CRAN Package Check Results for Package pagoo

Last updated on 2021-10-14 22:57:44 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.9 31.29 314.42 345.71 OK
r-devel-linux-x86_64-debian-gcc 0.3.9 24.78 231.81 256.59 OK
r-devel-linux-x86_64-fedora-clang 0.3.9 435.06 OK
r-devel-linux-x86_64-fedora-gcc 0.3.9 412.82 OK
r-devel-windows-x86_64 0.3.9 36.00 245.00 281.00 ERROR
r-devel-windows-x86_64-gcc10-UCRT 0.3.9 OK
r-patched-linux-x86_64 0.3.9 27.67 337.87 365.54 OK
r-patched-solaris-x86 0.3.9 501.90 NOTE
r-release-linux-x86_64 0.3.9 27.14 339.11 366.25 OK
r-release-macos-arm64 0.3.9 OK
r-release-macos-x86_64 0.3.9 NOTE
r-release-windows-ix86+x86_64 0.3.9 68.00 403.00 471.00 OK
r-oldrel-macos-x86_64 0.3.9 NOTE
r-oldrel-windows-ix86+x86_64 0.3.9 68.00 408.00 476.00 OK

Check Details

Version: 0.3.9
Check: tests
Result: ERROR
     Running 'testthat.R' [22s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(pagoo)
     Loading required package: S4Vectors
     Loading required package: stats4
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which.max, which.min
    
    
     Attaching package: 'S4Vectors'
    
     The following objects are masked from 'package:base':
    
     I, expand.grid, unname
    
     Loading required package: Biostrings
     Loading required package: IRanges
    
     Attaching package: 'IRanges'
    
     The following object is masked from 'package:grDevices':
    
     windows
    
     Loading required package: XVector
     Loading required package: GenomeInfoDb
    
     Attaching package: 'Biostrings'
    
     The following object is masked from 'package:base':
    
     strsplit
    
     Loading required package: ggplot2
     >
     > test_check("pagoo")
     == Failed tests ================================================================
     -- Error (test_input.R:101:3): Class of data fields (active bindings) are the expected --
     Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. +-testthat::expect_is(p$genes, "SplitDataFrameList") test_input.R:101:2
     2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
     3. | \-rlang::eval_bare(expr, quo_get_env(quo))
     4. \-(function () ...
     5. +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     6. \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     7. +-S4Vectors::splitAsList(x, f, drop = drop, ...)
     8. \-S4Vectors::splitAsList(x, f, drop = drop, ...)
     9. \-S4Vectors:::.local(x, f, drop, ...)
     10. \-IRanges:::default_splitAsList(x, f, drop = drop)
     11. \-IRanges:::.splitAsList_by_factor(x, f, drop)
     12. \-S4Vectors:::isNotSorted(f)
     -- Error (test_input.R:110:3): Data fields (active bindings) are consistent ----
     Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. +-testthat::expect_equal(length(p$genes), nrow(p$clusters)) test_input.R:110:2
     2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
     3. | \-rlang::eval_bare(expr, quo_get_env(quo))
     4. \-(function () ...
     5. +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     6. \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     7. +-S4Vectors::splitAsList(x, f, drop = drop, ...)
     8. \-S4Vectors::splitAsList(x, f, drop = drop, ...)
     9. \-S4Vectors:::.local(x, f, drop, ...)
     10. \-IRanges:::default_splitAsList(x, f, drop = drop)
     11. \-IRanges:::.splitAsList_by_factor(x, f, drop)
     12. \-S4Vectors:::isNotSorted(f)
     -- Error (test_input.R:119:3): $save_pangenomeRDS() and load_pangenome() works --
     Error in `h(simpleError(msg, call))`: error in evaluating the argument 'skeleton' in selecting a method for function 'relist': 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. +-p$save_pangenomeRDS(out_rds) test_input.R:119:2
     2. | +-base::split(sqs, mcols(sqs)$org)
     3. | \-S4Vectors::split(sqs, mcols(sqs)$org)
     4. | +-S4Vectors::splitAsList(x, f, drop = drop, ...)
     5. | \-S4Vectors::splitAsList(x, f, drop = drop, ...)
     6. | \-S4Vectors:::.local(x, f, drop, ...)
     7. | \-IRanges:::default_splitAsList(x, f, drop = drop)
     8. | \-IRanges:::as.factor2(f)
     9. | +-IRanges::PartitioningByEnd(relist(g))
     10. | | \-methods::is(x, "List")
     11. | +-utils::relist(g)
     12. | \-IRanges::relist(g)
     13. | +-utils::relist(...)
     14. | \-IRanges::PartitioningByEnd(attr(flesh, "ends"))
     15. | \-IRanges:::.numeric2end(x, NG)
     16. | \-S4Vectors:::isNotSorted(x)
     17. \-base::.handleSimpleError(...)
     18. \-base:::h(simpleError(msg, call))
     -- Error (test_input.R:167:3): Adding gene metadata after object creation works. --
     Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. +-testthat::expect_is(p$genes, "DFrameList") test_input.R:167:2
     2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
     3. | \-rlang::eval_bare(expr, quo_get_env(quo))
     4. \-(function () ...
     5. +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     6. \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     7. +-S4Vectors::splitAsList(x, f, drop = drop, ...)
     8. \-S4Vectors::splitAsList(x, f, drop = drop, ...)
     9. \-S4Vectors:::.local(x, f, drop, ...)
     10. \-IRanges:::default_splitAsList(x, f, drop = drop)
     11. \-IRanges:::.splitAsList_by_factor(x, f, drop)
     12. \-S4Vectors:::isNotSorted(f)
     -- Error (test_methods-plots.R:29:3): methods return expected objects ----------
     Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. +-p$core_seqs_4_phylo() test_methods-plots.R:29:2
     2. | \-base::unlist(self$core_sequences, use.names = FALSE)
     3. +-(function () ...
     4. | \-base::unlist(self$core_genes)
     5. \-(function () ...
     6. +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     7. \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     8. +-S4Vectors::splitAsList(x, f, drop = drop, ...)
     9. \-S4Vectors::splitAsList(x, f, drop = drop, ...)
     10. \-S4Vectors:::.local(x, f, drop, ...)
     11. \-IRanges:::default_splitAsList(x, f, drop = drop)
     12. \-IRanges:::.splitAsList_by_factor(x, f, drop)
     13. \-S4Vectors:::isNotSorted(f)
     -- Error (test_subset.R:8:3): predefined subsets for $genes are consistent -----
     Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. +-testthat::expect_is(p$core_genes, is(p$genes)) test_subset.R:8:2
     2. | \-base::stopifnot(is.character(class))
     3. +-methods::is(p$genes)
     4. \-(function () ...
     5. +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     6. \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     7. +-S4Vectors::splitAsList(x, f, drop = drop, ...)
     8. \-S4Vectors::splitAsList(x, f, drop = drop, ...)
     9. \-S4Vectors:::.local(x, f, drop, ...)
     10. \-IRanges:::default_splitAsList(x, f, drop = drop)
     11. \-IRanges:::.splitAsList_by_factor(x, f, drop)
     12. \-S4Vectors:::isNotSorted(f)
     -- Error (test_subset.R:19:3): predefined subsets for $clusters are consistent --
     Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. +-testthat::expect_is(p$shell_genes, is(p$clusters)) test_subset.R:19:2
     2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
     3. | \-rlang::eval_bare(expr, quo_get_env(quo))
     4. \-(function () ...
     5. +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     6. \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     7. +-S4Vectors::splitAsList(x, f, drop = drop, ...)
     8. \-S4Vectors::splitAsList(x, f, drop = drop, ...)
     9. \-S4Vectors:::.local(x, f, drop, ...)
     10. \-IRanges:::default_splitAsList(x, f, drop = drop)
     11. \-IRanges:::.splitAsList_by_factor(x, f, drop)
     12. \-S4Vectors:::isNotSorted(f)
     -- Error (test_subset.R:28:3): predefined subsets for $sequences are consistent --
     Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. +-testthat::expect_is(p$core_sequences, is(p$sequences)) test_subset.R:28:2
     2. | \-base::stopifnot(is.character(class))
     3. +-methods::is(p$sequences)
     4. +-(function () ...
     5. | \-base::unlist(self$genes)
     6. \-(function () ...
     7. +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     8. \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     9. +-S4Vectors::splitAsList(x, f, drop = drop, ...)
     10. \-S4Vectors::splitAsList(x, f, drop = drop, ...)
     11. \-S4Vectors:::.local(x, f, drop, ...)
     12. \-IRanges:::default_splitAsList(x, f, drop = drop)
     13. \-IRanges:::.splitAsList_by_factor(x, f, drop)
     14. \-S4Vectors:::isNotSorted(f)
     -- Error (test_subset.R:54:3): vector/list notation for subset works -----------
     Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. +-testthat::expect_equal(p[1], p[clus_1_char]) test_subset.R:54:2
     2. | +-testthat::compare(act$val, exp$val, ...)
     3. | \-testthat:::compare.default(act$val, exp$val, ...)
     4. | +-base::all.equal(x, y, ...)
     5. | \-base::all.equal.environment(x, y, ...)
     6. | \-base::as.list.environment(target, all.names = all.names, sorted = TRUE)
     7. \-(function () ...
     8. +-base::split(df, df$cluster, drop = TRUE)
     9. \-S4Vectors::split(df, df$cluster, drop = TRUE)
     10. +-S4Vectors::splitAsList(x, f, drop = drop, ...)
     11. \-S4Vectors::splitAsList(x, f, drop = drop, ...)
     12. \-S4Vectors:::.local(x, f, drop, ...)
     13. \-IRanges:::default_splitAsList(x, f, drop = drop)
     14. \-IRanges:::.splitAsList_by_factor(x, f, drop)
     15. \-S4Vectors:::isNotSorted(f)
     -- Error (test_subset.R:78:3): matrix notation for subset works ----------------
     Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. +-testthat::expect_equal(p[1, 1], p[orgs_1_char, clus_1_char]) test_subset.R:78:2
     2. | +-testthat::compare(act$val, exp$val, ...)
     3. | \-testthat:::compare.default(act$val, exp$val, ...)
     4. | +-base::all.equal(x, y, ...)
     5. | \-base::all.equal.environment(x, y, ...)
     6. | \-base::as.list.environment(target, all.names = all.names, sorted = TRUE)
     7. \-(function () ...
     8. +-base::split(df, df$cluster, drop = TRUE)
     9. \-S4Vectors::split(df, df$cluster, drop = TRUE)
     10. +-S4Vectors::splitAsList(x, f, drop = drop, ...)
     11. \-S4Vectors::splitAsList(x, f, drop = drop, ...)
     12. \-S4Vectors:::.local(x, f, drop, ...)
     13. \-IRanges:::default_splitAsList(x, f, drop = drop)
     14. \-IRanges:::.splitAsList_by_factor(x, f, drop)
     15. \-S4Vectors:::isNotSorted(f)
     -- Error (test_subset.R:103:3): dropping/recovering organisms works ------------
     Error in `..Internal(is.unsorted(x, FALSE))`: 2 arguments passed to .Internal(is.unsorted) which requires 3
     Backtrace:
     x
     1. +-testthat::expect_false(...) test_subset.R:103:2
     2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
     3. | \-rlang::eval_bare(expr, quo_get_env(quo))
     4. +-as.character(todrop) %in% as.character(unlist(p$genes, use.names = FALSE)$org)
     5. +-base::unlist(p$genes, use.names = FALSE)
     6. \-(function () ...
     7. +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     8. \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
     9. +-S4Vectors::splitAsList(x, f, drop = drop, ...)
     10. \-S4Vectors::splitAsList(x, f, drop = drop, ...)
     11. \-S4Vectors:::.local(x, f, drop, ...)
     12. \-IRanges:::default_splitAsList(x, f, drop = drop)
     13. \-IRanges:::.splitAsList_by_factor(x, f, drop)
     14. \-S4Vectors:::isNotSorted(f)
    
     [ FAIL 11 | WARN 0 | SKIP 0 | PASS 72 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-windows-x86_64

Version: 0.3.9
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'Input.Rmd' using rmarkdown
    Loading required package: S4Vectors
    Loading required package: stats4
    Loading required package: BiocGenerics
    Loading required package: parallel
    
    Attaching package: 'BiocGenerics'
    
    The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
    The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
    The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which.max, which.min
    
    
    Attaching package: 'S4Vectors'
    
    The following objects are masked from 'package:base':
    
     I, expand.grid, unname
    
    Loading required package: Biostrings
    Loading required package: IRanges
    
    Attaching package: 'IRanges'
    
    The following object is masked from 'package:grDevices':
    
     windows
    
    Loading required package: XVector
    Loading required package: GenomeInfoDb
    
    Attaching package: 'Biostrings'
    
    The following object is masked from 'package:base':
    
     strsplit
    
    Loading required package: ggplot2
    Checking class.
    Checking dimnames.
    Creating gid (gene ids).
    Checking provided organism metadata.
    Checking provided cluster metadata.
    Creating panmatrix.
    Populating class.
    Checking input sequences.
    Checking that sequence names matches with DataFrame.
    Adding metadata to sequences.
    --- finished re-building 'Input.Rmd'
    
    --- re-building 'Methods_Plots.Rmd' using rmarkdown
    Checking class.
    Checking dimnames.
    Creating gid (gene ids).
    Checking provided organism metadata.
    Checking provided cluster metadata.
    Creating panmatrix.
    Populating class.
    Checking input sequences.
    Checking that sequence names matches with DataFrame.
    Adding metadata to sequences.
    Warning: In prcomp.default(self$pan_matrix, center = center, scale. = scale.,
     ...) :
     extra argument 'size' will be disregarded
    --- finished re-building 'Methods_Plots.Rmd'
    
    --- re-building 'Querying_Data.Rmd' using rmarkdown
    Checking class.
    Checking dimnames.
    Creating gid (gene ids).
    Checking provided organism metadata.
    Checking provided cluster metadata.
    Creating panmatrix.
    Populating class.
    Checking input sequences.
    Checking that sequence names matches with DataFrame.
    Adding metadata to sequences.
    Quitting from lines 62-63 (Querying_Data.Rmd)
    Error: processing vignette 'Querying_Data.Rmd' failed with diagnostics:
    2 arguments passed to .Internal(is.unsorted) which requires 3
    --- failed re-building 'Querying_Data.Rmd'
    
    --- re-building 'Recipes.Rmd' using rmarkdown
    Checking class.
    Checking dimnames.
    Creating gid (gene ids).
    Checking provided organism metadata.
    Checking provided cluster metadata.
    Creating panmatrix.
    Populating class.
    Checking input sequences.
    Checking that sequence names matches with DataFrame.
    Adding metadata to sequences.
    Warning: In prcomp.default(self$pan_matrix, center = center, scale. = scale.,
     ...) :
     extra argument 'size' will be disregarded
    Scale for 'fill' is already present. Adding another scale for 'fill', which
    will replace the existing scale.
    --- finished re-building 'Recipes.Rmd'
    
    --- re-building 'Subseting.Rmd' using rmarkdown
    Checking class.
    Checking dimnames.
    Creating gid (gene ids).
    Checking provided organism metadata.
    Checking provided cluster metadata.
    Creating panmatrix.
    Populating class.
    Checking input sequences.
    Checking that sequence names matches with DataFrame.
    Adding metadata to sequences.
    Quitting from lines 57-63 (Subseting.Rmd)
    Error: processing vignette 'Subseting.Rmd' failed with diagnostics:
    2 arguments passed to .Internal(is.unsorted) which requires 3
    --- failed re-building 'Subseting.Rmd'
    
    --- re-building 'pagoo.Rmd' using rmarkdown
    Checking class.
    Checking dimnames.
    Creating gid (gene ids).
    Checking provided organism metadata.
    Checking provided cluster metadata.
    Creating panmatrix.
    Populating class.
    Checking input sequences.
    Checking that sequence names matches with DataFrame.
    Adding metadata to sequences.
    Quitting from lines 70-71 (pagoo.Rmd)
    Error: processing vignette 'pagoo.Rmd' failed with diagnostics:
    2 arguments passed to .Internal(is.unsorted) which requires 3
    --- failed re-building 'pagoo.Rmd'
    
    SUMMARY: processing the following files failed:
     'Querying_Data.Rmd' 'Subseting.Rmd' 'pagoo.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-windows-x86_64

Version: 0.3.9
Check: installed package size
Result: NOTE
     installed size is 5.1Mb
     sub-directories of 1Mb or more:
     extdata 4.1Mb
Flavor: r-patched-solaris-x86

Version: 0.3.9
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘DECIPHER’
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64