remotes::install_github(
"bhklab/AnnotationGx",
build_manual=TRUE,
build_vignettes=TRUE
)
Downloading GitHub repo bhklab/AnnotationGx@HEAD
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5: withr (2.5.2 -> 3.0.0 ) [CRAN]
6: tidyselect (1.2.0 -> 1.2.1 ) [CRAN]
7: glue (1.6.2 -> 1.7.0 ) [CRAN]
8: openssl (2.1.1 -> 2.1.2 ) [CRAN]
9: curl (5.2.0 -> 5.2.1 ) [CRAN]
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── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/8x/mq9t1w4d4kxdbj1837xwsx_m0000gn/T/RtmpgShzxp/remotes122a2268168fc/bhklab-AnnotationGx-27cbafe/DESCRIPTION’ (578ms)
─ preparing ‘AnnotationGx’:
✔ checking DESCRIPTION meta-information ...
─ installing the package to build vignettes
E creating vignettes (1m 3.9s)
--- re-building ‘Cellosaurus.Rmd’ using rmarkdown
--- finished re-building ‘Cellosaurus.Rmd’
--- re-building ‘ChEMBL.Rmd’ using rmarkdown
--- finished re-building ‘ChEMBL.Rmd’
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "1. Introduction to AnnotationGx", and the latter is "Introduction to AnnotationGx". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘Introduction.Rmd’
--- re-building ‘OncoTree.Rmd’ using rmarkdown
Quitting from lines 62-63 [getCancerSubtypes] (OncoTree.Rmd)
Error: processing vignette 'OncoTree.Rmd' failed with diagnostics:
replacement has 0 rows, data has 885
--- failed re-building ‘OncoTree.Rmd’
--- re-building ‘PubChemAPI.Rmd’ using rmarkdown
--- finished re-building ‘PubChemAPI.Rmd’
--- re-building ‘Unichem.Rmd’ using rmarkdown
--- finished re-building ‘Unichem.Rmd’
SUMMARY: processing the following file failed:
‘OncoTree.Rmd’
Error: Vignette re-building failed.
Execution halted
Error: Failed to install 'AnnotationGx' from GitHub:
! System command 'R' failed
Initially it asked to install 'sessioninfo'