Re: [Bioc-devel] Error from rmarkdown

2019-12-21 Thread 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: [Bioc-devel] dependency problem in the windows machine

2019-12-21 Thread 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

[Bioc-devel] dependency problem in the windows machine

2019-12-21 Thread 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