PF2-pasteur-fr/SARTools

error when generating HTML files

Closed this issue · 6 comments

mthernando commented

Hi! I have a problem when running sartools. I have run sartools before and it did not happened! At the last part (generating HTML report) I obtain this error:

> > # generating HTML report
> > writeReport.DESeq2(target=target, counts=counts, out.DESeq2=out.DESeq2, summaryResults=summaryResults,
> +                    majSequences=majSequences, workDir=workDir, projectName=projectName, author=author,
> +                    targetFile=targetFile, rawDir=rawDir, featuresToRemove=featuresToRemove, varInt=varInt,
> +                    condRef=condRef, batch=batch, fitType=fitType, cooksCutoff=cooksCutoff,
> +                    independentFiltering=independentFiltering, alpha=alpha, pAdjustMethod=pAdjustMethod,
> +                    typeTrans=typeTrans, locfunc=locfunc, colors=colors)
> Quitting from lines 63-100 (/home/azken/R/x86_64-pc-linux-gnu-library/3.3/SARTools/report_DESeq2.rmd) 
> Error in eval(expr, envir, enclos) : objeto 'nbNull' no encontrado

I would appreciate your help. Best regards,

Maria

hvaret commented

Dear Maria,

thank you very much for reporting this problem. Some colleagues already obtained this error message but I can't understand what happened because all went good when they re-ran SARTools with me.

Could you try to run the script again and tell me if you still have the error?

Best regards,

Hugo

mthernando commented

Dear Hugo, I have re-run the script in R environment (not Rstudio) and I find the same error:

Quitting from lines 63-100 (/home/azken/R/x86_64-pc-linux-gnu-library/3.3/SARTools/report_DESeq2.rmd) 
Error in eval(expr, envir, enclos) : objeto 'nbNull' no encontrado
Además: Warning message:
In descriptionPlots(counts = counts, group = target[, varInt], col = colors) :
  No pairwise scatter-plot produced because of a too high number of samples (>30).
hvaret commented

OK thank you for having re-run the script. If your data are not confidential, could you send me the target and count files at hugo.varet at pasteur.fr ? I will reproduce the bug and then try to fix it.

Hugo

mthernando commented

sent!

Deleted user commented

I just got the same error and for asking what the reason could be I just created a github profile. Interestingly, everything run smoothly after I deleted every output which was generated before. So kind of a "restart" of the script helped in my case.

hvaret commented

Thanks @fabiansan for your message! It is very strange because one line of code seems to be skipped when generating the HTML report (nbNull <- nrow(counts) - nrow(removeNull(counts)), see the rmd file containing the skeleton of the report.