[Bioc-devel] Permission denied warning when building vignette

Dan Tenenbaum dtenenba at fredhutch.org
Tue Jun 7 21:15:18 CEST 2016

I can't reproduce this.

One thing you can do is try and reproduce it in an interactive session in order to get more information.

So install your package:


Then do the following:

cd ASAFE/vignettes
R CMD Stangle ASAFE.Rmd

This will produce a file called ASAFE.R containing just the R code from your vignette, you can then start R and do:

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

Then see if the code fails again in the same place. If it does fail you can use traceback() and debug() and other tools to find the error.
Be sure that traceback() is the first command you run after the error.
Also at this point you can run sessionInfo() to see what you have installed. If you still have trouble and return to this list for help you should include the sessionInfo() and traceback() output. 


----- Original Message -----
> From: "Qian Sophia Zhang" <qszhang at uw.edu>
> To: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Tuesday, June 7, 2016 11:22:29 AM
> Subject: [Bioc-devel] Permission denied warning when building vignette

> Dear Bioc-devel list people,
> I am baffled about this 1 WARNING when I run “R CMD check ASAFE_0.99.0.tar.gz”
> and would be grateful if anyone could help me get rid of it.
> Excerpt from attached log file:
> "* checking re-building of vignette outputs ... WARNING
> Error in re-building vignettes:
>  ...
> Warning in file(file, ifelse(append, "a", "w")) :
>  cannot open file 'ASAFE.R': Permission denied
> Quitting from lines 163-172 (ASAFE.Rmd)
> Error: processing vignette 'ASAFE.Rmd' failed with diagnostics:
> cannot open the connection
> Execution halted”
> I don’t have a file called ASAFE.R. I looked at lines 163-172 of ASAFE.Rmd. Here
> are lines 162-172 in vim:
> 162 ```{r}
> 163
> 164 # Making the rsID column row names
> 165
> 166 row.names(adm_ancestries) <- adm_ancestries[,1]
> 167 row.names(adm_genotypes) <- adm_genotypes[,1]
> 168
> 169 adm_ancestries <- adm_ancestries[,-1]
> 170 adm_genotypes <- adm_genotypes[,-1]
> 171
> 172 ```
> I think adm_ancestries and adm_genotypes are successfully exported data objects
> because they are used earlier in the vignette and no warning occurred then.
> Hence, I don’t see why I’m getting a warning from these lines.
> The tar.gz file can be found here:
> https://github.com/BiostatQian/ASAFE/raw/master/ASAFE_0.99.0.tar.gz
> Thanks,
> Qian
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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