- using R Under development (unstable) (2025-09-11 r88810)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘harmony/DESCRIPTION’ ... OK
- this is package ‘harmony’ version ‘1.2.3’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘harmony’ can be installed ... [99s/97s] OK
See the install log for details.
- used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
- checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [15s/23s] OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [7s/11s] OK
Running ‘testthat.R’ [7s/10s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [163s/216s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘Seurat.Rmd’ using rmarkdown
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
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Calculating feature variances of standardized and clipped values
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**************************************************|
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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Using method 'umap'
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[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Seurat.Rmd’
--- re-building ‘detailedWalkthrough.Rmd’ using rmarkdown
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Quitting from detailedWalkthrough.Rmd:778-788 [unnamed-chunk-36]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! <ggplot2::labels> object is invalid:
- every label must be named.
---
Backtrace:
▆
1. └─ggplot2::labs(...)
2. └─ggplot2::class_labels(args)
3. └─S7::new_object(labels)
4. └─S7::validate(object, recursive = !parent_validated)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'detailedWalkthrough.Rmd' failed with diagnostics:
<ggplot2::labels> object is invalid:
- every label must be named.
--- failed re-building ‘detailedWalkthrough.Rmd’
--- re-building ‘quickstart.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘quickstart.Rmd’
SUMMARY: processing the following file failed:
‘detailedWalkthrough.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... OK
- checking HTML version of manual ... OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR