############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CatsCradle ### ############################################################################## ############################################################################## * checking for file ‘CatsCradle/DESCRIPTION’ ... OK * preparing ‘CatsCradle’: * checking DESCRIPTION meta-information ... OK * installing the package (it is needed to build vignettes) * creating vignettes ... ERROR --- re-building ‘CatsCradle.Rmd’ using rmarkdown 2025-11-17 16:21:33.921 R[8638:55058107] XType: Using static font registry. [0%] Downloaded 10836 bytes... [0%] Downloaded 12184 bytes... [0%] Downloaded 28568 bytes... [0%] Downloaded 39144 bytes... [0%] Downloaded 56668 bytes... [0%] Downloaded 73052 bytes... 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Timeout was reached [zenodo.org]: Operation timed out after 300002 milliseconds with 8842608 out of 33730584 bytes received --- Backtrace: ▆ 1. ├─CatsCradle (local) getExample("hallmark") 2. │ └─msigdbr::msigdbr(species = "mouse", category = "H") 3. │ └─msigdbr:::load_msigdb_df(target_species = db_species) 4. │ └─curl::curl_download(...) 5. └─curl:::raise_libcurl_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'CatsCradle.Rmd' failed with diagnostics: Timeout was reached [zenodo.org]: Operation timed out after 300002 milliseconds with 8842608 out of 33730584 bytes received --- failed re-building ‘CatsCradle.Rmd’ --- re-building ‘CatsCradleExampleData.Rmd’ using rmarkdown --- finished re-building ‘CatsCradleExampleData.Rmd’ --- re-building ‘CatsCradleQuickStart.Rmd’ using rmarkdown [0%] Downloaded 4096 bytes... [0%] Downloaded 12184 bytes... [0%] Downloaded 21620 bytes... [0%] Downloaded 33752 bytes... 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Timeout was reached [zenodo.org]: Operation timed out after 300003 milliseconds with 13057504 out of 33730584 bytes received --- Backtrace: ▆ 1. ├─CatsCradle (local) getExample("hallmark") 2. │ └─msigdbr::msigdbr(species = "mouse", category = "H") 3. │ └─msigdbr:::load_msigdb_df(target_species = db_species) 4. │ └─curl::curl_download(...) 5. └─curl:::raise_libcurl_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'CatsCradleQuickStart.Rmd' failed with diagnostics: Timeout was reached [zenodo.org]: Operation timed out after 300003 milliseconds with 13057504 out of 33730584 bytes received --- failed re-building ‘CatsCradleQuickStart.Rmd’ --- re-building ‘CatsCradleSingleCellExperimentQuickStart.Rmd’ using rmarkdown [0%] Downloaded 10836 bytes... [0%] Downloaded 14828 bytes... [0%] Downloaded 31212 bytes... [0%] Downloaded 36396 bytes... [0%] Downloaded 43136 bytes... [0%] Downloaded 45832 bytes... 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[50%] Downloaded 16936020 bytes... [50%] Downloaded 16952284 bytes... Quitting from CatsCradleSingleCellExperimentQuickStart.Rmd:92-107 [[SCE4]] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `curl::curl_download()`: ! Timeout was reached [zenodo.org]: Operation timed out after 300001 milliseconds with 16952284 out of 33730584 bytes received --- Backtrace: ▆ 1. ├─CatsCradle (local) getExample("hallmark") 2. │ └─msigdbr::msigdbr(species = "mouse", category = "H") 3. │ └─msigdbr:::load_msigdb_df(target_species = db_species) 4. │ └─curl::curl_download(...) 5. └─curl:::raise_libcurl_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'CatsCradleSingleCellExperimentQuickStart.Rmd' failed with diagnostics: Timeout was reached [zenodo.org]: Operation timed out after 300001 milliseconds with 16952284 out of 33730584 bytes received --- failed re-building ‘CatsCradleSingleCellExperimentQuickStart.Rmd’ --- re-building ‘CatsCradleSpatial.Rmd’ using rmarkdown 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| --- finished re-building ‘CatsCradleSpatial.Rmd’ SUMMARY: processing the following files failed: ‘CatsCradle.Rmd’ ‘CatsCradleQuickStart.Rmd’ ‘CatsCradleSingleCellExperimentQuickStart.Rmd’ Error: Vignette re-building failed. Execution halted