BioC 3.2: CHECK report for phyloseq on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings phyloseq_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/phyloseq.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘phyloseq’ can be installed ... [17s/18s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘phyloseq’
See ‘/Users/biocbuild/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
* 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 ... [76s/77s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot_richness 4.807  0.492   5.303
plot_heatmap  4.808  0.241   5.087
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [85s/88s]
 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: 1 ERROR, 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/phyloseq.Rcheck/00check.log’
for details.


R version 3.2.4 (2016-03-10) -- "Very Secure Dishes"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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] '1.14.0'
> # 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...
 /Users/biocbuild/bbs-3.2-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...
 /Users/biocbuild/bbs-3.2-bioc/meat/phyloseq.Rcheck/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

* 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’
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	3.412	0.176	3.620
JSD	0.001	0.000	0.001
UniFrac-methods	0.142	0.008	0.241
access	0.000	0.000	0.001
assign-otu_table	0.001	0.000	0.002
assign-phy_tree	0.048	0.007	0.055
assign-sample_data	0.386	0.024	0.410
assign-sample_names	0.011	0.004	0.015
assign-tax_table	0.001	0.000	0.001
assign-taxa_are_rows	0.004	0.004	0.007
assign-taxa_names	0.007	0.003	0.010
build_tax_table	0.015	0.001	0.015
capscale-phyloseq-methods	1.007	0.067	1.076
cca-rda-phyloseq-methods	0.001	0.000	0.000
chunkReOrder	0.001	0.000	0.001
data-GlobalPatterns	1.437	0.097	1.535
data-enterotype	1.573	0.031	1.606
data-esophagus	0.677	0.010	0.687
data-soilrep	1.699	0.157	1.864
distance	0.208	0.032	1.342
distanceMethodList	0.001	0.000	0.002
envHash2otu_table	0.001	0.000	0.001
estimate_richness	0.032	0.003	0.034
export_env_file	0.001	0.001	0.001
export_mothur_dist	0.097	0.018	0.116
extract-methods	0.008	0.002	0.010
filter_taxa	1.032	0.029	1.062
filterfun_sample	0.023	0.000	0.023
gapstat_ord	2.534	0.052	2.595
genefilter_sample-methods	0.001	0.000	0.001
get.component.classes	0.001	0.000	0.001
get_sample-methods	0.005	0.003	0.009
get_taxa-methods	0.004	0.002	0.006
get_taxa_unique	0.260	0.020	0.281
get_variable	0.222	0.008	0.231
getslots.phyloseq	0.215	0.014	0.231
import	0	0	0
import_RDP_otu	0.841	0.034	0.876
import_biom	0.223	0.002	0.261
import_env_file	0.001	0.000	0.000
import_mothur	0.001	0.000	0.001
import_mothur_dist	0.001	0.000	0.000
import_pyrotagger_tab	0.001	0.000	0.000
import_qiime	0.671	0.009	0.680
import_qiime_otu_tax	0.547	0.045	0.591
import_qiime_sample_data	0.018	0.001	0.019
import_usearch_uc	0.014	0.003	0.018
index_reorder	0	0	0
intersect_taxa	0.001	0.000	0.001
make_network	3.660	0.091	3.756
merge_phyloseq	0.001	0.000	0.001
merge_phyloseq_pair-methods	0.001	0.001	0.002
merge_samples-methods	1.283	0.174	1.458
merge_taxa-methods	0.084	0.006	0.089
microbio_me_qiime	0.698	0.022	0.768
mt-methods	1.484	0.016	1.500
nodeplotblank	0.375	0.008	0.384
nodeplotboot	0.002	0.000	0.003
nodeplotdefault	0.001	0.000	0.001
nsamples-methods	0.032	0.003	0.035
ntaxa-methods	0.005	0.003	0.008
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0.002	0.000	0.003
phy_tree-methods	0.215	0.013	0.228
phyloseq	0.034	0.005	0.040
phyloseq_to_deseq2	2.791	0.107	2.901
phyloseq_to_metagenomeSeq	1.791	0.119	1.911
plot_bar	2.788	0.136	2.991
plot_clusgap	4.251	0.136	4.432
plot_heatmap	4.808	0.241	5.087
plot_net	4.096	0.135	4.274
plot_network	2.667	0.035	2.707
plot_ordination	0.682	0.059	0.742
plot_phyloseq-methods	0.270	0.003	0.274
plot_richness	4.807	0.492	5.303
plot_scree	2.078	0.080	2.189
plot_tree	0.603	0.015	0.619
prune_samples-methods	0.561	0.101	0.662
prune_taxa-methods	0.031	0.003	0.035
psmelt	1.283	0.102	1.386
rank_names	0.020	0.004	0.025
rarefy_even_depth	0.094	0.004	0.097
read_tree	0.127	0.005	0.131
read_tree_greengenes	0.048	0.005	0.053
reconcile_categories	0.001	0.000	0.001
refseq-methods	0.160	0.014	0.174
rm_outlierf	0.025	0.001	0.025
sample_data-methods	0.055	0.010	0.065
sample_names-methods	0.002	0.007	0.009
sample_sums	0.030	0.019	0.048
sample_variables	0.026	0.008	0.034
show-methods	0.001	0.000	0.001
splat.phyloseq.objects	0.001	0.000	0.000
subset_ord_plot	0	0	0
subset_samples-methods	0.001	0.000	0.001
subset_taxa-methods	0.000	0.000	0.001
tax_glom	0.001	0.000	0.001
tax_table-methods	0.000	0.001	0.000
taxa_names-methods	0.034	0.010	0.044
taxa_sums	0.035	0.022	0.056
threshrank	2.481	0.924	3.409
threshrankfun	0.070	0.003	0.073
tip_glom	0.854	0.009	0.862
topf	0.022	0.000	0.022
topk	0.021	0.000	0.021
topp	0.017	0.001	0.017
transformcounts	0.132	0.002	0.134
transpose-methods	0.754	0.532	1.286
tree_layout	0.570	0.007	0.595

BioC 3.2: CHECK report for phyloseq on oaxaca

Summary

Command output