CRAN Package Check Results for Package HTSSIP

Last updated on 2021-10-15 22:54:17 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.4.1 0.73 3.08 3.81 ERROR --no-vignettes
r-devel-linux-x86_64-debian-gcc 1.4.1 6.01 160.22 166.23 OK --no-vignettes
r-devel-linux-x86_64-fedora-clang 1.4.1 1166.72 NOTE
r-devel-linux-x86_64-fedora-gcc 1.4.1 1170.26 NOTE
r-devel-windows-x86_64 1.4.1 15.00 134.00 149.00 ERROR --no-vignettes
r-devel-windows-x86_64-gcc10-UCRT 1.4.1 ERROR
r-patched-linux-x86_64 1.4.1 8.73 209.33 218.06 OK --no-vignettes
r-patched-solaris-x86 1.4.1 354.70 NOTE
r-release-linux-x86_64 1.4.1 6.78 202.94 209.72 OK --no-vignettes
r-release-macos-arm64 1.4.1 NOTE
r-release-macos-x86_64 1.4.1 NOTE
r-release-windows-ix86+x86_64 1.4.1 19.00 274.00 293.00 OK --no-vignettes
r-oldrel-macos-x86_64 1.4.1 NOTE
r-oldrel-windows-ix86+x86_64 1.4.1 20.00 215.00 235.00 OK --no-vignettes

Check Details

Version: 1.4.1
Flags: --no-vignettes
Check: package dependencies
Result: ERROR
    Package required but not available: 'DESeq2'
    
    See section 'The DESCRIPTION file' in the 'Writing R Extensions'
    manual.
Flavor: r-devel-linux-x86_64-debian-clang

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-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.4.1
Flags: --no-vignettes
Check: tests
Result: ERROR
     Running 'testthat.R' [27s]
    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
     Sparsity threshold: 0.25
     Density window: 1.71-1.75
     Sparsity threshold: 0
     Density window: 1.7-1.75
     == Skipped tests ===============================================================
     * On CRAN (17)
     * empty test (1)
    
     == Failed tests ================================================================
     -- Error (test-DESeq2_l2fc.R:2:3): DESeq2_l2fc runs with default params --------
     Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. \-HTSSIP::DESeq2_l2fc(...) test-DESeq2_l2fc.R:2:2
     2. \-phyloseq::phyloseq_to_deseq2(physeq, design)
     3. \-DESeq2::DESeqDataSetFromMatrix(countData, colData, design, ...)
     4. \-DESeq2::DESeqDataSet(se, design = design, ignoreRank)
     5. \-methods::as(se, "RangedSummarizedExperiment")
     6. \-SummarizedExperiment:::asMethod(object)
     7. \-IRanges::PartitioningByEnd(integer(length(from)), names = names(from))
     8. \-IRanges:::.numeric2end(x, NG)
     9. \-S4Vectors:::isNotSorted(x)
     -- Error (test-DESeq2_l2fc.R:15:3): DESeq2_l2fc runs with sparsity_apply=heavy --
     Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. \-HTSSIP::DESeq2_l2fc(...) test-DESeq2_l2fc.R:15:2
     2. \-phyloseq::phyloseq_to_deseq2(physeq, design)
     3. \-DESeq2::DESeqDataSetFromMatrix(countData, colData, design, ...)
     4. \-DESeq2::DESeqDataSet(se, design = design, ignoreRank)
     5. \-methods::as(se, "RangedSummarizedExperiment")
     6. \-SummarizedExperiment:::asMethod(object)
     7. \-IRanges::PartitioningByEnd(integer(length(from)), names = names(from))
     8. \-IRanges:::.numeric2end(x, NG)
     9. \-S4Vectors:::isNotSorted(x)
     -- Error (test-HRSIP.R:3:3): HRSIP runs with default ---------------------------
     Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. \-HTSSIP::HRSIP(...) test-HRSIP.R:3:2
     2. \-plyr::mdply(...)
     3. \-plyr::adply(...)
     4. \-plyr::ldply(...)
     5. \-plyr::llply(...)
     6. +-plyr:::loop_apply(n, do.ply)
     7. \-(function (i) ...
     8. \-plyr:::.fun(piece, ...)
     9. +-base::do.call(flat, c(args, list(...)))
     10. \-(function (physeq, density_min, density_max, design, l2fc_threshold = 0.25, ...
     11. \-phyloseq::phyloseq_to_deseq2(physeq, design)
     12. \-DESeq2::DESeqDataSetFromMatrix(countData, colData, design, ...)
     13. \-DESeq2::DESeqDataSet(se, design = design, ignoreRank)
     14. \-methods::as(se, "RangedSummarizedExperiment")
     15. \-SummarizedExperiment:::asMethod(object)
     16. \-IRanges::PartitioningByEnd(integer(length(from)), names = names(from))
     17. \-IRanges:::.numeric2end(x, NG)
     18. \-S4Vectors:::isNotSorted(x)
    
     [ FAIL 3 | WARN 10 | SKIP 18 | PASS 102 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-windows-x86_64

Version: 1.4.1
Check: package dependencies
Result: ERROR
    Package required but not available: 'DESeq2'
    
    See section 'The DESCRIPTION file' in the 'Writing R Extensions'
    manual.
Flavor: r-devel-windows-x86_64-gcc10-UCRT