BioC 2.13: CHECK report for phyloseq on zin1

Package: phyloseq

Version: 1.6.1

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.6.1.tar.gz

StartedAt: 2014-04-05 03:01:37 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:09:23 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 466.1 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/phyloseq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.6.1’
* 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 ... [20s/20s] OK
* checking installed package size ... OK
* checking package 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 ... NOTE
Packages in Depends field not imported from:
  ‘ade4’ ‘methods’ ‘picante’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘JSD.pair’ ‘UFwi’ ‘internal2tips.self’ ‘ufnum’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
JSD: no visible binding for global variable ‘i’
fastUniFrac: no visible binding for global variable ‘i’
import_qiime_otu_tax: no visible binding for global variable ‘i’
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_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 ‘type’
plot_tree_only: no visible binding for global variable ‘type’
plot_tree_only: no visible binding for global variable ‘x’
plot_tree_only: no visible binding for global variable ‘y’
plot_tree_only: no visible binding for global variable ‘xend’
plot_tree_only: no visible binding for global variable ‘yend’
plot_tree_sampledodge: no visible binding for global variable ‘type’
plot_tree_sampledodge: no visible binding for global variable ‘value’
plot_tree_sampledodge: no visible binding for global variable ‘x’
plot_tree_sampledodge: no visible binding for global variable ‘x.adj’
plot_tree_sampledodge: no visible binding for global variable ‘y’
plot_tree_sampledodge: no visible binding for global variable
  ‘tipLabels’
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 ... 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 ... NOTE
  Note: the specification for S3 class "AsIs" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO': not turning on duplicate class definitions for this class.
  Note: the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO': not turning on duplicate class definitions for this class.
  Note: the specification for S3 class "file" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO': not turning on duplicate class definitions for this class.
  Note: the specification for S3 class "pipe" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO': not turning on duplicate class definitions for this class.
  Note: the specification for S3 class "textConnection" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO': not turning on duplicate class definitions for this class.
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [226s/227s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
rarefy_even_depth   99.666  0.084 100.039
plot_scree          21.397  0.028  21.486
plot_tree           14.941  0.008  14.992
plot_ordination     10.776  0.056  10.938
data-GlobalPatterns  6.916  0.044   6.972
nodeplotblank        5.897  0.040   5.942
plot_clusgap         5.644  0.084   5.753
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [41s/41s]
 [41s/42s] OK
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/phyloseq.Rcheck/00check.log’
for details.

* installing *source* package ‘phyloseq’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “file” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “pipe” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “textConnection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “file” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “pipe” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “textConnection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	0.008	0.004	0.008
JSD	0.004	0.000	0.004
UniFrac-methods	0.008	0.000	0.008
access	0.004	0.000	0.004
assign-otu_table	0.000	0.000	0.003
assign-phy_tree	0.008	0.000	0.006
assign-sample_data	0.004	0.000	0.004
assign-sample_names	0.012	0.004	0.016
assign-tax_table	0.004	0.004	0.006
assign-taxa_are_rows	0.000	0.000	0.001
assign-taxa_names	0.016	0.000	0.016
build_tax_table	0.024	0.000	0.025
cca-rda-phyloseq-methods	0.000	0.000	0.003
data-GlobalPatterns	6.916	0.044	6.972
data-enterotype	3.825	0.008	3.838
data-esophagus	1.548	0.004	1.554
data-soilrep	1.888	0.044	1.933
distance	1.324	0.016	1.446
edgelist2clique	0.004	0.000	0.002
envHash2otu_table	0.000	0.004	0.002
estimate_richness	3.544	0.072	3.620
export_env_file	0.004	0.000	0.001
export_mothur_dist	0.000	0.000	0.001
extract-methods	0.012	0.000	0.012
filter_taxa	1.068	0.068	1.138
filterfun_sample	0.028	0.004	0.034
gapstat_ord	4.949	0.040	4.999
genefilter_sample-methods	0.000	0.000	0.002
get.component.classes	0.004	0.000	0.004
get_sample-methods	0.004	0.000	0.004
get_taxa-methods	0.004	0.000	0.006
get_taxa_unique	0.236	0.004	0.244
get_variable	0.184	0.008	0.191
getslots.phyloseq	0.204	0.000	0.202
import	0.004	0.000	0.001
import_RDP_otu	0.4	0.0	0.4
import_biom	0.184	0.004	0.185
import_env_file	0	0	0
import_mothur	0.004	0.000	0.006
import_mothur_dist	0.004	0.000	0.006
import_pyrotagger_tab	0.000	0.000	0.001
import_qiime	0.864	0.004	0.868
import_qiime_otu_tax	0.736	0.032	0.770
import_qiime_sample_data	0.024	0.000	0.024
index_reorder	0.000	0.000	0.001
intersect_taxa	0.000	0.000	0.001
make_network	3.588	0.000	3.596
merge_phyloseq	0.004	0.000	0.005
merge_phyloseq_pair-methods	0.016	0.000	0.016
merge_samples-methods	2.344	0.000	2.348
merge_taxa-methods	1.460	0.004	1.473
microbio_me_qiime	0.732	0.056	0.816
mt-methods	0.008	0.000	0.007
nodeplotblank	5.897	0.040	5.942
nodeplotboot	0.004	0.000	0.002
nodeplotdefault	0.008	0.000	0.005
nsamples-methods	0.000	0.000	0.001
ntaxa-methods	0.004	0.000	0.005
ordinate	0.000	0.004	0.004
otu_table-methods	0.004	0.000	0.004
parseTaxonomy-functions	0.000	0.000	0.002
phy_tree-methods	0.176	0.000	0.179
phyloseq	0.028	0.000	0.029
plot_bar	2.688	0.008	2.697
plot_clusgap	5.644	0.084	5.753
plot_heatmap	2.220	0.000	2.225
plot_network	2.997	0.004	3.005
plot_ordination	10.776	0.056	10.938
plot_phyloseq-methods	3.016	0.004	3.023
plot_richness	3.809	0.032	3.851
plot_scree	21.397	0.028	21.486
plot_tree	14.941	0.008	14.992
prune_samples-methods	0.744	0.004	0.753
prune_taxa-methods	0.056	0.004	0.061
psmelt	1.072	0.012	1.086
rank_names	0.032	0.000	0.030
rarefy_even_depth	99.666	0.084	100.039
read_tree	0.152	0.004	0.154
read_tree_greengenes	0.052	0.000	0.050
reconcile_categories	0.000	0.000	0.001
refseq-methods	0.168	0.004	0.170
rm_outlierf	0.02	0.00	0.02
sample_data-methods	0.004	0.000	0.006
sample_names-methods	0.000	0.000	0.001
sample_sums	0.032	0.004	0.034
sample_variables	0.024	0.000	0.024
show-methods	0.000	0.000	0.001
splat.phyloseq.objects	0.000	0.000	0.001
subset_ord_plot	0.004	0.000	0.005
subset_samples-methods	0	0	0
subset_taxa-methods	0.000	0.000	0.001
tax_glom	0.000	0.000	0.001
tax_table-methods	0.004	0.000	0.006
taxa_names-methods	0.000	0.000	0.001
taxa_sums	0.028	0.012	0.038
threshrank	2.496	0.540	3.039
threshrankfun	0.060	0.000	0.058
tip_glom-methods	0.004	0.000	0.002
topf	0.020	0.000	0.019
topk	0.02	0.00	0.02
topp	0.02	0.00	0.02
transformcounts	0.120	0.004	0.123
transpose-methods	0.681	0.364	1.044
tree.get.tags	0.008	0.000	0.005
tree.has.tags	0.000	0.000	0.001