade game where fake mole
> heads
> > pop up and the contestant is challenged to smash them down as more and
> more
> > keep popping up.)
> >
> > I made some changes to a package and when I run the R CMD check, I get
> one
> > error with this lead-in notification:
> >
> > Running examples in 'radsafer-Ex.R' failed
> >  The error most likely occurred in:
> > *base::assign(".ptime", proc.time(), pos = "CheckExEnv")*
> >
> > When I do something with the affected function, I get a similar error on
> > another function.
> >
> > Could it have something to do with my having added argument checks on
> these
> > functions? Could someone advise where to go to understand this error
> > better? And is it normal to get only one error at a time like this?
> >
> > Thanks,
> >
> > Mark
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: pda...@gmail.com
>
>
>
>
>
>
>
>
>
>

[[alternative HTML version deleted]]

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Re: [R-pkg-devel] Need help for Debian check error

2019-04-30 Thread Ivan Krylov
On Tue, 30 Apr 2019 19:53:49 +
"Zhang, Lixiang"  wrote:

> I don't know why is that happening and how should I fix it. Thanks a
> lot for your help.

The e-mail from CRAN also said,

>> More details are given in the directory:

followed by a link scrambled by your e-mail software. When you follow
the link, you can find this file:

https://win-builder.r-project.org/incoming_pretest/cps_1.0_20190425_175509/Debian/00install.out

which lists the messages from the compiler produced when trying to
build your package on a Debian machine. "HUGE" is not an identifier
defined anywhere in C++ standard (AFAIK), but in standard 
header you can find HUGE_VAL
, which seems
to do what you mean.

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] Need help for Debian check error

2019-04-30 Thread Duncan Murdoch

On 30/04/2019 3:53 p.m., Zhang, Lixiang wrote:

Sorry to interrupt, but I have some problems that I don't understand about the 
check result. It shows that it passes the check using R CMD check --as-cran. 
But when I submit to cran, it shows me an error on Debian:

* checking whether package ‘cps’ can be installed ... [8s/8s] ERROR
Installation failed.

I don't know why is that happening and how should I fix it. Thanks a lot for 
your help.


I can't see your package, but the file

https://win-builder.r-project.org/incoming_pretest/cps_1.0_20190425_175509/Debian/00install.out

contains an explanation of the build error:

huge.cpp: In function ‘float match_fast(float*, float*, float*, int, 
int, float*)’:

huge.cpp:374:16: error: ‘HUGE’ was not declared in this scope
 minval=HUGE;


So you need to work out why HUGE is defined on Windows but not on Debian.

Duncan Murdoch

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[R-pkg-devel] Need help for Debian check error

2019-04-30 Thread Zhang, Lixiang
Sorry to interrupt, but I have some problems that I don't understand about the 
check result. It shows that it passes the check using R CMD check --as-cran. 
But when I submit to cran, it shows me an error on Debian:

* checking whether package ‘cps’ can be installed ... [8s/8s] ERROR
Installation failed.

I don't know why is that happening and how should I fix it. Thanks a lot for 
your help.

Best,
Lixiang

PS: here are the details

Dear maintainer,

package cps_1.0.tar.gz does not pass the incoming checks automatically, please 
see the following pre-tests:
Windows: 

Status: 1 NOTE
Debian: 

Status: 1 ERROR, 1 NOTE



Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the 
R-package-devel mailing list:

If you are fairly certain the rejection is a false positive, please reply-all 
to this message and explain.

More details are given in the directory:

The files will be removed after roughly 7 days.

No strong reverse dependencies to be checked.

Best regards,
CRAN teams' auto-check service
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: NOTE
  Maintainer: 'Lixiang Zhang '
  
  New submission
  
  The Title field should be in title case. Current version is:
  'An validation tool for both clustering results and visualization methods'
  In title case that is:
  'An Validation Tool for both Clustering Results and Visualization Methods'

Flavor: r-devel-linux-x86_64-debian-gcc
Check: whether package can be installed, Result: ERROR
  Installation failed.
  See '/srv/hornik/tmp/CRAN/cps.Rcheck/00install.out' for details.
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Re: [R-pkg-devel] parallel computing slower than sequential computing

2019-04-30 Thread Wang, Zhu
-Original Message-
From: Ivan Krylov  
Sent: Tuesday, April 30, 2019 10:17 AM
To: Wang, Zhu 
Cc: R-package-devel@r-project.org
Subject: Re: [R-pkg-devel] parallel computing slower than sequential computing

On Mon, 29 Apr 2019 23:44:42 +
"Wang, Zhu"  wrote:

> sessionInfo()
> R version 3.5.2 (2018-12-20)
> Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.2 
> LTS

Which BLAS implementation do you use? One popular implementation, OpenBLAS, 
spawns multiple threads to do some operations faster; the threads can compete 
against each other for CPU resources if resulting number of processes * threads 
per process is more than what CPU can handle.

>>BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
>>LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1


How many CPU cores does your system have? Does this include SMT (also known as 
hyper-threading on Intel processors)? While some problems benefit from 
processor pipeline being able to fetch from multiple threads at the same time, 
for others it's more of a bottleneck.

>>8 CPU cores and 16 logical processors. The Linux system is on a Virtualbox. I 
>>realized this might be a factor.

It may help to decrease the n.cores parameter.
>> n.cores=3, 4, 5 would have similar user/elapsed time compared with 
>> sequential computing.  Thanks Ivan.
--
Best regards,
Ivan

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Re: [R-pkg-devel] parallel computing slower than sequential computing

2019-04-30 Thread Ivan Krylov
On Mon, 29 Apr 2019 23:44:42 +
"Wang, Zhu"  wrote:

> sessionInfo()  
> R version 3.5.2 (2018-12-20)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 18.04.2 LTS

Which BLAS implementation do you use? One popular implementation,
OpenBLAS, spawns multiple threads to do some operations faster; the
threads can compete against each other for CPU resources if resulting
number of processes * threads per process is more than what CPU can
handle.

How many CPU cores does your system have? Does this include SMT (also
known as hyper-threading on Intel processors)? While some problems
benefit from processor pipeline being able to fetch from multiple
threads at the same time, for others it's more of a bottleneck.

It may help to decrease the n.cores parameter.

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] Whack-a-mole base::assign(".ptime", proc.time(), pos = "CheckExEnv")

2019-04-30 Thread peter dalgaard
That line is a generic part of the timing (it records current time so that at 
the end you can do what amounts to "Time used:" proc.time() - .ptime). 

It is not likely to contain the actual error -- notice that the message just 
gives you a best guess of the error location and that may fail. You probably 
need to have a look at the actual radsafer-Ex.R file and its output to find the 
true culprit.

If you have catastrophic failures, yes, you see them only one at a time.

-pd

> On 30 Apr 2019, at 03:16 , Mark Hogue  wrote:
> 
> (The subject title is in reference to the arcade game where fake mole heads
> pop up and the contestant is challenged to smash them down as more and more
> keep popping up.)
> 
> I made some changes to a package and when I run the R CMD check, I get one
> error with this lead-in notification:
> 
> Running examples in 'radsafer-Ex.R' failed
>  The error most likely occurred in:
> *base::assign(".ptime", proc.time(), pos = "CheckExEnv")*
> 
> When I do something with the affected function, I get a similar error on
> another function.
> 
> Could it have something to do with my having added argument checks on these
> functions? Could someone advise where to go to understand this error
> better? And is it normal to get only one error at a time like this?
> 
> Thanks,
> 
> Mark
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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