BioC 2.12: CHECK report for phyloseq on george2

Package: phyloseq

Version: 1.4.5

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.4.5.tar.gz

StartedAt: 2013-10-09 03:59:14 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:09:55 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 640.5 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/phyloseq.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.4.5’
* 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 ... [30s/33s] 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 for unstated 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
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’
originalUniFrac: no visible binding for global variable ‘i’
otu2df : trimdf: no visible binding for global variable ‘TaxaGroup’
otu2df : trimdf: no visible binding for global variable ‘Abundance’
plot_heatmap: no visible binding for global variable ‘x’
plot_heatmap: no visible binding for global variable ‘y’
plot_heatmap: no visible binding for global variable ‘value’
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 ‘variable’
plot_richness: no visible binding for global variable ‘value’
plot_richness: no visible binding for global variable ‘se’
plot_richness_estimates: no visible binding for global variable
  ‘variable’
plot_richness_estimates: no visible binding for global variable ‘value’
plot_richness_estimates: no visible binding for global variable ‘se’
plot_scree: no visible binding for global variable ‘eigenvalue’
plot_taxa_bar: no visible binding for global variable ‘Abundance’
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 ‘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’
taxaplot: no visible binding for global variable ‘Abundance’
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [265s/267s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plot_scree            48.691  0.120  49.315
plot_ordination       28.438  0.112  28.618
plot_tree             26.566  0.024  26.728
data-soilrep          18.413  0.180  18.984
data-GlobalPatterns   16.905  0.120  17.097
plot_richness         13.885  0.072  14.161
nodeplotblank         10.545  0.004  10.555
merge_samples-methods  9.385  0.056   9.443
data-enterotype        7.481  0.060   7.546
make_network           6.936  0.008   6.947
rarefy_even_depth      6.244  0.020   6.312
plot_phyloseq-methods  6.120  0.000   6.142
plot_bar               5.552  0.052   5.603
threshrank             4.397  0.908   5.428
plot_network           5.256  0.028   5.296
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [74s/75s]
 [74s/75s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/phyloseq.Rcheck/00check.log’
for details.

* installing *source* package ‘phyloseq’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’ and is 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
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	0.020	0.008	0.027
JSD	0.016	0.004	0.019
UniFrac-methods	0.036	0.000	0.039
access	0.016	0.000	0.015
assign-otu_table	0.024	0.004	0.027
assign-phy_tree	0.024	0.000	0.022
assign-sample_data	0.020	0.000	0.023
assign-sample_names	0.064	0.000	0.063
assign-tax_table	0.028	0.008	0.037
assign-taxa_are_rows	0.012	0.004	0.016
assign-taxa_names	0.052	0.004	0.055
build_tax_table	0.088	0.000	0.088
cca-rda-phyloseq-methods	0.020	0.008	0.031
data-GlobalPatterns	16.905	0.120	17.097
data-enterotype	7.481	0.060	7.546
data-esophagus	2.640	0.008	2.647
data-soilrep	18.413	0.180	18.984
distance	2.560	0.036	2.722
edgelist2clique	0.016	0.004	0.020
envHash2otu_table	0.004	0.004	0.007
estimate_richness	1.864	0.096	1.981
export_env_file	0.004	0.000	0.006
export_mothur_dist	0.008	0.000	0.007
filter_taxa	1.820	0.032	1.953
filterfun_sample	0.14	0.00	0.14
genefilter_sample-methods	0.028	0.000	0.026
get.component.classes	0.008	0.000	0.005
get_sample-methods	0.032	0.000	0.033
get_taxa-methods	0.012	0.004	0.015
get_taxa_unique	0.284	0.032	0.316
get_variable	0.208	0.024	0.233
getslots.phyloseq	0.229	0.032	0.260
import	0.024	0.000	0.022
import_RDP_otu	1.636	0.008	1.644
import_biom	0.220	0.004	0.225
import_env_file	0.016	0.000	0.014
import_mothur	0.024	0.000	0.026
import_mothur_dist	0.008	0.004	0.012
import_pyrotagger_tab	0.012	0.000	0.013
import_qiime	1.624	0.004	1.632
import_qiime_otu_tax	1.608	0.036	1.642
import_qiime_sample_data	0.036	0.004	0.041
index_reorder	0.004	0.000	0.005
intersect_taxa	0.004	0.000	0.005
make_network	6.936	0.008	6.947
merge_phyloseq	0.016	0.000	0.015
merge_phyloseq_pair-methods	0.016	0.000	0.018
merge_samples-methods	9.385	0.056	9.443
merge_taxa-methods	2.560	0.004	2.570
mt-methods	0.012	0.000	0.012
nodeplotblank	10.545	0.004	10.555
nodeplotboot	0.008	0.000	0.008
nodeplotdefault	0.032	0.000	0.034
nsamples-methods	0.008	0.004	0.012
ntaxa-methods	0.020	0.000	0.019
ordinate	0.028	0.004	0.029
otu_table-methods	0.004	0.000	0.005
parseTaxonomy-functions	0.024	0.000	0.025
phy_tree-methods	0.212	0.016	0.226
phyloseq	0.076	0.000	0.076
plot-taxa-bar	4.404	0.048	4.453
plot_bar	5.552	0.052	5.603
plot_heatmap	4.261	0.032	4.456
plot_network	5.256	0.028	5.296
plot_ordination	28.438	0.112	28.618
plot_phyloseq-methods	6.120	0.000	6.142
plot_richness	13.885	0.072	14.161
plot_scree	48.691	0.120	49.315
plot_tree	26.566	0.024	26.728
prune_samples-methods	1.316	0.060	1.414
prune_taxa-methods	0.092	0.004	0.098
psmelt	2.596	0.016	2.675
rank_names	0.028	0.004	0.033
rarefy_even_depth	6.244	0.020	6.312
read_tree	0.232	0.004	0.246
reconcile_categories	0.008	0.000	0.004
refseq-methods	0.200	0.012	0.212
rm_outlierf	0.048	0.000	0.049
sample_data-methods	0.020	0.000	0.018
sample_names-methods	0.004	0.000	0.004
sample_sums	0.036	0.004	0.041
sample_variables	0.044	0.000	0.043
show-methods	0.004	0.000	0.004
splat.phyloseq.objects	0.000	0.004	0.004
subset_ord_plot	0.020	0.000	0.019
subset_samples-methods	0.008	0.000	0.005
subset_taxa-methods	0.020	0.000	0.017
tax_glom	0.008	0.000	0.007
tax_table-methods	0.008	0.000	0.006
taxa_names-methods	0.024	0.000	0.026
taxa_sums	0.044	0.000	0.045
threshrank	4.397	0.908	5.428
threshrankfun	0.180	0.004	0.183
tip_glom-methods	0.692	0.008	0.703
topf	0.064	0.004	0.064
topk	0.044	0.000	0.048
topp	0.040	0.000	0.041
transformcounts	0.260	0.004	0.265
transpose-methods	1.032	0.644	1.679
tree.get.tags	0.020	0.000	0.021
tree.has.tags	0.008	0.000	0.009