* using log directory 'd:/Rcompile/CRANpkg/local/3.3/HTSSIP.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HTSSIP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTSSIP' version '1.3.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'HTSSIP' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [20s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [89s] ERROR
  Running 'testthat.R' [88s]
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_ordination
  Incorrect number of arguments (7), expecting 5 for 'node_depth_edgelength'
  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: structure(lapply(pieces, .fun, ...), dim = dim(pieces))
  4: lapply(pieces, .fun, ...)
  5: FUN(X[[i]], ...)
  6: FUN(X[[i]], ...)
  7: UniFrac(physeq, ...)
  8: UniFrac(physeq, ...)
  9: fastUniFrac(physeq, weighted, normalized, parallel)
  10: ape_node_depth_edge_length(Ntip = length(tree$tip.label), Nnode = tree$Nnode, edge = z$edge, 
         Nedge = nrow(tree$edge)[1], edge.length = z$edge.length)
  
  -- 2. Error: Beta diversity from a list of phyloseq objects (parallel) (@test-BD
  Incorrect number of arguments (7), expecting 5 for 'node_depth_edgelength'
  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: structure(lapply(pieces, .fun, ...), dim = dim(pieces))
  4: lapply(pieces, .fun, ...)
  5: FUN(X[[i]], ...)
  6: FUN(X[[i]], ...)
  7: UniFrac(physeq, ...)
  8: UniFrac(physeq, ...)
  9: fastUniFrac(physeq, weighted, normalized, parallel)
  10: ape_node_depth_edge_length(Ntip = length(tree$tip.label), Nnode = tree$Nnode, edge = z$edge, 
         Nedge = nrow(tree$edge)[1], edge.length = z$edge.length)
  
  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 
  Sparsity threshold: 0.15 
  Density window: 1.7-1.75 
  Sparsity threshold: 0.3 
  Density window: 1.7-1.75 
  -- 3. Error: phyloseq sim (@test-HTSSIP_sim.R#59)  -----------------------------
  could not find function "sample_data"
  1: physeq %>% sample_data %>% .$Buoyant_density at testthat/test-HTSSIP_sim.R:59
  2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3: eval(quote(`_fseq`(`_lhs`)), env, env)
  4: eval(expr, envir, enclos)
  5: `_fseq`(`_lhs`)
  6: freduce(value, `_function_list`)
  7: function_list[[i]](value)
  
  -- 4. Error: phyloseq sim w/ metadata (@test-HTSSIP_sim.R#75)  -----------------
  could not find function "sample_data"
  1: physeq %>% sample_data %>% .$Buoyant_density at testthat/test-HTSSIP_sim.R:75
  2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3: eval(quote(`_fseq`(`_lhs`)), env, env)
  4: eval(expr, envir, enclos)
  5: `_fseq`(`_lhs`)
  6: freduce(value, `_function_list`)
  7: function_list[[i]](value)
  
  -- 5. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#10
  could not find function "sample_data"
  1: suppressWarnings(as.data.frame(as.matrix(sample_data(physeq_S2D2)))) at testthat/test-Util.R:10
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: as.data.frame(as.matrix(sample_data(physeq_S2D2)))
  4: as.matrix(sample_data(physeq_S2D2))
  
  -- 6. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#18) 
  could not find function "tax_table"
  1: suppressWarnings(as.data.frame(as.matrix(tax_table(physeq_S2D2)))) at testthat/test-Util.R:18
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: as.data.frame(as.matrix(tax_table(physeq_S2D2)))
  4: as.matrix(tax_table(physeq_S2D2))
  
  -- 7. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#25) 
  could not find function "otu_table"
  1: suppressWarnings(as.data.frame(as.matrix(otu_table(physeq_S2D2)))) at testthat/test-Util.R:25
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: as.data.frame(as.matrix(otu_table(physeq_S2D2)))
  4: as.matrix(otu_table(physeq_S2D2))
  
  -- 8. Error: phyloseq_re sample_data can be converted to dataframe (@test-Util.R
  could not find function "sample_data"
  1: suppressWarnings(as.data.frame(as.matrix(sample_data(physeq_rep3)))) at testthat/test-Util.R:35
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: as.data.frame(as.matrix(sample_data(physeq_rep3)))
  4: as.matrix(sample_data(physeq_rep3))
  
  -- 9. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#48) 
  could not find function "otu_table"
  1: suppressWarnings(as.data.frame(as.matrix(otu_table(physeq_rep3)))) at testthat/test-Util.R:48
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: as.data.frame(as.matrix(otu_table(physeq_rep3)))
  4: as.matrix(otu_table(physeq_rep3))
  
  -- 10. Error: physeq_format runs (@test-chk.R#5)  ------------------------------
  could not find function "sample_data"
  1: expect_equal(x %>% sample_data %>% colnames, physeq_S2D2 %>% sample_data %>% colnames) at testthat/test-chk.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: x %>% sample_data %>% colnames
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(expr, envir, enclos)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: function_list[[i]](value)
  
  -- 11. Error: qPCR OTU table transformation (@test-qSIP_trans.R#39)  -----------
  could not find function "otu_table"
  1: physeq_rep3 %>% otu_table %>% colnames at testthat/test-qSIP_trans.R:39
  2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3: eval(quote(`_fseq`(`_lhs`)), env, env)
  4: eval(expr, envir, enclos)
  5: `_fseq`(`_lhs`)
  6: freduce(value, `_function_list`)
  7: function_list[[i]](value)
  
  == testthat results  ===========================================================
  OK: 83 SKIPPED: 17 FAILED: 11
  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: phyloseq sim (@test-HTSSIP_sim.R#59) 
  4. Error: phyloseq sim w/ metadata (@test-HTSSIP_sim.R#75) 
  5. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#10) 
  6. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#18) 
  7. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#25) 
  8. Error: phyloseq_re sample_data can be converted to dataframe (@test-Util.R#35) 
  9. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#48) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE