############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r GBScleanR -R && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GBScleanR ### ############################################################################## ############################################################################## * checking for file 'GBScleanR/DESCRIPTION' ... OK * preparing 'GBScleanR': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'BasicUsageOfGBScleanR.rmd' using rmarkdown Loading required package: SeqArray Loading required package: gdsfmt `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. Set the number of threads: 1 Start cleaning... Now cleaning chr 1... Cycle 1: Forward path... Cycle 1: Backward path... Cycle 1: Estimating allele read bias and mismapping pattern... Cycle 2: Forward path... Cycle 2: Backward path... Cycle 2: Estimating allele read bias and mismapping pattern... Cycle 3: Forward path... Cycle 3: Backward path... Cycle 3: Estimating allele read bias and mismapping pattern... Cycle 4: Forward path... Cycle 4: Backward path... Summarizing output... Done! Quitting from lines 679-681 (BasicUsageOfGBScleanR.rmd) Error: processing vignette 'BasicUsageOfGBScleanR.rmd' failed with diagnostics: Stream Read Error, need 12 byte(s) but receive 0 --- failed re-building 'BasicUsageOfGBScleanR.rmd' SUMMARY: processing the following file failed: 'BasicUsageOfGBScleanR.rmd' Error: Vignette re-building failed. Execution halted