| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:03:42 -0400 (Tue, 09 Apr 2019).
| Package 1185/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| phyloseq 1.27.2 Paul J. McMurdie
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: phyloseq |
| Version: 1.27.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings phyloseq_1.27.2.tar.gz |
| StartedAt: 2019-04-09 04:23:13 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:30:34 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 440.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: phyloseq.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings phyloseq_1.27.2.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/phyloseq.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.27.2’
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘phyloseq’ can be installed ... OK
* checking installed package size ... OK
* 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 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 ... NOTE
DPCoA: no visible global function definition for ‘as.dist’
chunkReOrder: no visible global function definition for ‘tail’
chunkReOrder: no visible global function definition for ‘head’
export_env_file: no visible global function definition for
‘write.table’
export_mothur_dist: no visible global function definition for ‘as.dist’
export_mothur_dist: no visible global function definition for
‘write.table’
fastUniFrac: no visible global function definition for ‘combn’
fastUniFrac: no visible global function definition for ‘as.dist’
import_RDP_otu: no visible global function definition for ‘read.table’
import_env_file: no visible global function definition for ‘read.table’
import_mothur_constaxonomy: no visible global function definition for
‘read.table’
import_mothur_dist: no visible global function definition for ‘as.dist’
import_mothur_groups: no visible global function definition for
‘read.table’
import_mothur_shared: no visible global function definition for
‘read.table’
import_qiime_otu_tax: no visible global function definition for ‘:=’
import_qiime_otu_tax: no visible binding for global variable ‘Consensus
Lineage’
import_qiime_otu_tax: no visible binding for global variable ‘#OTU ID’
import_qiime_sample_data: no visible global function definition for
‘read.table’
import_uparse: no visible global function definition for ‘:=’
import_uparse: no visible binding for global variable ‘count’
import_uparse: no visible binding for global variable ‘queryString’
import_uparse: no visible binding for global variable ‘queryID’
import_uparse: no visible binding for global variable ‘Classification’
import_uparse: no visible global function definition for
‘dcast.data.table’
import_uparse: no visible binding for global variable ‘OTULabel’
import_usearch_uc: no visible global function definition for ‘:=’
import_usearch_uc: no visible binding for global variable ‘read’
microbio_me_qiime: no visible global function definition for
‘download.file’
microbio_me_qiime: no visible global function definition for ‘unzip’
microbio_me_qiime: no visible global function definition for ‘untar’
nodeplotboot : <anonymous>: no visible global function definition for
‘complete.cases’
nodeplotboot : <anonymous>: no visible binding for global variable ‘x’
nodeplotboot : <anonymous>: no visible binding for global variable ‘y’
nodeplotdefault : <anonymous>: no visible binding for global variable
‘x’
nodeplotdefault : <anonymous>: no visible binding for global variable
‘y’
nodeplotdefault : <anonymous>: no visible binding for global variable
‘label’
ordinate: no visible global function definition for ‘as.formula’
plot_clusgap: no visible binding for global variable ‘k’
plot_clusgap: no visible binding for global variable ‘gap’
plot_clusgap: no visible binding for global variable ‘SE.sim’
plot_heatmap: no visible global function definition for
‘capture.output’
plot_heatmap: no visible binding for global variable ‘Sample’
plot_heatmap: no visible binding for global variable ‘OTU’
plot_heatmap: no visible binding for global variable ‘Abundance’
plot_net : vertex_layout: no visible binding for global variable ‘x’
plot_net : link_layout: no visible binding for global variable ‘x’
plot_net : link_layout: no visible binding for global variable ‘y’
plot_net: no visible binding for global variable ‘x’
plot_net: no visible binding for global variable ‘y’
plot_net: no visible binding for global variable ‘xend’
plot_net: no visible binding for global variable ‘yend’
plot_network: no visible binding for global variable ‘x’
plot_network: no visible binding for global variable ‘y’
plot_richness: no visible binding for global variable ‘value’
plot_richness: no visible binding for global variable ‘se’
plot_scree: no visible binding for global variable ‘axis’
plot_scree: no visible binding for global variable ‘eigenvalue’
plot_tree: no visible binding for global variable ‘xleft’
plot_tree: no visible binding for global variable ‘xright’
plot_tree: no visible binding for global variable ‘y’
plot_tree: no visible binding for global variable ‘x’
plot_tree: no visible binding for global variable ‘vmin’
plot_tree: no visible binding for global variable ‘vmax’
plot_tree: no visible binding for global variable ‘OTU’
plot_tree: no visible binding for global variable ‘label’
plot_tree: no visible binding for global variable ‘Abundance’
plot_tree: no visible binding for global variable ‘Sample’
plot_tree: no visible global function definition for ‘:=’
plot_tree: no visible binding for global variable ‘h.adj.index’
plot_tree: no visible binding for global variable ‘xdodge’
plot_tree: no visible binding for global variable ‘xfartiplab’
plot_tree: no visible binding for global variable ‘.SD’
rp.joint.fill: no visible global function definition for ‘relevel’
tip_glom: no visible global function definition for ‘as.dist’
tip_glom: no visible global function definition for ‘cutree’
tip_glom: no visible global function definition for ‘as.hclust’
tree_layout: no visible global function definition for ‘:=’
tree_layout: no visible binding for global variable ‘OTU’
tree_layout: no visible binding for global variable ‘V2’
tree_layout: no visible binding for global variable ‘xleft’
tree_layout: no visible binding for global variable ‘V1’
tree_layout: no visible binding for global variable ‘xright’
tree_layout: no visible binding for global variable ‘y’
tree_layout: no visible binding for global variable ‘x’
tree_layout: no visible binding for global variable ‘label’
tree_layout: no visible global function definition for ‘J’
tree_layout: no visible binding for global variable ‘vmin’
tree_layout: no visible binding for global variable ‘vmax’
JSD,matrix: no visible global function definition for ‘combn’
JSD,matrix: no visible binding for global variable ‘i’
JSD,matrix: no visible global function definition for ‘as.dist’
capscale.phyloseq,phyloseq-formula-character: no visible global
function definition for ‘as.formula’
capscale.phyloseq,phyloseq-formula-dist: no visible global function
definition for ‘as.formula’
cca.phyloseq,phyloseq-formula: no visible global function definition
for ‘as.formula’
distance,phyloseq-character: no visible global function definition for
‘as.dist’
merge_phyloseq_pair,sample_data-sample_data : <anonymous>: no visible
binding for global variable ‘X0’
merge_samples,sample_data: no visible global function definition for
‘aggregate’
plot_phyloseq,phyloseq: no visible binding for global variable
‘esophagus’
Undefined global functions or variables:
#OTU ID .SD := Abundance Classification Consensus Lineage J OTU
OTULabel SE.sim Sample V1 V2 X0 aggregate as.dist as.formula
as.hclust axis capture.output combn complete.cases count cutree
dcast.data.table download.file eigenvalue esophagus gap h.adj.index
head i k label queryID queryString read read.table relevel se tail
untar unzip value vmax vmin write.table x xdodge xend xfartiplab
xleft xright y yend
Consider adding
importFrom("graphics", "axis")
importFrom("stats", "aggregate", "as.dist", "as.formula", "as.hclust",
"complete.cases", "cutree", "relevel")
importFrom("utils", "capture.output", "combn", "download.file", "head",
"read.table", "tail", "untar", "unzip", "write.table")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_net 11.544 5.416 4.760
plot_heatmap 8.963 0.522 9.521
plot_richness 5.522 0.926 6.471
phyloseq_to_deseq2 5.311 0.244 5.557
threshrank 3.013 2.449 5.485
DPCoA 4.539 0.521 5.062
plot_bar 4.484 0.535 5.020
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat-phyloseq.R’
ERROR
Running the tests in ‘tests/testthat-phyloseq.R’ failed.
Last 13 lines of output:
══ testthat results ═══════════════════════════════════════════════════════════
OK: 599 SKIPPED: 0 FAILED: 9
1. Failure: Test that empty OTUs and samples were automatically pruned (@test-rarefy.R#22)
2. Failure: Test that empty OTUs and samples were automatically pruned (@test-rarefy.R#23)
3. Failure: Test that empty OTUs and samples were automatically pruned (@test-rarefy.R#24)
4. Failure: Test that empty OTUs and samples were automatically pruned (@test-rarefy.R#27)
5. Failure: Test that empty OTUs and samples were automatically pruned (@test-rarefy.R#28)
6. Failure: Test values (@test-rarefy.R#36)
7. Failure: Test values (@test-rarefy.R#37)
8. Error: Test values (@test-rarefy.R#38)
9. Failure: The same samples should have been cut in each results (@test-rarefy.R#58)
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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/phyloseq.Rcheck/00check.log’
for details.
phyloseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL phyloseq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘phyloseq’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘phyloseq-FAQ.Rmd’ using ‘UTF-8’ ‘phyloseq-analysis.Rmd’ ‘phyloseq-basics.Rmd’ ‘phyloseq-mixture-models.Rmd’ ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (phyloseq)
phyloseq.Rcheck/tests/testthat-phyloseq.Rout.fail
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library("testthat")
> packageVersion("phyloseq")
[1] '1.27.2'
> # As suggested for opt-out option on testing by users, recommended by CRAN
> # http://adv-r.had.co.nz/Testing.html
> # Previously, best practice was to put all test files in inst/tests and ensure that R CMD check ran them by putting the following code in tests/test-all.R:
> # library(testthat)
> # library(yourpackage)
> # test_package("yourpackage")
> # Now, recommended practice is to put your tests in tests/testthat, and ensure R CMD check runs them by putting the following code in tests/test-all.R:
> # library(testthat)
> # test_check("yourpackage")
> # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, but now you have the flexibility as requested by CRAN maintainers.
> test_check("phyloseq")
Loading required package: phyloseq
Found biom-format file, now parsing it...
Done parsing biom...
Importing Sample Metdadata from mapping file...
Merging the imported objects...
Successfully merged, phyloseq-class created.
Returning...
Found biom-format file, now parsing it...
Done parsing biom...
Importing Sample Metdadata from mapping file...
Merging the imported objects...
Successfully merged, phyloseq-class created.
Returning...
Reading `ucfile` into memory and parsing into table
Initially read 100 entries.
... Now removing unassigned OTUs (* or NA)...
Removed 7 entries that had no OTU assignment.
A total of 93 will be assigned to the OTU table.
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 2
Converting input file to a table...
Defining OTU table...
Parsing taxonomy table...
Processing phylogenetic tree...
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing map file...
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 2
Converting input file to a table...
Defining OTU table...
Parsing taxonomy table...
Processing phylogenetic tree...
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
── 1. Failure: Test that empty OTUs and samples were automatically pruned (@test
length(rmOTU) not equal to 20.
1/1 mismatches
[1] 35 - 20 == 15
── 2. Failure: Test that empty OTUs and samples were automatically pruned (@test
rmOTU[1:5] not equal to c("534601", "408325", "325564", "8112", "571917").
5/5 mismatches
x[1]: "552540"
y[1]: "534601"
x[2]: "332271"
y[2]: "408325"
x[3]: "251292"
y[3]: "325564"
x[4]: "76574"
y[4]: "8112"
x[5]: "9555"
y[5]: "571917"
── 3. Failure: Test that empty OTUs and samples were automatically pruned (@test
taxa_names(GP100)[taxa_sums(GP100) <= 0] %in% rmOTU isn't true.
── 4. Failure: Test that empty OTUs and samples were automatically pruned (@test
length(rmsam) not equal to 12.
1/1 mismatches
[1] 15 - 12 == 3
── 5. Failure: Test that empty OTUs and samples were automatically pruned (@test
rmsam[1:5] not equal to c("M11Fcsw", "M31Tong", "M11Tong", "NP2", "TRRsed1").
5/5 mismatches
x[1]: "M31Fcsw"
y[1]: "M11Fcsw"
x[2]: "M11Fcsw"
y[2]: "M31Tong"
x[3]: "M31Plmr"
y[3]: "M11Tong"
x[4]: "M11Plmr"
y[4]: "NP2"
x[5]: "F21Plmr"
y[5]: "TRRsed1"
── 6. Failure: Test values (@test-rarefy.R#36) ────────────────────────────────
as(otu_table(rGP)[1, 3:10], "vector") not equal to rep(0, 8).
1/8 mismatches
[3] 3 - 0 == 3
── 7. Failure: Test values (@test-rarefy.R#37) ────────────────────────────────
as(otu_table(rGP)[2, 1:10], "vector") not equal to c(rep(0, 9), 2).
2/10 mismatches (average diff: 1.5)
[4] 1 - 0 == 1
[10] 0 - 2 == -2
── 8. Error: Test values (@test-rarefy.R#38) ──────────────────────────────────
subscript out of bounds
1: expect_equal(as(otu_table(rGP)[3, 8:12], "vector"), c(892, 956, 56, 10, 25)) at testthat/test-rarefy.R:38
2: quasi_label(enquo(object), label)
3: eval_bare(get_expr(quo), get_env(quo))
4: as(otu_table(rGP)[3, 8:12], "vector")
5: .class1(object)
6: otu_table(rGP)[3, 8:12]
7: otu_table(rGP)[3, 8:12]
── 9. Failure: The same samples should have been cut in each results (@test-rare
nsamples(rGP) not equal to 14.
