############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ReactomeContentService4R ### ############################################################################## ############################################################################## * checking for file ‘ReactomeContentService4R/DESCRIPTION’ ... OK * preparing ‘ReactomeContentService4R’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘ReactomeContentService4R.Rmd’ using rmarkdown starting worker pid=21445 on localhost:11999 at 07:17:48.572 starting worker pid=21444 on localhost:11999 at 07:17:48.572 Loading required package: ReactomeContentService4R Loading required package: ReactomeContentService4R loaded ReactomeContentService4R and set parent environment loaded ReactomeContentService4R and set parent environment | | |= | 1% |= | 2% | |== | 3% | |== | 4% | |=== | 4% | |==== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 10% | |======= | 11% | |======== | 12% | |========= | 12% | |========= | 13% | |========== | 14% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============ | 18% | |============= | 19% | |============== | 19% | |============== | 20% | |=============== | 21% | |=============== | 22% | |================ | 23% | |================= | 24% | |================= | 25% | |=================== | 27% | |================== | 26% | 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|================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100%Warning message: Warning message: In fun(libname, pkgname) : Package 'ReactomeContentService4R' is deprecated and will be removed from Bioconductor version 3.22 In fun(libname, pkgname) : Package 'ReactomeContentService4R' is deprecated and will be removed from Bioconductor version 3.22 Quitting from ReactomeContentService4R.Rmd:146-152 [getPathways] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `{ ancestors.url <- file.path(getOption("base.address"), "data/event", id, "ancestors") ancestors <- .retrieveData(ancestors.url, as = "text") ancestors <- ancestors[[1]] ancestors[ancestors$schemaClass == "TopLevelPathway", ] }`: ! task 1 failed - "Server returned nothing (no headers, no data) [reactome.org]: Empty reply from server" --- Backtrace: ▆ 1. └─ReactomeContentService4R::getPathways("R-HSA-176949", top.level = TRUE) 2. └─... %dopar% ... 3. └─e$fun(obj, substitute(ex), parent.frame(), e$data) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'ReactomeContentService4R.Rmd' failed with diagnostics: task 1 failed - "Server returned nothing (no headers, no data) [reactome.org]: Empty reply from server" --- failed re-building ‘ReactomeContentService4R.Rmd’ SUMMARY: processing the following file failed: ‘ReactomeContentService4R.Rmd’ Error: Vignette re-building failed. Execution halted