Rapid builds (Linux only) of a subset of BioC 3.23<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences"	925
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BUILD results for phyloseq on teran2

To the developers/maintainers of the phyloseq package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: phyloseq

Version: 1.55.0

Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data phyloseq

StartedAt: 2025-12-09 12:44:52 -0500 (Tue, 09 Dec 2025)

EndedAt: 2025-12-09 12:44:53 -0500 (Tue, 09 Dec 2025)

EllapsedTime: 1.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data phyloseq
###
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##############################################################################


* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* preparing ‘phyloseq’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
      -----------------------------------
* installing *source* package ‘phyloseq’ ...
** this is package ‘phyloseq’ version ‘1.55.0’
** using staged installation
** R
** data
** inst
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/doc/Unweighted_UniFrac.RData', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/GP_otu_table_rand_short.txt.gz', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/GP_tree_rand_short.newick.gz', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/biom-refseq.fasta', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/biom-tree.phy', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/esophagus.fn.list.gz', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/esophagus.fn.shared.gz', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/esophagus.good.groups.gz', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/esophagus.tree.gz', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/gg13-5-73.tree.gz', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/gp500-pycogent.py', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/gp500-uuf.csv', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/gp500-wuf.csv', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/gp500-wufu.csv', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/gp500test.env.txt', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/gp500test.tree', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/master_map.txt', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/min_dense_otu_table.biom', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/min_sparse_otu_table.biom', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/mothur_example.cons.taxonomy.gz', reason 'No such file or directory'
Warning in file.create(to[okay]) :
  cannot create file '/tmp/Rtmp7nLQaZ/Rinst205d36368cfb64/00LOCK-phyloseq/00new/phyloseq/extdata/phyloseq.png', reaso
      -----------------------------------
ERROR: package installation failed