############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RNAmodR.AlkAnilineSeq ### ############################################################################## ############################################################################## * checking for file ‘RNAmodR.AlkAnilineSeq/DESCRIPTION’ ... OK * preparing ‘RNAmodR.AlkAnilineSeq’: * checking DESCRIPTION meta-information ... OK * installing the package (it is needed to build vignettes) * creating vignettes ... ERROR --- re-building ‘RNAmodR.AlkAnilineSeq.Rmd’ using rmarkdown [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d324f6ef4_2545' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d335136d5_2547' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d7166d77a_2549' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d510c7644_2537' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d5d01f63e_2539' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d33e9b46b_2541' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d57e436fe_2543' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d324f6ef4_2545' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d510c7644_2537' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d33e9b46b_2541' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d33e9b46b_2541' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d510c7644_2537' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d324f6ef4_2545' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d57e436fe_2543' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d5d01f63e_2539' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d5d01f63e_2539' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d57e436fe_2543' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d335136d5_2547' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d510c7644_2537' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d335136d5_2547' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d5d01f63e_2539' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d7166d77a_2549' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d7166d77a_2549' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d33e9b46b_2541' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d324f6ef4_2545' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d57e436fe_2543' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d335136d5_2547' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d7166d77a_2549' Quitting from RNAmodR.AlkAnilineSeq.Rmd:84-87 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! BiocParallel errors 3 remote errors, element index: 1, 2, 3 0 unevaluated and other errors first remote error: Error in h(simpleError(msg, call)): error in evaluating the argument 'table' in selecting a method for function '%in%': error in evaluating the argument 'x' in selecting a method for function 'shortName': Biostrings internal error, please report --- Backtrace: ▆ 1. └─RNAmodR.AlkAnilineSeq::ModSetAlkAnilineSeq(...) 2. ├─RNAmodR::ModifierSet(...) 3. └─RNAmodR::ModifierSet(...) 4. └─RNAmodR:::.bamfiles_to_ModifierSet(...) 5. ├─BiocParallel::bpmapply(...) 6. └─BiocParallel::bpmapply(...) 7. ├─BiocParallel::bpmapply(...) 8. └─BiocParallel::bpmapply(...) 9. ├─BiocParallel::bplapply(...) 10. └─BiocParallel::bplapply(...) 11. └─BiocParallel:::.bpinit(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'RNAmodR.AlkAnilineSeq.Rmd' failed with diagnostics: BiocParallel errors 3 remote errors, element index: 1, 2, 3 0 unevaluated and other errors first remote error: Error in h(simpleError(msg, call)): error in evaluating the argument 'table' in selecting a method for function '%in%': error in evaluating the argument 'x' in selecting a method for function 'shortName': Biostrings internal error, please report --- failed re-building ‘RNAmodR.AlkAnilineSeq.Rmd’ SUMMARY: processing the following file failed: ‘RNAmodR.AlkAnilineSeq.Rmd’ Error: Vignette re-building failed. Execution halted