Package: phyloseq

Version: 1.22.3

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.22.3.tar.gz

StartedAt: 2018-04-12 01:48:24 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:52:30 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 246.6 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.22.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/phyloseq.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.22.3’
* 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 ... NOTE
  installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’
 OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/phyloseq.Rcheck/00check.log’
for details.

* installing *source* package ‘phyloseq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (phyloseq)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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] '1.22.3'
> # 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...
 /home/biocbuild/bbs-3.6-bioc/meat/phyloseq.Rcheck/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...
 /home/biocbuild/bbs-3.6-bioc/meat/phyloseq.Rcheck/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 613 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 61.288   0.416  61.301 

name	user	system	elapsed
DPCoA	4.016	0.024	4.043
JSD	0	0	0
UniFrac-methods	0.420	0.008	0.425
access	0	0	0
assign-otu_table	0.000	0.000	0.001
assign-phy_tree	0.196	0.000	0.197
assign-sample_data	0.464	0.012	0.478
assign-sample_names	0.008	0.000	0.007
assign-tax_table	0.000	0.000	0.001
assign-taxa_are_rows	0.004	0.000	0.003
assign-taxa_names	0.000	0.004	0.006
build_tax_table	0.020	0.000	0.022
capscale-phyloseq-methods	0.960	0.008	0.968
cca-rda-phyloseq-methods	0.000	0.000	0.001
chunkReOrder	0.000	0.000	0.001
data-GlobalPatterns	1.996	0.020	2.018
data-enterotype	1.396	0.000	1.400
data-esophagus	0.440	0.000	0.441
data-soilrep	1.636	0.020	1.658
distance	0.196	0.032	0.606
distanceMethodList	0.000	0.000	0.001
envHash2otu_table	0.000	0.000	0.001
estimate_richness	0.080	0.008	0.089
export_env_file	0	0	0
export_mothur_dist	0.080	0.028	0.111
extract-methods	0.004	0.004	0.011
filter_taxa	1.392	0.036	1.444
filterfun_sample	0.028	0.000	0.029
gapstat_ord	1.740	0.052	1.797
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0.004	0.000	0.003
get_taxa-methods	0.004	0.000	0.003
get_taxa_unique	0.196	0.012	0.209
get_variable	0.164	0.004	0.171
getslots.phyloseq	0.148	0.012	0.164
import	0	0	0
import_RDP_otu	0.844	0.000	0.851
import_biom	0.476	0.004	0.481
import_env_file	0	0	0
import_mothur	0.004	0.000	0.001
import_mothur_dist	0.000	0.000	0.001
import_pyrotagger_tab	0.000	0.000	0.001
import_qiime	0.856	0.000	0.861
import_qiime_otu_tax	0.564	0.020	0.586
import_qiime_sample_data	0.016	0.000	0.013
import_uparse	0	0	0
import_usearch_uc	0.012	0.000	0.012
index_reorder	0.004	0.000	0.000
intersect_taxa	0.000	0.000	0.001
make_network	1.856	0.000	1.859
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0.000	0.000	0.001
merge_samples-methods	0.664	0.012	0.676
merge_taxa-methods	0.068	0.000	0.069
microbio_me_qiime	0.864	0.064	0.938
mt-methods	1.292	0.012	1.305
nodeplotblank	0.808	0.000	0.667
nodeplotboot	0.040	0.000	0.039
nodeplotdefault	0.000	0.000	0.001
nsamples-methods	0.036	0.000	0.035
ntaxa-methods	0.004	0.000	0.004
ordinate	0	0	0
otu_table-methods	0.000	0.000	0.001
parseTaxonomy-functions	0.004	0.000	0.003
phy_tree-methods	0.168	0.008	0.177
phyloseq	0.02	0.00	0.02
phyloseq_to_deseq2	2.840	0.052	2.897
phyloseq_to_metagenomeSeq	1.752	0.016	1.769
plot_bar	1.988	0.008	1.997
plot_clusgap	3.448	0.048	3.506
plot_heatmap	3.648	0.024	3.678
plot_net	3.352	0.008	3.135
plot_network	1.696	0.000	1.699
plot_ordination	0.64	0.00	0.64
plot_phyloseq-methods	0.308	0.004	0.233
plot_richness	3.620	0.024	3.649
plot_scree	2.316	0.008	2.327
plot_tree	0.652	0.004	0.495
prune_samples-methods	1.304	0.004	1.310
prune_taxa-methods	0.040	0.000	0.038
psmelt	0.628	0.000	0.627
rank_names	0.024	0.000	0.022
rarefy_even_depth	0.100	0.000	0.103
read_tree	0.02	0.00	0.02
read_tree_greengenes	0.008	0.000	0.010
reconcile_categories	0	0	0
refseq-methods	0.144	0.004	0.148
rm_outlierf	0.024	0.000	0.025
sample_data-methods	0.044	0.004	0.050
sample_names-methods	0.004	0.000	0.003
sample_sums	0.024	0.004	0.026
sample_variables	0.024	0.000	0.023
show-methods	0.000	0.000	0.001
splat.phyloseq.objects	0.000	0.000	0.001
subset_ord_plot	0.000	0.000	0.001
subset_samples-methods	0.000	0.000	0.001
subset_taxa-methods	0.000	0.000	0.001
tax_glom	0.000	0.000	0.001
tax_table-methods	0	0	0
taxa_names-methods	0.036	0.000	0.038
taxa_sums	0.020	0.008	0.031
threshrank	1.404	0.424	1.829
threshrankfun	0.072	0.000	0.072
tip_glom	0.992	0.004	0.700
topf	0.012	0.000	0.011
topk	0.012	0.000	0.011
topp	0.008	0.000	0.011
transformcounts	0.088	0.000	0.087
transpose-methods	0.968	0.312	1.283
tree_layout	0.532	0.000	0.519