Closed dimalvovs closed 5 months ago
Ensembl fails often and is used in the vignettes. Find a way to make vignette builds more stable.
Example from bioconductor devel build:
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CoGAPS ### ############################################################################## ############################################################################## * checking for file ‘CoGAPS/DESCRIPTION’ ... OK * preparing ‘CoGAPS’: * checking DESCRIPTION meta-information ... OK * cleaning src * running ‘cleanup’ * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘CoGAPS.Rmd’ using rmarkdown Data Model: Dense, Normal Sampler Type: Sequential Loading Data...Done! (00:00:00) -- Equilibration Phase -- 10000 of 50000, Atoms: 67(A), 31(P), ChiSq: 439, Time: 00:00:00 / 00:00:00 20000 of 50000, Atoms: 81(A), 35(P), ChiSq: 140, Time: 00:00:00 / 00:00:00 30000 of 50000, Atoms: 88(A), 42(P), ChiSq: 138, Time: 00:00:01 / 00:00:03 40000 of 50000, Atoms: 91(A), 37(P), ChiSq: 101, Time: 00:00:01 / 00:00:02 50000 of 50000, Atoms: 82(A), 36(P), ChiSq: 122, Time: 00:00:02 / 00:00:04 -- Sampling Phase -- 10000 of 50000, Atoms: 89(A), 40(P), ChiSq: 113, Time: 00:00:02 / 00:00:03 20000 of 50000, Atoms: 90(A), 36(P), ChiSq: 145, Time: 00:00:03 / 00:00:04 30000 of 50000, Atoms: 83(A), 31(P), ChiSq: 113, Time: 00:00:03 / 00:00:03 40000 of 50000, Atoms: 86(A), 38(P), ChiSq: 104, Time: 00:00:04 / 00:00:04 50000 of 50000, Atoms: 87(A), 36(P), ChiSq: 129, Time: 00:00:04 / 00:00:04 Quitting from lines 428-429 [get hallmarks] (CoGAPS.Rmd) Error: processing vignette 'CoGAPS.Rmd' failed with diagnostics: Unable to query any Ensembl site --- failed re-building ‘CoGAPS.Rmd’ SUMMARY: processing the following file failed: ‘CoGAPS.Rmd’ Error: Vignette re-building failed. Execution halted
Ensembl fails often and is used in the vignettes. Find a way to make vignette builds more stable.
Example from bioconductor devel build: