AnnotationGx installation error
Urooj-M opened this issue · comments
remotes::install_github(
"bhklab/AnnotationGx",
build_manual=TRUE,
build_vignettes=TRUE
)
Downloading GitHub repo bhklab/AnnotationGx@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: rlang (1.1.2 -> 1.1.3 ) [CRAN]
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]
10: readr (2.1.4 -> 2.1.5 ) [CRAN]
11: data.table (1.14.10 -> 1.15.4) [CRAN]
Enter one or more numbers, or an empty line to skip updates:
── 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'
thanks for this.
can you also post the output of the sessionInfo() command?
sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.7
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] remotes_2.5.0 stringr_1.5.1 data.table_1.14.10 dplyr_1.1.4
loaded via a namespace (and not attached):
[1] rstudioapi_0.15.0 magrittr_2.0.3 tidyselect_1.2.0 R6_2.5.1 rlang_1.1.2 fansi_1.0.6
[7] tools_4.2.3 pkgbuild_1.4.2 utf8_1.2.4 cli_3.6.2 rprojroot_2.0.4 tibble_3.2.1
[13] lifecycle_1.0.4 crayon_1.5.2 processx_3.8.3 BiocManager_1.30.22 callr_3.7.6 vctrs_0.6.5
[19] ps_1.7.5 curl_5.2.0 glue_1.6.2 stringi_1.8.3 compiler_4.2.3 pillar_1.9.0
[25] desc_1.4.3 prettyunits_1.2.0 generics_0.1.3 pkgconfig_2.0.3
Just to confirm, when it prompts to update the packages, do you install all of them or by chance are you skipping them?
@Urooj-M I haven't been able to reproduce this error yet, for now can you please try installing without building vignettes and see what happens