[Bioc-devel] Permission denied warning when building vignette

Qian Sophia Zhang qszhang at uw.edu
Tue Jun 7 20:22:29 CEST 2016

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}
164 # Making the rsID column row names
166 row.names(adm_ancestries) <- adm_ancestries[,1]
167 row.names(adm_genotypes) <- adm_genotypes[,1]
169 adm_ancestries <- adm_ancestries[,-1]
170 adm_genotypes <- adm_genotypes[,-1]
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: 



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