Re: [Bioc-devel] Error from rmarkdown

[Martin Morgan]

I checked out your package

  git clone https://git.bioconductor.org/packages/anamiR

and then, on R-devel (since that is the version being used in the current 
Bioconductor 'devel' release) and with BiocManager::version() returning 3.11 
and BiocManager::valid() returning TRUE, I did

  cd anamiR/vignettes
  R -f Stangle IntroductionToanamiR.Rmd

This gave me the R file IntroductinoToanamiR.R, which I then 'source'd' in R 
with

  R
  > source("IntroductionToanamiR.R", echo = TRUE, max = Inf)

This lead to

> mrna_d <- differExp_discrete(se = mrna_se,
+ class = "ER", method = "t.test",
+ t_test.var = FALSE, log2 = FALSE,
+ p_value.cutoff = 0.05,  logratio = 0.5
+ )
Error in t.test.default(da[gp_1], da[gp_2], var.equal = t_test.var) :
  not enough 'x' observations

While the error comes from t.test

> traceback()
10: stop("not enough 'x' observations")
9: t.test.default(da[gp_1], da[gp_2], var.equal = t_test.var)
8: stats::t.test(da[gp_1], da[gp_2], var.equal = t_test.var)
7: FUN(newX[, i], ...)
6: apply(data, 1, t_test, gp1, gp2)
5: differExp_discrete(se = mrna_se, class = "ER", method = "t.test",
   t_test.var = FALSE, log2 = FALSE, p_value.cutoff = 0.05,
   logratio = 0.5) at IntroductionToanamiR.R#47
4: eval(ei, envir)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("IntroductionToanamiR.R", echo = TRUE, max = Inf)

It seems likely that the problem is somewhere else in your code.

Since the error is reproducible outside the build system and using a standard 
bioc-devel installation, further troubleshooting is really the maintainer's 
responsibility. If the above isn't enough, respond here and I'll work on this 
further.

Martin

On 12/21/19, 12:48 AM, "Bioc-devel on behalf of r04945...@ntu.edu.tw" 
 wrote:

Hi all,

I am the maintainer of anamiR.
I keep getting this error on build report, which I don't get it on my  
local environment. Also, the weird part is that it did not show up  
until this September. Does anyone how to fix this? it looks like  
something went wrong with t.test from stats, and I don't think this  
package has been changed...

Quitting from lines 187-198 (IntroductionToanamiR.Rmd)
Error: processing vignette 'IntroductionToanamiR.Rmd' failed with 
diagnostics:
not enough 'x' observations
--- failed re-building ‘IntroductionToanamiR.Rmd’

Any suggestion would be helpful,
Thank you!

Ti-Tai

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Rd] Downsized R configuration for flat deployment

[Gábor Csárdi]

Hi,

FWIW this recent project of mine has somewhat similar goals:
https://github.com/r-hub/r-minimal

Gabor

On Sat, Dec 21, 2019 at 2:40 PM  wrote:
>
> Dear folks,
>
> I'm testing a downsized R build - in features and obviously sizes -
> for a "modern" flat deployment (eg. like python virtualenv, just to
> name one).
>
> Questions:
>
> 1) Is flat style possible?
> 2) With this setup, R and packages can be installed/updated?
> 3) The directory can be easy renamed or moved?
>
> ---
>
> I didn't find any official git repo, so I downloaded latest stable
> R release (3.6.2), exploring different setups of configure options.
>
> # tested in debian 10
> # $ sudo apt-get build-dep r-base
>
> $ mkdir ~/r-virtual
> $ cd R-3.6.2/
> $ ./configure --prefix=/home/dmedri/r-virtual/ \
> --exec-prefix=/home/dmedri/r-virtual/ \
> --without-recommended-packages \
> --without-cairo \
> --without-libtiff \
> --without-jpeglib \
> --without-x \
> --without-aqua \
> --without-tcltk \
> --disable-rpath
>
> $ make && make install
>
> This minimal R could run inside a container, no desktop just cli,
> with just one graphical formats in output (png). Java support was
> leaved in. I didn't find options to disable html docs. Recommended
> packages were leaved out, for a 2nd stage.
>
> $ cd r-virtual/
> $ ./bin/R
>
> The environment was there, "yes" to question 1).
>
> I can install/update packages, obviously with required includes
> installed in the system, not fetched online -- a limit, looking at
> python pip, partially by design/choice. BTW answer to question 2)
> is "yes" for packages, "no" for the core.
>
> Without the "--disable-rpath" option, abs paths break everything
> with the easy case of "renaming r-virtual directory". IMHO this option
> should be a general default, and another "yes" to question 3).
>
> While I'm still investigating, tips are welcome...
>
> HTH
>
> Best Regards,
>
> DM
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Bioc-devel] dependency problem in the windows machine

