| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L M N O [P] Q R S T U V W X Y Z |
This page was generated on 2016-04-23 10:18:19 -0700 (Sat, 23 Apr 2016).
| Package 772/1103 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| phyloseq 1.14.0 Paul J. McMurdie
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | ||||||
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | ||||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: phyloseq |
| Version: 1.14.0 |
| Command: rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.14.0.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.14.0.tar.gz |
| StartedAt: 2016-04-23 05:55:44 -0700 (Sat, 23 Apr 2016) |
| EndedAt: 2016-04-23 06:08:04 -0700 (Sat, 23 Apr 2016) |
| EllapsedTime: 740.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: phyloseq.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.14.0.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/phyloseq.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phyloseq/DESCRIPTION' ... OK
* this is package 'phyloseq' version '1.14.0'
* 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 'phyloseq' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'phyloseq'
See 'D:/biocbld/bbs-3.2-bioc/meat/phyloseq.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
':::' calls which should be '::':
'ape:::node_depth_edgelength' 'ape:::node_height'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
.C(ape:::node_depth_edgelength, ..., PACKAGE = "ape")
.C(ape:::node_height, ..., PACKAGE = "ape")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
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_usearch_uc: no visible global function definition for ':='
import_usearch_uc: no visible binding for global variable 'read'
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'
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 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
'vertex'
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 : links_to_ggplot: no visible binding for global variable 'x'
plot_net : links_to_ggplot: no visible binding for global variable 'y'
plot_net : links_to_ggplot: no visible binding for global variable
'xend'
plot_net : links_to_ggplot: 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 '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'
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 binding for global variable 'i'
merge_phyloseq_pair,sample_data-sample_data : <anonymous>: no visible
binding for global variable 'X0'
plot_phyloseq,phyloseq: no visible binding for global variable
'esophagus'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'psmelt.Rd':
'ggplot2'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ...
** running examples for arch 'i386' ... [103s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_richness 7.24 0.13 7.79
plot_net 7.06 0.02 7.08
plot_heatmap 5.94 0.06 6.01
plot_clusgap 5.10 0.03 5.83
make_network 4.87 0.02 5.04
** running examples for arch 'x64' ... [109s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_heatmap 7.44 0.04 7.99
plot_richness 6.66 0.07 6.74
plot_clusgap 6.08 0.10 6.35
plot_net 5.43 0.00 5.62
DPCoA 4.76 0.02 5.54
plot_network 3.82 0.00 6.16
gapstat_ord 3.34 0.06 5.13
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat-phyloseq.R' [97s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/i386/R" CMD BATCH --vanilla "testthat-phyloseq.R" "testthat-phyloseq.Rout"' had status 1
ERROR
Running the tests in 'tests/testthat-phyloseq.R' failed.
Last 13 lines of output:
The following object is masked from 'package:base':
anyNA
testthat results ================================================================
OK: 611 SKIPPED: 0 FAILED: 2
1. Failure: import_mothur: show method output tests (@test-IO.R#52)
2. Failure: the import_RDP_otu function can properly read gzipped-example (@test-IO.R#72)
Error: testthat unit tests failed
In addition: Warning message:
replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'phyloseq'
Execution halted
** running tests for arch 'x64' ...
Running 'testthat-phyloseq.R' [110s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/x64/R" CMD BATCH --vanilla "testthat-phyloseq.R" "testthat-phyloseq.Rout"' had status 1
ERROR
Running the tests in 'tests/testthat-phyloseq.R' failed.
Last 13 lines of output:
The following object is masked from 'package:base':
anyNA
testthat results ================================================================
OK: 611 SKIPPED: 0 FAILED: 2
1. Failure: import_mothur: show method output tests (@test-IO.R#52)
2. Failure: the import_RDP_otu function can properly read gzipped-example (@test-IO.R#72)
Error: testthat unit tests failed
In addition: Warning message:
replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'phyloseq'
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: 2 ERRORs, 2 WARNINGs, 3 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/phyloseq.Rcheck/00check.log'
for details.
testthat-phyloseq.Rout.fail:
R version 3.2.4 (2016-03-10) -- "Very Secure Dishes"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
Warning message:
package 'testthat' was built under R version 3.2.5
> packageVersion("phyloseq")
[1] '1.14.0'
> # 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
1. Failure: import_mothur: show method output tests (@test-IO.R#52) ------------
`esophman` produced no output
2. Failure: the import_RDP_otu function can properly read gzipped-example (@test-IO.R#72)
head(t(ex_otu)) produced no output
Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics'
Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics'
Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics'
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...
D:/biocbld/bbs-3.2-bioc/meat/phyloseq.buildbin-libdir/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...
D:/biocbld/bbs-3.2-bioc/meat/phyloseq.buildbin-libdir/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
Attaching package: 'genefilter'
The following object is masked from 'package:base':
anyNA
testthat results ================================================================
OK: 611 SKIPPED: 0 FAILED: 2
1. Failure: import_mothur: show method output tests (@test-IO.R#52)
2. Failure: the import_RDP_otu function can properly read gzipped-example (@test-IO.R#72)
Error: testthat unit tests failed
In addition: Warning message:
replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'phyloseq'
Execution halted
testthat-phyloseq.Rout.fail:
R version 3.2.4 (2016-03-10) -- "Very Secure Dishes"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
Warning message:
package 'testthat' was built under R version 3.2.5
> packageVersion("phyloseq")
[1] '1.14.0'
> # 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
1. Failure: import_mothur: show method output tests (@test-IO.R#52) ------------
`esophman` produced no output
2. Failure: the import_RDP_otu function can properly read gzipped-example (@test-IO.R#72)
head(t(ex_otu)) produced no output
Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics'
Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics'
Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics'
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...
D:/biocbld/bbs-3.2-bioc/meat/phyloseq.buildbin-libdir/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...
D:/biocbld/bbs-3.2-bioc/meat/phyloseq.buildbin-libdir/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
Attaching package: 'genefilter'
The following object is masked from 'package:base':
anyNA
testthat results ================================================================
OK: 611 SKIPPED: 0 FAILED: 2
1. Failure: import_mothur: show method output tests (@test-IO.R#52)
2. Failure: the import_RDP_otu function can properly read gzipped-example (@test-IO.R#72)
Error: testthat unit tests failed
In addition: Warning message:
replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'phyloseq'
Execution halted
phyloseq.Rcheck/00install.out:
install for i386 * installing *source* package 'phyloseq' ... ** R ** data ** inst ** preparing package for lazy loading Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'phyloseq' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'phyloseq' install for x64 * installing *source* package 'phyloseq' ... ** testing if installed package can be loaded Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'phyloseq' * MD5 sums packaged installation of 'phyloseq' as phyloseq_1.14.0.zip * DONE (phyloseq)
phyloseq.Rcheck/examples_i386/phyloseq-Ex.timings:
| name | user | system | elapsed | |
| DPCoA | 4.50 | 0.04 | 4.68 | |
| JSD | 0 | 0 | 0 | |
| UniFrac-methods | 0.20 | 0.00 | 0.27 | |
| access | 0 | 0 | 0 | |
| assign-otu_table | 0 | 0 | 0 | |
| assign-phy_tree | 0.07 | 0.02 | 0.08 | |
| assign-sample_data | 0.70 | 0.03 | 0.73 | |
| assign-sample_names | 0.01 | 0.00 | 0.02 | |
| assign-tax_table | 0 | 0 | 0 | |
| assign-taxa_are_rows | 0 | 0 | 0 | |
| assign-taxa_names | 0.02 | 0.00 | 0.01 | |
| build_tax_table | 0.02 | 0.00 | 0.02 | |
| capscale-phyloseq-methods | 0.74 | 0.00 | 0.75 | |
| cca-rda-phyloseq-methods | 0 | 0 | 0 | |
| chunkReOrder | 0 | 0 | 0 | |
| data-GlobalPatterns | 2.11 | 0.00 | 2.11 | |
| data-enterotype | 2.09 | 0.03 | 2.12 | |
| data-esophagus | 0.92 | 0.00 | 0.92 | |
| data-soilrep | 2.30 | 0.02 | 2.30 | |
| distance | 0.26 | 0.00 | 3.22 | |
| distanceMethodList | 0 | 0 | 0 | |
| envHash2otu_table | 0.02 | 0.00 | 0.01 | |
| estimate_richness | 0.03 | 0.00 | 0.04 | |
| export_env_file | 0 | 0 | 0 | |
| export_mothur_dist | 0.11 | 0.01 | 0.13 | |
| extract-methods | 0.00 | 0.02 | 0.01 | |
| filter_taxa | 1.33 | 0.03 | 1.36 | |
| filterfun_sample | 0.03 | 0.00 | 0.03 | |
| gapstat_ord | 2.54 | 0.05 | 3.31 | |
| genefilter_sample-methods | 0.02 | 0.00 | 0.01 | |
| get.component.classes | 0 | 0 | 0 | |
| get_sample-methods | 0 | 0 | 0 | |
| get_taxa-methods | 0 | 0 | 0 | |
| get_taxa_unique | 0.38 | 0.00 | 0.37 | |
| get_variable | 0.35 | 0.00 | 0.34 | |
| getslots.phyloseq | 0.32 | 0.03 | 0.36 | |
| import | 0 | 0 | 0 | |
| import_RDP_otu | 2.70 | 0.00 | 2.69 | |
| import_biom | 0.20 | 0.00 | 0.72 | |
| import_env_file | 0 | 0 | 0 | |
| import_mothur | 0 | 0 | 0 | |
| import_mothur_dist | 0 | 0 | 0 | |
| import_pyrotagger_tab | 0 | 0 | 0 | |
| import_qiime | 0.59 | 0.00 | 0.59 | |
| import_qiime_otu_tax | 0.56 | 0.00 | 0.56 | |
| import_qiime_sample_data | 0.02 | 0.00 | 0.01 | |
| import_usearch_uc | 0.01 | 0.00 | 0.02 | |
| index_reorder | 0 | 0 | 0 | |
| intersect_taxa | 0 | 0 | 0 | |
| make_network | 4.87 | 0.02 | 5.04 | |
| merge_phyloseq | 0.02 | 0.00 | 0.01 | |
| merge_phyloseq_pair-methods | 0 | 0 | 0 | |
| merge_samples-methods | 1.42 | 0.06 | 1.49 | |
| merge_taxa-methods | 0.04 | 0.02 | 0.06 | |
| microbio_me_qiime | 0.84 | 0.00 | 0.89 | |
| mt-methods | 4.76 | 0.01 | 4.77 | |
| nodeplotblank | 0.29 | 0.00 | 0.29 | |
| nodeplotboot | 0 | 0 | 0 | |
| nodeplotdefault | 0 | 0 | 0 | |
| nsamples-methods | 0.04 | 0.00 | 0.03 | |
| ntaxa-methods | 0.01 | 0.00 | 0.02 | |
| ordinate | 0 | 0 | 0 | |
| otu_table-methods | 0 | 0 | 0 | |
| parseTaxonomy-functions | 0 | 0 | 0 | |
| phy_tree-methods | 0.24 | 0.00 | 0.23 | |
| phyloseq | 0.03 | 0.00 | 0.03 | |
| phyloseq_to_deseq2 | 2.80 | 0.08 | 2.89 | |
| phyloseq_to_metagenomeSeq | 2.05 | 0.00 | 2.04 | |
| plot_bar | 2.45 | 0.02 | 2.47 | |
| plot_clusgap | 5.10 | 0.03 | 5.83 | |
| plot_heatmap | 5.94 | 0.06 | 6.01 | |
| plot_net | 7.06 | 0.02 | 7.08 | |
| plot_network | 3.09 | 0.00 | 3.09 | |
| plot_ordination | 0.86 | 0.01 | 0.87 | |
| plot_phyloseq-methods | 0.2 | 0.0 | 0.2 | |
| plot_richness | 7.24 | 0.13 | 7.79 | |
| plot_scree | 2.84 | 0.01 | 2.85 | |
| plot_tree | 0.53 | 0.00 | 0.53 | |
| prune_samples-methods | 1.05 | 0.00 | 1.05 | |
| prune_taxa-methods | 0.04 | 0.02 | 0.06 | |
| psmelt | 1.19 | 0.01 | 1.20 | |
| rank_names | 0.05 | 0.00 | 0.05 | |
| rarefy_even_depth | 0.14 | 0.00 | 0.14 | |
| read_tree | 0.21 | 0.00 | 0.21 | |
| read_tree_greengenes | 0.06 | 0.00 | 0.06 | |
| reconcile_categories | 0 | 0 | 0 | |
| refseq-methods | 0.35 | 0.00 | 0.35 | |
| rm_outlierf | 0.03 | 0.00 | 0.03 | |
| sample_data-methods | 0.11 | 0.00 | 0.11 | |
| sample_names-methods | 0 | 0 | 0 | |
| sample_sums | 0.06 | 0.00 | 0.06 | |
| sample_variables | 0.05 | 0.00 | 0.05 | |
| show-methods | 0 | 0 | 0 | |
| splat.phyloseq.objects | 0 | 0 | 0 | |
| subset_ord_plot | 0.01 | 0.00 | 0.01 | |
| subset_samples-methods | 0 | 0 | 0 | |
| subset_taxa-methods | 0 | 0 | 0 | |
| tax_glom | 0 | 0 | 0 | |
| tax_table-methods | 0 | 0 | 0 | |
| taxa_names-methods | 0.05 | 0.00 | 0.05 | |
| taxa_sums | 0.05 | 0.03 | 0.08 | |
| threshrank | 3.71 | 0.30 | 4.01 | |
| threshrankfun | 0.05 | 0.02 | 0.06 | |
| tip_glom | 0.74 | 0.00 | 0.75 | |
| topf | 0 | 0 | 0 | |
| topk | 0 | 0 | 0 | |
| topp | 0 | 0 | 0 | |
| transformcounts | 0.09 | 0.02 | 0.11 | |
| transpose-methods | 1.37 | 0.11 | 1.49 | |
| tree_layout | 0.86 | 0.00 | 1.29 | |
phyloseq.Rcheck/examples_x64/phyloseq-Ex.timings:
| name | user | system | elapsed | |
| DPCoA | 4.76 | 0.02 | 5.54 | |
| JSD | 0 | 0 | 0 | |
| UniFrac-methods | 0.17 | 0.01 | 0.22 | |
| access | 0 | 0 | 0 | |
| assign-otu_table | 0 | 0 | 0 | |
| assign-phy_tree | 0.07 | 0.02 | 0.08 | |
| assign-sample_data | 0.56 | 0.00 | 0.56 | |
| assign-sample_names | 0.01 | 0.00 | 0.01 | |
| assign-tax_table | 0 | 0 | 0 | |
| assign-taxa_are_rows | 0.02 | 0.00 | 0.02 | |
| assign-taxa_names | 0.02 | 0.00 | 0.01 | |
| build_tax_table | 0.01 | 0.00 | 0.02 | |
| capscale-phyloseq-methods | 0.97 | 0.00 | 0.97 | |
| cca-rda-phyloseq-methods | 0 | 0 | 0 | |
| chunkReOrder | 0.01 | 0.00 | 0.01 | |
| data-GlobalPatterns | 2.45 | 0.03 | 2.50 | |
| data-enterotype | 2.48 | 0.03 | 2.73 | |
| data-esophagus | 1.02 | 0.03 | 1.04 | |
| data-soilrep | 1.59 | 0.05 | 1.64 | |
| distance | 0.31 | 0.05 | 0.36 | |
| distanceMethodList | 0 | 0 | 0 | |
| envHash2otu_table | 0 | 0 | 0 | |
| estimate_richness | 0.05 | 0.00 | 0.05 | |
| export_env_file | 0 | 0 | 0 | |
| export_mothur_dist | 0.15 | 0.01 | 0.17 | |
| extract-methods | 0.02 | 0.00 | 0.01 | |
| filter_taxa | 1.51 | 0.02 | 1.53 | |
| filterfun_sample | 0.05 | 0.00 | 0.05 | |
| gapstat_ord | 3.34 | 0.06 | 5.13 | |
| genefilter_sample-methods | 0 | 0 | 0 | |
| get.component.classes | 0 | 0 | 0 | |
| get_sample-methods | 0 | 0 | 0 | |
| get_taxa-methods | 0.02 | 0.00 | 0.01 | |
| get_taxa_unique | 0.33 | 0.05 | 0.38 | |
| get_variable | 0.28 | 0.03 | 0.31 | |
