CRAN Package Check Results for Package HTSSIP

Last updated on 2019-12-11 22:51:09 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.4.1 8.60 398.36 406.96 OK --no-vignettes
r-devel-linux-x86_64-debian-gcc 1.4.1 5.98 294.18 300.16 OK --no-vignettes
r-devel-linux-x86_64-fedora-clang 1.4.1 472.65 NOTE --no-vignettes
r-devel-linux-x86_64-fedora-gcc 1.4.1 467.53 NOTE --no-vignettes
r-devel-windows-ix86+x86_64 1.4.1 15.00 472.00 487.00 OK --no-vignettes
r-devel-windows-ix86+x86_64-gcc8 1.4.1 22.00 322.00 344.00 ERROR --no-vignettes
r-patched-linux-x86_64 1.4.1 6.43 336.01 342.44 OK --no-vignettes
r-patched-solaris-x86 1.4.1 4494.10 NOTE
r-release-linux-x86_64 1.4.1 5.20 311.05 316.25 OK --no-vignettes
r-release-windows-ix86+x86_64 1.4.1 16.00 343.00 359.00 OK --no-vignettes
r-release-osx-x86_64 1.4.1 ERROR
r-oldrel-windows-ix86+x86_64 1.4.1 10.00 420.00 430.00 OK --no-vignettes
r-oldrel-osx-x86_64 1.4.1 NOTE

Check Details

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
Flags: --no-vignettes
Check: tests
Result: ERROR
     Running 'testthat.R' [163s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > # Work-around for bug (https://github.com/hadley/testthat/issues/144)
     > Sys.setenv("R_TESTS" = "")
     >
     > # library
     > library(testthat)
     > library(HTSSIP)
     >
     > # test check
     > test_check('HTSSIP')
     Sparsity threshold: 0.25
     Density window: 1.71-1.75
     -- 1. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2) -----
     failed to coerce 'list(value)' to a DESeqResults object of length 1
     Backtrace:
     1. HTSSIP::DESeq2_l2fc(...)
     2. DESeq2::results(dds, independentFiltering = FALSE)
     3. DESeq2:::pvalueAdjustment(...)
     5. S4Vectors:::`$<-`(...)
     7. S4Vectors:::`[[<-`(...)
     11. S4Vectors:::.nextMethod(x, i, value = value)
     13. S4Vectors::setListElement(x, i, value)
     14. S4Vectors:::.append_list_element(x, value, name)
     15. S4Vectors:::.wrap_in_length_one_list_like_object(...)
    
     Sparsity threshold: 0.25
     Density window: 1.71-1.75
     -- 2. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15)
     failed to coerce 'list(value)' to a DESeqResults object of length 1
     Backtrace:
     1. HTSSIP::DESeq2_l2fc(...)
     2. DESeq2::results(dds, independentFiltering = FALSE)
     3. DESeq2:::pvalueAdjustment(...)
     5. S4Vectors:::`$<-`(...)
     7. S4Vectors:::`[[<-`(...)
     11. S4Vectors:::.nextMethod(x, i, value = value)
     13. S4Vectors::setListElement(x, i, value)
     14. S4Vectors:::.append_list_element(x, value, name)
     15. S4Vectors:::.wrap_in_length_one_list_like_object(...)
    
     Sparsity threshold: 0
     Density window: 1.7-1.75
     -- 3. Error: HRSIP runs with default (@test-HRSIP.R#3) ------------------------
     failed to coerce 'list(value)' to a DESeqResults object of length 1
     Backtrace:
     1. HTSSIP::HRSIP(...)
     2. plyr::mdply(...)
     3. plyr::adply(...)
     4. plyr::ldply(...)
     5. plyr::llply(...)
     8. plyr:::.fun(piece, ...)
     11. DESeq2::results(dds, independentFiltering = FALSE)
     12. DESeq2:::pvalueAdjustment(...)
     14. S4Vectors:::`$<-`(...)
     16. S4Vectors:::`[[<-`(...)
     20. S4Vectors:::.nextMethod(x, i, value = value)
     22. S4Vectors::setListElement(x, i, value)
     23. S4Vectors:::.append_list_element(x, value, name)
     24. S4Vectors:::.wrap_in_length_one_list_like_object(...)
    
     == testthat results ===========================================================
     [ OK: 102 | SKIPPED: 18 | WARNINGS: 3 | 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-devel-windows-ix86+x86_64-gcc8

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-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.4.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [52s/52s]
    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: 3 | 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-release-osx-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-release-osx-x86_64