BioC 3.2: CHECK report for phyloseq on zin1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/phyloseq.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.14.0’
* 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 ... [13s/13s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘phyloseq’
See ‘/home/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 ... [60s/60s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [62s/62s]
 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/phyloseq.Rcheck/00check.log’
for details.


R version 3.2.4 Revised (2016-03-16 r70336) -- "Very Secure Dishes"
Copyright (C) 2016 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] '1.14.0'
> # 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...
 /home/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...
 /home/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

name	user	system	elapsed
DPCoA	2.773	0.020	2.818
JSD	0	0	0
UniFrac-methods	0.102	0.008	0.110
access	0	0	0
assign-otu_table	0.001	0.000	0.001
assign-phy_tree	0.038	0.000	0.038
assign-sample_data	0.337	0.008	0.344
assign-sample_names	0.006	0.000	0.007
assign-tax_table	0.000	0.000	0.001
assign-taxa_are_rows	0.001	0.000	0.003
assign-taxa_names	0.006	0.000	0.006
build_tax_table	0.008	0.000	0.010
capscale-phyloseq-methods	0.621	0.004	0.626
cca-rda-phyloseq-methods	0.001	0.000	0.000
chunkReOrder	0.000	0.000	0.001
data-GlobalPatterns	1.355	0.012	1.366
data-enterotype	1.696	0.004	1.699
data-esophagus	0.564	0.000	0.564
data-soilrep	0.862	0.016	0.877
distance	0.150	0.013	0.392
distanceMethodList	0.001	0.000	0.001
envHash2otu_table	0.001	0.000	0.001
estimate_richness	0.024	0.000	0.024
export_env_file	0.001	0.000	0.001
export_mothur_dist	0.080	0.008	0.088
extract-methods	0.007	0.000	0.007
filter_taxa	1.031	0.016	1.047
filterfun_sample	0.015	0.000	0.015
gapstat_ord	1.987	0.036	2.022
genefilter_sample-methods	0.001	0.000	0.000
get.component.classes	0.001	0.000	0.000
get_sample-methods	0.003	0.000	0.003
get_taxa-methods	0.003	0.000	0.004
get_taxa_unique	0.199	0.000	0.198
get_variable	0.150	0.004	0.155
getslots.phyloseq	0.164	0.004	0.167
import	0	0	0
import_RDP_otu	0.812	0.004	0.818
import_biom	0.136	0.004	0.147
import_env_file	0.000	0.000	0.001
import_mothur	0.001	0.000	0.000
import_mothur_dist	0.001	0.000	0.001
import_pyrotagger_tab	0.000	0.000	0.001
import_qiime	0.564	0.000	0.563
import_qiime_otu_tax	0.483	0.032	0.515
import_qiime_sample_data	0.014	0.000	0.014
import_usearch_uc	0.009	0.004	0.013
index_reorder	0.001	0.000	0.001
intersect_taxa	0	0	0
make_network	2.813	0.016	2.833
merge_phyloseq	0.001	0.000	0.001
merge_phyloseq_pair-methods	0.001	0.000	0.001
merge_samples-methods	0.772	0.012	0.785
merge_taxa-methods	0.049	0.000	0.049
microbio_me_qiime	0.485	0.060	0.547
mt-methods	1.458	0.012	1.471
nodeplotblank	0.248	0.000	0.248
nodeplotboot	0.001	0.000	0.001
nodeplotdefault	0.001	0.000	0.001
nsamples-methods	0.022	0.000	0.022
ntaxa-methods	0.004	0.000	0.004
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0.002	0.000	0.002
phy_tree-methods	0.150	0.008	0.158
phyloseq	0.018	0.000	0.022
phyloseq_to_deseq2	2.144	0.180	2.320
phyloseq_to_metagenomeSeq	1.412	0.012	1.422
plot_bar	1.968	0.036	2.003
plot_clusgap	3.333	0.044	3.395
plot_heatmap	3.277	0.016	3.291
plot_net	3.957	0.012	3.978
plot_network	2.505	0.060	2.563
plot_ordination	0.624	0.004	0.628
plot_phyloseq-methods	0.204	0.000	0.203
plot_richness	3.958	0.144	4.099
plot_scree	1.664	0.016	1.691
plot_tree	0.459	0.000	0.460
prune_samples-methods	0.543	0.016	0.558
prune_taxa-methods	0.028	0.000	0.028
psmelt	1.152	0.012	1.163
rank_names	0.023	0.004	0.027
rarefy_even_depth	0.08	0.00	0.08
read_tree	0.109	0.000	0.109
read_tree_greengenes	0.035	0.000	0.035
reconcile_categories	0.001	0.000	0.001
refseq-methods	0.159	0.000	0.162
rm_outlierf	0.013	0.004	0.017
sample_data-methods	0.057	0.000	0.057
sample_names-methods	0.000	0.004	0.002
sample_sums	0.023	0.004	0.028
sample_variables	0.019	0.004	0.023
show-methods	0.001	0.000	0.001
splat.phyloseq.objects	0.000	0.000	0.001
subset_ord_plot	0	0	0
subset_samples-methods	0	0	0
subset_taxa-methods	0.001	0.000	0.000
tax_glom	0.001	0.000	0.001
tax_table-methods	0	0	0
taxa_names-methods	0.023	0.004	0.023
taxa_sums	0.023	0.008	0.033
threshrank	2.611	0.552	3.162
threshrankfun	0.05	0.00	0.05
tip_glom	0.612	0.000	0.612
topf	0.011	0.004	0.015
topk	0.013	0.000	0.014
topp	0.014	0.000	0.014
transformcounts	0.098	0.004	0.102
transpose-methods	0.629	0.337	0.964
tree_layout	0.483	0.004	0.494

BioC 3.2: CHECK report for phyloseq on zin1

Summary

Command output