Last updated on 2020-08-07 01:50:32 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| HTSSIP | 1 | 4 | 7 |
Current CRAN status: ERROR: 1, NOTE: 4, OK: 7
Version: 1.4.1
Flags: --no-vignettes
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘igraph’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.4.1
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘igraph’
All declared Imports should be used.
Flavors: r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 1.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [53s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
18. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
20. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
22. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
23. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
24. base:::withOneRestart(expr, restarts[[1L]])
25. base:::doWithOneRestart(return(expr), restart)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 102 | SKIPPED: 18 | WARNINGS: 10 | FAILED: 3 ]
1. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2)
2. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15)
3. Error: HRSIP runs with default (@test-HRSIP.R#3)
Error: testthat unit tests failed
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 1.4.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘BD_shifts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: phyloseq
--- finished re-building ‘BD_shifts.Rmd’
--- re-building ‘HTSSIP_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
--- finished re-building ‘HTSSIP_intro.Rmd’
--- re-building ‘HTSSIP_sim.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
--- finished re-building ‘HTSSIP_sim.Rmd’
--- re-building ‘MW_HR_SIP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required namespace: DESeq2
Failed with error: 'there is no package called 'GenomeInfoDbData''
Quitting from lines 84-89 (MW_HR_SIP.Rmd)
Error: processing vignette 'MW_HR_SIP.Rmd' failed with diagnostics:
there is no package called 'GenomeInfoDbData'
--- failed re-building ‘MW_HR_SIP.Rmd’
--- re-building ‘beta_diversity_ordinations.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: phyloseq
--- finished re-building ‘beta_diversity_ordinations.Rmd’
--- re-building ‘heavy_SIP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
--- finished re-building ‘heavy_SIP.Rmd’
--- re-building ‘qSIP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
--- finished re-building ‘qSIP.Rmd’
--- re-building ‘quant_incorp.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
--- finished re-building ‘quant_incorp.Rmd’
SUMMARY: processing the following file failed:
‘MW_HR_SIP.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64