BioC 2.12: CHECK report for phyloseq on petty

Package: phyloseq

Version: 1.4.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phyloseq_1.4.5.tar.gz

StartedAt: 2013-10-08 23:26:03 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:36:39 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 635.4 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/phyloseq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [28s/29s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [276s/281s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plot_scree            43.269  5.590  49.246
plot_tree             33.537  0.460  34.677
plot_ordination       26.854  2.811  30.020
data-soilrep          14.906  1.129  16.624
plot_richness         12.470  2.176  14.749
data-GlobalPatterns   12.107  1.408  13.710
nodeplotblank         12.691  0.167  13.049
data-enterotype        8.560  0.224   9.030
make_network           7.368  0.140   7.588
rarefy_even_depth      7.106  0.379   7.525
plot_phyloseq-methods  7.081  0.114   7.218
threshrank             4.761  1.816   6.883
plot_bar               6.299  0.277   6.714
plot_network           6.044  0.098   6.159
merge_samples-methods  5.331  0.454   5.827
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'testthat-phyloseq.R' [68s/70s]
 [69s/71s] 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
  '/Users/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	0.015	0.003	0.020
JSD	0.010	0.001	0.011
UniFrac-methods	0.035	0.002	0.038
access	0.010	0.001	0.009
assign-otu_table	0.014	0.001	0.016
assign-phy_tree	0.019	0.001	0.020
assign-sample_data	0.019	0.001	0.021
assign-sample_names	0.046	0.007	0.052
assign-tax_table	0.020	0.001	0.022
assign-taxa_are_rows	0.292	0.002	0.295
assign-taxa_names	0.038	0.014	0.053
build_tax_table	0.065	0.004	0.070
cca-rda-phyloseq-methods	0.012	0.004	0.016
data-GlobalPatterns	12.107	1.408	13.710
data-enterotype	8.560	0.224	9.030
data-esophagus	3.512	0.060	3.595
data-soilrep	14.906	1.129	16.624
distance	2.932	0.042	3.298
edgelist2clique	0.003	0.003	0.006
envHash2otu_table	0.003	0.005	0.008
estimate_richness	1.708	0.279	1.997
export_env_file	0.002	0.004	0.005
export_mothur_dist	0.003	0.002	0.005
filter_taxa	2.046	0.129	2.194
filterfun_sample	0.052	0.008	0.061
genefilter_sample-methods	0.003	0.005	0.010
get.component.classes	0.002	0.004	0.006
get_sample-methods	0.008	0.011	0.019
get_taxa-methods	0.009	0.010	0.019
get_taxa_unique	0.413	0.059	0.480
get_variable	0.706	0.041	0.752
getslots.phyloseq	0.354	0.037	0.395
import	0.002	0.001	0.003
import_RDP_otu	1.705	0.038	1.748
import_biom	0.187	0.041	0.249
import_env_file	0.002	0.002	0.003
import_mothur	0.010	0.009	0.018
import_mothur_dist	0.003	0.005	0.008
import_pyrotagger_tab	0.002	0.003	0.005
import_qiime	1.282	0.031	1.324
import_qiime_otu_tax	1.029	0.084	1.124
import_qiime_sample_data	0.053	0.007	0.059
index_reorder	0.002	0.002	0.005
intersect_taxa	0.002	0.005	0.007
make_network	7.368	0.140	7.588
merge_phyloseq	0.009	0.006	0.015
merge_phyloseq_pair-methods	0.010	0.009	0.020
merge_samples-methods	5.331	0.454	5.827
merge_taxa-methods	3.091	0.057	3.191
mt-methods	0.004	0.006	0.009
nodeplotblank	12.691	0.167	13.049
nodeplotboot	0.003	0.004	0.007
nodeplotdefault	0.002	0.003	0.006
nsamples-methods	0.007	0.007	0.015
ntaxa-methods	0.003	0.005	0.008
ordinate	0.012	0.014	0.026
otu_table-methods	0.002	0.002	0.005
parseTaxonomy-functions	0.011	0.011	0.023
phy_tree-methods	0.337	0.032	0.370
phyloseq	0.063	0.025	0.087
plot-taxa-bar	4.668	0.275	4.974
plot_bar	6.299	0.277	6.714
plot_heatmap	3.843	0.312	4.174
plot_network	6.044	0.098	6.159
plot_ordination	26.854	2.811	30.020
plot_phyloseq-methods	7.081	0.114	7.218
plot_richness	12.470	2.176	14.749
plot_scree	43.269	5.590	49.246
plot_tree	33.537	0.460	34.677
prune_samples-methods	1.445	0.314	1.783
prune_taxa-methods	0.096	0.027	0.125
psmelt	2.108	0.345	2.478
rank_names	0.041	0.018	0.059
rarefy_even_depth	7.106	0.379	7.525
read_tree	0.314	0.008	0.323
reconcile_categories	0.013	0.005	0.019
refseq-methods	0.345	0.031	0.377
rm_outlierf	0.072	0.013	0.085
sample_data-methods	0.003	0.004	0.007
sample_names-methods	0.003	0.005	0.007
sample_sums	0.051	0.026	0.077
sample_variables	0.043	0.012	0.055
show-methods	0.002	0.004	0.005
splat.phyloseq.objects	0.012	0.004	0.016
subset_ord_plot	0.011	0.004	0.016
subset_samples-methods	0.002	0.003	0.005
subset_taxa-methods	0.002	0.002	0.004
tax_glom	0.004	0.004	0.007
tax_table-methods	0.002	0.003	0.006
taxa_names-methods	0.003	0.004	0.007
taxa_sums	0.051	0.033	0.084
threshrank	4.761	1.816	6.883
threshrankfun	0.155	0.040	0.196
tip_glom-methods	0.012	0.008	0.021
topf	0.044	0.009	0.053
topk	0.047	0.021	0.069
topp	0.044	0.009	0.053
transformcounts	0.254	0.069	0.346
transpose-methods	1.115	0.974	2.496
tree.get.tags	0.011	0.012	0.024
tree.has.tags	0.003	0.004	0.007