| getslots.phyloseq | 0.32 | 0.00 | 0.33 | |
| import | 0 | 0 | 0 | |
| import_RDP_otu | 2.41 | 0.00 | 2.40 | |
| import_biom | 0.25 | 0.01 | 0.58 | |
| import_env_file | 0 | 0 | 0 | |
| import_mothur | 0 | 0 | 0 | |
| import_mothur_dist | 0 | 0 | 0 | |
| import_pyrotagger_tab | 0 | 0 | 0 | |
| import_qiime | 0.84 | 0.02 | 0.86 | |
| import_qiime_otu_tax | 0.61 | 0.00 | 0.61 | |
| import_qiime_sample_data | 0.01 | 0.00 | 0.01 | |
| import_usearch_uc | 0.02 | 0.00 | 0.02 | |
| index_reorder | 0 | 0 | 0 | |
| intersect_taxa | 0.01 | 0.00 | 0.01 | |
| make_network | 4.5 | 0.0 | 4.5 | |
| merge_phyloseq | 0.01 | 0.00 | 0.01 | |
| merge_phyloseq_pair-methods | 0 | 0 | 0 | |
| merge_samples-methods | 1.28 | 0.01 | 1.30 | |
| merge_taxa-methods | 0.16 | 0.00 | 0.15 | |
| microbio_me_qiime | 0.90 | 0.00 | 0.98 | |
| mt-methods | 2.64 | 0.04 | 2.67 | |
| nodeplotblank | 0.44 | 0.00 | 0.44 | |
| nodeplotboot | 0 | 0 | 0 | |
| nodeplotdefault | 0 | 0 | 0 | |
| nsamples-methods | 0.03 | 0.01 | 0.05 | |
| ntaxa-methods | 0.01 | 0.00 | 0.01 | |
| ordinate | 0 | 0 | 0 | |
| otu_table-methods | 0 | 0 | 0 | |
| parseTaxonomy-functions | 0.00 | 0.02 | 0.02 | |
| phy_tree-methods | 0.28 | 0.01 | 0.29 | |
| phyloseq | 0.05 | 0.00 | 0.05 | |
| phyloseq_to_deseq2 | 3.10 | 0.03 | 3.13 | |
| phyloseq_to_metagenomeSeq | 2.67 | 0.04 | 2.70 | |
| plot_bar | 3.73 | 0.04 | 3.82 | |
| plot_clusgap | 6.08 | 0.10 | 6.35 | |
| plot_heatmap | 7.44 | 0.04 | 7.99 | |
| plot_net | 5.43 | 0.00 | 5.62 | |
| plot_network | 3.82 | 0.00 | 6.16 | |
| plot_ordination | 0.86 | 0.02 | 0.88 | |
| plot_phyloseq-methods | 0.25 | 0.01 | 0.26 | |
| plot_richness | 6.66 | 0.07 | 6.74 | |
| plot_scree | 2.23 | 0.04 | 2.28 | |
| plot_tree | 0.88 | 0.00 | 1.22 | |
| prune_samples-methods | 0.95 | 0.02 | 0.97 | |
| prune_taxa-methods | 0.04 | 0.00 | 0.04 | |
| psmelt | 2.15 | 0.00 | 2.15 | |
| rank_names | 0.03 | 0.00 | 0.04 | |
| rarefy_even_depth | 0.11 | 0.00 | 0.11 | |
| read_tree | 0.14 | 0.00 | 0.14 | |
| read_tree_greengenes | 0.07 | 0.00 | 0.06 | |
| reconcile_categories | 0 | 0 | 0 | |
| refseq-methods | 0.29 | 0.01 | 0.32 | |
| rm_outlierf | 0.03 | 0.00 | 0.03 | |
| sample_data-methods | 0.08 | 0.00 | 0.08 | |
| sample_names-methods | 0.01 | 0.00 | 0.02 | |
| sample_sums | 0.03 | 0.00 | 0.03 | |
| sample_variables | 0.04 | 0.00 | 0.03 | |
| 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 | 0 | 0 | |
| tax_glom | 0 | 0 | 0 | |
| tax_table-methods | 0 | 0 | 0 | |
| taxa_names-methods | 0.03 | 0.00 | 0.03 | |
| taxa_sums | 0.03 | 0.02 | 0.04 | |
| threshrank | 4.08 | 0.44 | 4.51 | |
| threshrankfun | 0.07 | 0.00 | 0.08 | |
| tip_glom | 1.06 | 0.00 | 1.06 | |
| topf | 0.04 | 0.00 | 0.03 | |
| topk | 0.03 | 0.00 | 0.03 | |
| topp | 0.03 | 0.00 | 0.03 | |
| transformcounts | 0.12 | 0.00 | 0.13 | |
| transpose-methods | 0.88 | 0.25 | 1.12 | |
| tree_layout | 0.90 | 0.01 | 0.92 | |