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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data lcmsPlot
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* checking for file ‘lcmsPlot/DESCRIPTION’ ... OK
* preparing ‘lcmsPlot’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘creating_publication_ready_plots.Rmd’ using rmarkdown

Quitting from creating_publication_ready_plots.Rmd:95-112 [data-overview]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `dyn.load()`:
! unable to load shared object '/home/biocbuild/R/R-devel_2025-02-19/site-library/ncdf4/libs/ncdf4.so':
  libnetcdf.so.19: cannot open shared object file: No such file or directory
---
Backtrace:
     ▆
  1. ├─... + ...
  2. ├─... + ...
  3. │ └─lcmsPlot (local) e2(e1)
  4. │   └─lcmsPlot (local) fn(obj)
  5. │     ├─lcmsPlot:::create_chromatograms(...)
  6. │     └─lcmsPlot:::create_chromatograms(...)
  7. │       └─lcmsPlot:::io_get_raw_data(metadata$sample_path)
  8. │         └─lcmsPlot:::open_raw_reader(sample_path)
  9. │           └─methods::new("MzrReader", connection = mzR::openMSfile(path))
 10. │             ├─methods::initialize(value, ...)
 11. │             └─methods::initialize(value, ...)
 12. └─base::loadNamespace(x)
 13.   ├─base::namespaceImport(...)
 14.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
 15.     └─base::library.dynam(lib, package, package.lib)
 16.       └─base::dyn.load(file, DLLpath = DLLpath, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'creating_publication_ready_plots.Rmd' failed with diagnostics:
unable to load shared object '/home/biocbuild/R/R-devel_2025-02-19/site-library/ncdf4/libs/ncdf4.so':
  libnetcdf.so.19: cannot open shared object file: No such file or directory
--- failed re-building ‘creating_publication_ready_plots.Rmd’

--- re-building ‘lcms_data_plotting.Rmd’ using rmarkdown

Quitting from lcms_data_plotting.Rmd:29-34 [init]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'faahKO' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/biocbuild/R/R-devel_2025-02-19/site-library/ncdf4/libs/ncdf4.so':
  libnetcdf.so.19: cannot open shared object file: No such file or directory
---
Backtrace:
    ▆
 1. └─base::library(faahKO)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'lcms_data_plotting.Rmd' failed with diagnostics:
package or namespace load failed for 'faahKO' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/biocbuild/R/R-devel_2025-02-19/site-library/ncdf4/libs/ncdf4.so':
  libnetcdf.so.19: cannot open shared object file: No such file or directory
--- failed re-building ‘lcms_data_plotting.Rmd’

SUMMARY: processing the following files failed:
  ‘creating_publication_ready_plots.Rmd’ ‘lcms_data_plotting.Rmd’

Error: Vignette re-building failed.
Execution halted