1/1 mismatches
[1] 11 - 14 == -3
══ testthat results ═══════════════════════════════════════════════════════════
OK: 599 SKIPPED: 0 FAILED: 9
1. Failure: Test that empty OTUs and samples were automatically pruned (@test-rarefy.R#22)
2. Failure: Test that empty OTUs and samples were automatically pruned (@test-rarefy.R#23)
3. Failure: Test that empty OTUs and samples were automatically pruned (@test-rarefy.R#24)
4. Failure: Test that empty OTUs and samples were automatically pruned (@test-rarefy.R#27)
5. Failure: Test that empty OTUs and samples were automatically pruned (@test-rarefy.R#28)
6. Failure: Test values (@test-rarefy.R#36)
7. Failure: Test values (@test-rarefy.R#37)
8. Error: Test values (@test-rarefy.R#38)
9. Failure: The same samples should have been cut in each results (@test-rarefy.R#58)
Error: testthat unit tests failed
Execution halted
phyloseq.Rcheck/phyloseq-Ex.timings
| name | user | system | elapsed | |
| DPCoA | 4.539 | 0.521 | 5.062 | |
| JSD | 0.000 | 0.001 | 0.001 | |
| UniFrac-methods | 0.136 | 0.012 | 0.148 | |
| access | 0.001 | 0.000 | 0.000 | |
| assign-otu_table | 0.000 | 0.000 | 0.001 | |
| assign-phy_tree | 0.042 | 0.003 | 0.044 | |
| assign-sample_data | 0.145 | 0.020 | 0.165 | |
| assign-sample_names | 0.007 | 0.001 | 0.008 | |
| assign-tax_table | 0.000 | 0.000 | 0.001 | |
| assign-taxa_are_rows | 0.003 | 0.002 | 0.004 | |
| assign-taxa_names | 0.007 | 0.003 | 0.010 | |
| build_tax_table | 0.011 | 0.001 | 0.012 | |
| capscale-phyloseq-methods | 0.753 | 0.078 | 0.831 | |
| cca-rda-phyloseq-methods | 0 | 0 | 0 | |
| chunkReOrder | 0.000 | 0.001 | 0.003 | |
| data-GlobalPatterns | 1.772 | 0.184 | 1.956 | |
| data-enterotype | 2.372 | 0.133 | 2.506 | |
| data-esophagus | 0.943 | 0.009 | 0.955 | |
| data-soilrep | 1.225 | 0.220 | 1.446 | |
| distance | 0.329 | 0.069 | 0.433 | |
| distanceMethodList | 0.001 | 0.000 | 0.002 | |
| envHash2otu_table | 0 | 0 | 0 | |
| estimate_richness | 0.041 | 0.009 | 0.050 | |
| export_env_file | 0.000 | 0.000 | 0.001 | |
| export_mothur_dist | 0.133 | 0.063 | 0.197 | |
| extract-methods | 0.011 | 0.002 | 0.013 | |
| filter_taxa | 1.534 | 0.080 | 1.615 | |
| filterfun_sample | 0.017 | 0.000 | 0.017 | |
| gapstat_ord | 2.501 | 0.075 | 2.577 | |
| genefilter_sample-methods | 0.000 | 0.000 | 0.001 | |
| get.component.classes | 0 | 0 | 0 | |
| get_sample-methods | 0.003 | 0.002 | 0.005 | |
| get_taxa-methods | 0.003 | 0.002 | 0.005 | |
| get_taxa_unique | 0.284 | 0.039 | 0.323 | |
| get_variable | 0.230 | 0.014 | 0.244 | |
| getslots.phyloseq | 0.237 | 0.027 | 0.263 | |
| import | 0.001 | 0.001 | 0.001 | |
| import_RDP_otu | 0.792 | 0.031 | 0.823 | |
| import_biom | 0.806 | 0.026 | 0.831 | |
| import_env_file | 0 | 0 | 0 | |
| import_mothur | 0.001 | 0.000 | 0.001 | |
| import_mothur_dist | 0.000 | 0.000 | 0.001 | |
| import_pyrotagger_tab | 0.001 | 0.000 | 0.000 | |
| import_qiime | 0.987 | 0.009 | 1.000 | |