[Shepherd, Lori]

Please ignore and see the announcement

https://stat.ethz.ch/pipermail/bioc-devel/2019-December/015962.html

Get Outlook for Android


From: Bioc-devel  on behalf of Yue Zhao 
(Jason) 
Sent: Saturday, December 21, 2019 9:32:44 AM
To: bioc-devel 
Subject: [Bioc-devel] dependency problem in the windows machine

Hello all,

Recently, a package I submitted to Bioconductor failed with an
error message in the Windows system:

ERROR: dependencies 'DESeq2', 'MultiAssayExperiment',
'SummarizedExperiment' are not available for package 'animalcules'.

This is the link for the build:
http://bioconductor.org/checkResults/release/bioc-LATEST/animalcules/tokay1-install.html

Any suggestions on how I can proceed?

Best and thanks,
Jason


*--*

*Yue (Jason) Zhao*

PhD Candidate, Bioinformatics Program

Boston University

yu...@bu.edu

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Rd] Downsized R configuration for flat deployment

[dmedri]

Dear folks,

I'm testing a downsized R build - in features and obviously sizes -
for a "modern" flat deployment (eg. like python virtualenv, just to
name one).

Questions:

1) Is flat style possible?
2) With this setup, R and packages can be installed/updated?
3) The directory can be easy renamed or moved?

---

I didn't find any official git repo, so I downloaded latest stable
R release (3.6.2), exploring different setups of configure options. 

# tested in debian 10
# $ sudo apt-get build-dep r-base

$ mkdir ~/r-virtual
$ cd R-3.6.2/
$ ./configure --prefix=/home/dmedri/r-virtual/ \
--exec-prefix=/home/dmedri/r-virtual/ \
--without-recommended-packages \
--without-cairo \
--without-libtiff \
--without-jpeglib \
--without-x \
--without-aqua \
--without-tcltk \
--disable-rpath

$ make && make install

This minimal R could run inside a container, no desktop just cli,
with just one graphical formats in output (png). Java support was
leaved in. I didn't find options to disable html docs. Recommended
packages were leaved out, for a 2nd stage.

$ cd r-virtual/
$ ./bin/R

The environment was there, "yes" to question 1).

I can install/update packages, obviously with required includes
installed in the system, not fetched online -- a limit, looking at
python pip, partially by design/choice. BTW answer to question 2)
is "yes" for packages, "no" for the core.

Without the "--disable-rpath" option, abs paths break everything
with the easy case of "renaming r-virtual directory". IMHO this option
should be a general default, and another "yes" to question 3).

While I'm still investigating, tips are welcome... 

HTH

Best Regards,

DM

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

[Bioc-devel] dependency problem in the windows machine

[Yue Zhao (Jason)]

Hello all,

Recently, a package I submitted to Bioconductor failed with an
error message in the Windows system:

ERROR: dependencies 'DESeq2', 'MultiAssayExperiment',
'SummarizedExperiment' are not available for package 'animalcules'.

This is the link for the build:
http://bioconductor.org/checkResults/release/bioc-LATEST/animalcules/tokay1-install.html

Any suggestions on how I can proceed?

Best and thanks,
Jason


*--*

*Yue (Jason) Zhao*

PhD Candidate, Bioinformatics Program

Boston University

yu...@bu.edu

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel