CRAN Package Check Results for Package HTSSIP

Last updated on 2017-07-18 17:47:13.

Check Details

Version: 1.1.1
Check: installed package size
Result: NOTE
     installed size is 5.2Mb
     sub-directories of 1Mb or more:
     data 4.1Mb
Flavor: r-patched-solaris-x86

Version: 1.1.1
Check: for missing documentation entries
Result: ERROR
    Error in .requirePackage(package) :
     unable to find required package ‘phyloseq’
    Calls: <Anonymous> ... withCallingHandlers -> is -> getClassDef -> .requirePackage
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.1.1
Check: data for non-ASCII characters
Result: NOTE
     Error in .requirePackage(package) :
     unable to find required package 'phyloseq'
     Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
     Execution halted
Flavor: r-patched-solaris-x86

Version: 1.1.1
Check: examples
Result: ERROR
    Running examples in ‘HTSSIP-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: OTU_qPCR_trans
    > ### Title: Transform OTU counts based on qPCR data
    > ### Aliases: OTU_qPCR_trans
    >
    > ### ** Examples
    >
    > # qPCR data simulation
    > data(physeq_rep3)
    > data(physeq_rep3_qPCR)
    > physeq_rep3_t = OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR)
    Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
     there is no package called ‘igraph’
    Calls: OTU_qPCR_trans ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.1.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [14s/14s]
    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')
     1. Error: Beta diversity from a list of phyloseq objects (@test-BD_ordinations.R#2)
     there is no package called 'igraph'
     1: physeq_list_betaDiv(physeq_S2D2_l) at testthat/test-BD_ordinations.R:2
     2: plyr::llply(physeq_l, phyloseq::distance, method = method, weighted = weighted, fast = fast,
     normalized = normalized, parallel = parallel)
     3: phyloseq::distance
     4: getExportedValue(pkg, name)
     5: asNamespace(ns)
     6: getNamespace(ns)
     7: tryCatch(loadNamespace(name), error = function(e) stop(e))
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     10: value[[3L]](cond)
    
     2. Error: Beta diversity from a list of phyloseq objects (parallel) (@test-BD_ordinations.R#9)
     there is no package called 'igraph'
     1: physeq_list_betaDiv(physeq_S2D2_l, parallel = TRUE) at testthat/test-BD_ordinations.R:9
     2: plyr::llply(physeq_l, phyloseq::distance, method = method, weighted = weighted, fast = fast,
     normalized = normalized, parallel = parallel)
     3: phyloseq::distance
     4: getExportedValue(pkg, name)
     5: asNamespace(ns)
     6: getNamespace(ns)
     7: tryCatch(loadNamespace(name), error = function(e) stop(e))
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     10: value[[3L]](cond)
    
     3. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2) ---------
     there is no package called 'igraph'
     1: DESeq2_l2fc(physeq_S2D2_l[[1]], sparsity_threshold = 0.25, density_min = 1.71, density_max = 1.75,
     design = ~Substrate) at testthat/test-DESeq2_l2fc.R:2
     2: phyloseq::sample_data
     3: getExportedValue(pkg, name)
     4: asNamespace(ns)
     5: getNamespace(ns)
     6: tryCatch(loadNamespace(name), error = function(e) stop(e))
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     9: value[[3L]](cond)
    
     4. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15) --
     there is no package called 'igraph'
     1: DESeq2_l2fc(physeq_S2D2_l[[1]], sparsity_threshold = 0.25, density_min = 1.71, density_max = 1.75,
     design = ~Substrate, sparsity_apply = "heavy") at testthat/test-DESeq2_l2fc.R:15
     2: phyloseq::sample_data
     3: getExportedValue(pkg, name)
     4: asNamespace(ns)
     5: getNamespace(ns)
     6: tryCatch(loadNamespace(name), error = function(e) stop(e))
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     9: value[[3L]](cond)
    
     5. Error: HRSIP runs with default (@test-HRSIP.R#3) ----------------------------
     there is no package called 'igraph'
     1: HRSIP(physeq_S2D2_l[[1]], sparsity_threshold = c(0, 0.15, 0.3), design = ~Substrate) at testthat/test-HRSIP.R:3
     2: plyr::mdply(m, DESeq2_l2fc, physeq = physeq, design = design, l2fc_threshold = l2fc_threshold,
     sparsity_apply = sparsity_apply, .parallel = parallel)
     3: adply(.data = .data, .margins = 1, .fun = f, ..., .expand = .expand, .progress = .progress,
     .inform = .inform, .parallel = .parallel, .paropts = .paropts)
     4: ldply(.data = pieces, .fun = .fun, ..., .progress = .progress, .inform = .inform,
     .parallel = .parallel, .paropts = .paropts, .id = .id)
     5: llply(.data = .data, .fun = .fun, ..., .progress = .progress, .inform = .inform,
     .parallel = .parallel, .paropts = .paropts)
     6: loop_apply(n, do.ply)
     7: (function (i)
     {
     piece <- pieces[[i]]
     if (.inform) {
     res <- try(.fun(piece, ...))
     if (inherits(res, "try-error")) {
     piece <- paste(utils::capture.output(print(piece)), collapse = "\n")
     stop("with piece ", i, ": \n", piece, call. = FALSE)
     }
     }
     else {
     res <- .fun(piece, ...)
     }
     progress$step()
     res
     })(1L)
     8: .fun(piece, ...)
     9: do.call(flat, c(args, list(...)))
     10: (function (physeq, density_min, density_max, design, l2fc_threshold = 0.25, sparsity_threshold = 0.25,
     sparsity_apply = "all")
     {
     l2fc_threshold = as.numeric(l2fc_threshold)
     stopifnot(l2fc_threshold >= 0 & l2fc_threshold <= 1)
     sparsity_apply = tolower(sparsity_apply)
     stopifnot(sparsity_apply %in% c("all", "heavy"))
     physeq.md = phyloseq::sample_data(physeq)
     stopifnot(!is.null(physeq.md$Buoyant_density))
     cat("Sparsity threshold:", sparsity_threshold, "\n")
     cat("Density window:", paste(c(density_min, density_max), collapse = "-"), "\n")
     prn = function(x) sum(x > 0) > sparsity_threshold * length(x)
     if (sparsity_apply == "all") {
     physeq = phyloseq::filter_taxa(physeq, prn, TRUE)
     }
     physeq = phyloseq::prune_samples((physeq.md$Buoyant_density >= density_min) &
     (physeq.md$Buoyant_density <= density_max), physeq)
     physeq = phyloseq::filter_taxa(physeq, function(x) sum(x > 0) > 0 * length(x),
     TRUE)
     if (sparsity_apply == "heavy") {
     physeq = phyloseq::filter_taxa(physeq, prn, TRUE)
     }
     dds = phyloseq::phyloseq_to_deseq2(physeq, design)
     dds = DESeq2::DESeq(dds, quiet = TRUE, fitType = "local")
     theta = l2fc_threshold
     res = DESeq2::results(dds, independentFiltering = FALSE)
     res$OTU = rownames(res)
     beta = res$log2FoldChange
     betaSE = res$lfcSE
     p = stats::pnorm(beta, theta, betaSE, lower.tail = FALSE)
     res$p = p
     d = data.frame(res[, c("OTU", "log2FoldChange", "p")])
     d$padj = stats::p.adjust(p, method = "BH")
     TT = phyloseq::tax_table(physeq)
     if (!is.null(TT)) {
     TT = as.data.frame(as.matrix(TT))
     TT$OTU = rownames(TT)
     d = dplyr::left_join(d, TT, c("OTU"))
     }
     d$density_min = density_min
     d$density_max = density_max
     d$sparsity_threshold = sparsity_threshold
     d$sparsity_apply = sparsity_apply
     d$l2fc_threshold = l2fc_threshold
     return(d)
     })(density_min = 1.7, density_max = 1.75, sparsity_threshold = 0, physeq = <S4 object of class structure("phyloseq", package = "phyloseq")>,
     design = ~Substrate, l2fc_threshold = 0.25, sparsity_apply = "all")
     11: phyloseq::sample_data
     12: getExportedValue(pkg, name)
     13: asNamespace(ns)
     14: getNamespace(ns)
     15: tryCatch(loadNamespace(name), error = function(e) stop(e))
     16: tryCatchList(expr, classes, parentenv, handlers)
     17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     18: value[[3L]](cond)
    
     6. Error: phyloseq sim (@test-HTSSIP_sim.R#57) ---------------------------------
     there is no package called 'igraph'
     1: HTSSIP_sim(L$locs, L$params) at testthat/test-HTSSIP_sim.R:57
     2: phyloseq::phyloseq
     3: getExportedValue(pkg, name)
     4: asNamespace(ns)
     5: getNamespace(ns)
     6: tryCatch(loadNamespace(name), error = function(e) stop(e))
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     9: value[[3L]](cond)
    
     7. Error: phyloseq sim w/ metadata (@test-HTSSIP_sim.R#73) ---------------------
     there is no package called 'igraph'
     1: HTSSIP_sim(L$locs, L$params, meta = meta) at testthat/test-HTSSIP_sim.R:73
     2: phyloseq::phyloseq
     3: getExportedValue(pkg, name)
     4: asNamespace(ns)
     5: getNamespace(ns)
     6: tryCatch(loadNamespace(name), error = function(e) stop(e))
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     9: value[[3L]](cond)
    
     8. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#9) --
     there is no package called 'igraph'
     1: phyloseq2df(physeq_S2D2, phyloseq::sample_data) at testthat/test-Util.R:9
     2: phyloseq::sample_data
     3: getExportedValue(pkg, name)
     4: asNamespace(ns)
     5: getNamespace(ns)
     6: tryCatch(loadNamespace(name), error = function(e) stop(e))
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     9: value[[3L]](cond)
    
     9. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#17) ---
     there is no package called 'igraph'
     1: phyloseq2df(physeq_S2D2, phyloseq::tax_table) at testthat/test-Util.R:17
     2: phyloseq::tax_table
     3: getExportedValue(pkg, name)
     4: asNamespace(ns)
     5: getNamespace(ns)
     6: tryCatch(loadNamespace(name), error = function(e) stop(e))
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     9: value[[3L]](cond)
    
     10. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#24) --
     there is no package called 'igraph'
     1: phyloseq2df(physeq_S2D2, phyloseq::otu_table) at testthat/test-Util.R:24
     2: phyloseq::otu_table
     3: getExportedValue(pkg, name)
     4: asNamespace(ns)
     5: getNamespace(ns)
     6: tryCatch(loadNamespace(name), error = function(e) stop(e))
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     9: value[[3L]](cond)
    
     11. Error: phyloseq_re sample_data can be converted to dataframe (@test-Util.R#34)
     there is no package called 'igraph'
     1: phyloseq2df(physeq_rep3, phyloseq::sample_data) at testthat/test-Util.R:34
     2: phyloseq::sample_data
     3: getExportedValue(pkg, name)
     4: asNamespace(ns)
     5: getNamespace(ns)
     6: tryCatch(loadNamespace(name), error = function(e) stop(e))
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     9: value[[3L]](cond)
    
     12. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#47) --
     there is no package called 'igraph'
     1: phyloseq2df(physeq_rep3, phyloseq::otu_table) at testthat/test-Util.R:47
     2: phyloseq::otu_table
     3: getExportedValue(pkg, name)
     4: asNamespace(ns)
     5: getNamespace(ns)
     6: tryCatch(loadNamespace(name), error = function(e) stop(e))
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     9: value[[3L]](cond)
    
     13. Error: physeq_format runs (@test-chk.R#3) ----------------------------------
     there is no package called 'igraph'
     1: physeq_format(physeq_S2D2) at testthat/test-chk.R:3
     2: phyloseq::sample_data
     3: getExportedValue(pkg, name)
     4: asNamespace(ns)
     5: getNamespace(ns)
     6: tryCatch(loadNamespace(name), error = function(e) stop(e))
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     9: value[[3L]](cond)
    
     14. Error: delta BD on rep3 dataset (@test-delta_BD.R#27) ----------------------
     there is no package called 'igraph'
     1: delta_BD(physeq_rep3, control_expr = "Treatment==\"12C-Con\"") at testthat/test-delta_BD.R:27
     2: qSIP_atom_excess_format(physeq, control_expr, treatment_rep = NULL)
     3: phyloseq2table(physeq, include_sample_data = TRUE, sample_col_keep = cols, control_expr = control_expr)
     4: phyloseq::otu_table
     5: getExportedValue(pkg, name)
     6: asNamespace(ns)
     7: getNamespace(ns)
     8: tryCatch(loadNamespace(name), error = function(e) stop(e))
     9: tryCatchList(expr, classes, parentenv, handlers)
     10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11: value[[3L]](cond)
    
     15. Error: Getting params for subsetting (@test-phyloseq_subset.R#3) -----------
     there is no package called 'igraph'
     1: get_treatment_params(physeq_S2D2, X) at testthat/test-phyloseq_subset.R:3
     2: phyloseq2df(physeq, phyloseq::sample_data)
     3: phyloseq::sample_data
     4: getExportedValue(pkg, name)
     5: asNamespace(ns)
     6: getNamespace(ns)
     7: tryCatch(loadNamespace(name), error = function(e) stop(e))
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     10: value[[3L]](cond)
    
     16. Error: Subsetting phyloseq object (@test-phyloseq_subset.R#43) -------------
     there is no package called 'igraph'
     1: get_treatment_params(physeq_S2D2, c("Substrate", "Day")) at testthat/test-phyloseq_subset.R:43
     2: phyloseq2df(physeq, phyloseq::sample_data)
     3: phyloseq::sample_data
     4: getExportedValue(pkg, name)
     5: asNamespace(ns)
     6: getNamespace(ns)
     7: tryCatch(loadNamespace(name), error = function(e) stop(e))
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     10: value[[3L]](cond)
    
     17. Error: Subsetting phyloseq object (@test-phyloseq_subset.R#60) -------------
     there is no package called 'igraph'
     1: get_treatment_params(physeq_rep3, c("Treatment", "Replicate")) at testthat/test-phyloseq_subset.R:60
     2: phyloseq2df(physeq, phyloseq::sample_data)
     3: phyloseq::sample_data
     4: getExportedValue(pkg, name)
     5: asNamespace(ns)
     6: getNamespace(ns)
     7: tryCatch(loadNamespace(name), error = function(e) stop(e))
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     10: value[[3L]](cond)
    
     18. Error: Naming phyloseq object (@test-phyloseq_subset.R#77) -----------------
     there is no package called 'igraph'
     1: get_treatment_params(physeq_S2D2, c("Substrate", "Day")) at testthat/test-phyloseq_subset.R:77
     2: phyloseq2df(physeq, phyloseq::sample_data)
     3: phyloseq::sample_data
     4: getExportedValue(pkg, name)
     5: asNamespace(ns)
     6: getNamespace(ns)
     7: tryCatch(loadNamespace(name), error = function(e) stop(e))
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     10: value[[3L]](cond)
    
     19. Error: qPCR simulation warnings (@test-qPCR.R#101) -------------------------
     there is no package called 'igraph'
     1: expect_warning(qPCR_sim(physeq_S2D2, control_expr = "Substrate==\"XXX\"", control_mean_fun = L$control_mean_fun,
     control_sd_fun = L$control_sd_fun, treat_mean_fun = L$treat_mean_fun, treat_sd_fun = L$treat_sd_fun)) at testthat/test-qPCR.R:101
     2: capture_warnings(object)
     3: withCallingHandlers(code, warning = function(condition) {
     out$push(condition)
     invokeRestart("muffleWarning")
     })
     4: qPCR_sim(physeq_S2D2, control_expr = "Substrate==\"XXX\"", control_mean_fun = L$control_mean_fun,
     control_sd_fun = L$control_sd_fun, treat_mean_fun = L$treat_mean_fun, treat_sd_fun = L$treat_sd_fun)
     5: phyloseq2df(physeq, phyloseq::sample_data)
     6: phyloseq::sample_data
     7: getExportedValue(pkg, name)
     8: asNamespace(ns)
     9: getNamespace(ns)
     10: tryCatch(loadNamespace(name), error = function(e) stop(e))
     11: tryCatchList(expr, classes, parentenv, handlers)
     12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     13: value[[3L]](cond)
    
     20. Error: bootstrap iteration is working (@test-qSIP_atom_excess.R#31) --------
     there is no package called 'igraph'
     1: OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR) at testthat/test-qSIP_atom_excess.R:31
     2: colnames(phyloseq::otu_table(physeq))
     3: is.data.frame(x)
     4: phyloseq::otu_table
     5: getExportedValue(pkg, name)
     6: asNamespace(ns)
     7: getNamespace(ns)
     8: tryCatch(loadNamespace(name), error = function(e) stop(e))
     9: tryCatchList(expr, classes, parentenv, handlers)
     10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11: value[[3L]](cond)
    
     21. Error: qPCR OTU table transformation (@test-qSIP_trans.R#38) ---------------
     there is no package called 'igraph'
     1: OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR) at testthat/test-qSIP_trans.R:38
     2: colnames(phyloseq::otu_table(physeq))
     3: is.data.frame(x)
     4: phyloseq::otu_table
     5: getExportedValue(pkg, name)
     6: asNamespace(ns)
     7: getNamespace(ns)
     8: tryCatch(loadNamespace(name), error = function(e) stop(e))
     9: tryCatchList(expr, classes, parentenv, handlers)
     10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11: value[[3L]](cond)
    
     testthat results ================================================================
     OK: 26 SKIPPED: 15 FAILED: 21
     1. Error: Beta diversity from a list of phyloseq objects (@test-BD_ordinations.R#2)
     2. Error: Beta diversity from a list of phyloseq objects (parallel) (@test-BD_ordinations.R#9)
     3. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2)
     4. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15)
     5. Error: HRSIP runs with default (@test-HRSIP.R#3)
     6. Error: phyloseq sim (@test-HTSSIP_sim.R#57)
     7. Error: phyloseq sim w/ metadata (@test-HTSSIP_sim.R#73)
     8. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#9)
     9. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#17)
     1. ...
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-solaris-x86

Version: 1.1.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    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
    Error: package or namespace load failed for 'phyloseq' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
     there is no package called 'igraph'
    Quitting from lines 78-79 (BD_shifts.Rmd)
    Error: processing vignette 'BD_shifts.Rmd' failed with diagnostics:
    unable to find required package 'phyloseq'
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.1.1
Check: package dependencies
Result: ERROR
    Packages required but not available: ‘DESeq2’ ‘phyloseq’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64