| import_qiime_otu_tax | 0.991 | 0.157 | 1.147 | |
| import_qiime_sample_data | 0.028 | 0.004 | 0.031 | |
| import_uparse | 0.000 | 0.000 | 0.001 | |
| import_usearch_uc | 0.119 | 0.117 | 0.047 | |
| index_reorder | 0.001 | 0.002 | 0.001 | |
| intersect_taxa | 0.002 | 0.002 | 0.000 | |
| make_network | 3.538 | 0.496 | 3.288 | |
| merge_phyloseq | 0.000 | 0.000 | 0.001 | |
| merge_phyloseq_pair-methods | 0.001 | 0.000 | 0.001 | |
| merge_samples-methods | 0.968 | 0.252 | 1.221 | |
| merge_taxa-methods | 0.057 | 0.002 | 0.058 | |
| microbio_me_qiime | 2.093 | 0.028 | 2.124 | |
| mt-methods | 1.301 | 0.023 | 1.324 | |
| nodeplotblank | 2.904 | 0.963 | 0.624 | |
| nodeplotboot | 0.010 | 0.009 | 0.003 | |
| nodeplotdefault | 0.004 | 0.004 | 0.002 | |
| nsamples-methods | 0.037 | 0.004 | 0.044 | |
| ntaxa-methods | 0.004 | 0.003 | 0.008 | |
| ordinate | 0 | 0 | 0 | |
| otu_table-methods | 0 | 0 | 0 | |
| parseTaxonomy-functions | 0.003 | 0.001 | 0.004 | |
| phy_tree-methods | 0.208 | 0.023 | 0.231 | |
| phyloseq | 0.022 | 0.005 | 0.027 | |
| phyloseq_to_deseq2 | 5.311 | 0.244 | 5.557 | |
| phyloseq_to_metagenomeSeq | 2.642 | 0.219 | 2.861 | |
| plot_bar | 4.484 | 0.535 | 5.020 | |
| plot_clusgap | 3.795 | 0.190 | 3.988 | |
| plot_heatmap | 8.963 | 0.522 | 9.521 | |
| plot_net | 11.544 | 5.416 | 4.760 | |
| plot_network | 2.894 | 0.037 | 2.954 | |
| plot_ordination | 1.038 | 0.101 | 1.139 | |
| plot_phyloseq-methods | 1.031 | 0.793 | 0.364 | |
| plot_richness | 5.522 | 0.926 | 6.471 | |
| plot_scree | 2.173 | 0.134 | 2.310 | |
| plot_tree | 2.520 | 1.588 | 1.119 | |
| prune_samples-methods | 0.549 | 0.138 | 0.688 | |
| prune_taxa-methods | 0.065 | 0.004 | 0.068 | |
| psmelt | 1.197 | 0.178 | 1.376 | |
| rank_names | 0.022 | 0.007 | 0.030 | |
| rarefy_even_depth | 0.088 | 0.006 | 0.093 | |
| read_tree | 0.027 | 0.001 | 0.027 | |
| read_tree_greengenes | 0.015 | 0.001 | 0.018 | |
| reconcile_categories | 0.000 | 0.000 | 0.001 | |
| refseq-methods | 0.220 | 0.030 | 0.251 | |
| rm_outlierf | 0.027 | 0.001 | 0.029 | |
| sample_data-methods | 0.063 | 0.017 | 0.081 | |
| sample_names-methods | 0.004 | 0.011 | 0.014 | |
| sample_sums | 0.026 | 0.021 | 0.047 | |
| sample_variables | 0.027 | 0.013 | 0.039 | |
| show-methods | 0 | 0 | 0 | |
| splat.phyloseq.objects | 0 | 0 | 0 | |
| subset_ord_plot | 0 | 0 | 0 | |
| subset_samples-methods | 0 | 0 | 0 | |
| subset_taxa-methods | 0.001 | 0.000 | 0.000 | |
| tax_glom | 0.000 | 0.000 | 0.001 | |
| tax_table-methods | 0.000 | 0.001 | 0.001 | |
| taxa_names-methods | 0.025 | 0.013 | 0.037 | |
| taxa_sums | 0.039 | 0.034 | 0.073 | |
| threshrank | 3.013 | 2.449 | 5.485 | |
| threshrankfun | 0.086 | 0.006 | 0.092 | |
| tip_glom | 2.791 | 1.674 | 1.064 | |
| topf | 0.012 | 0.000 | 0.013 | |
| topk | 0.012 | 0.000 | 0.012 | |
| topp | 0.012 | 0.001 | 0.013 | |
| transformcounts | 0.098 | 0.007 | 0.104 | |
| transpose-methods | 2.252 | 1.477 | 3.731 | |
| tree_layout | 2.517 | 1.756 | 0.904 | |