BioC 2.12: CHECK report for phyloseq on pelham

Package: phyloseq

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phyloseq_1.4.2.tar.gz

StartedAt: 2013-05-01 09:16:44 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 09:26:27 -0700 (Wed, 01 May 2013)

EllapsedTime: 583.3 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 3.0.0 Patched (2013-04-08 r62531)
* 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 '1.4.2'
* 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 ... [23s/25s] 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 ... [269s/273s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plot_scree            49.504  6.137  56.034
plot_ordination       27.423  3.491  31.179
plot_tree             25.101  0.588  25.888
data-soilrep          15.217  1.420  16.833
data-GlobalPatterns   13.925  1.779  15.973
plot_richness         12.772  2.460  15.367
nodeplotblank          9.633  0.246  10.108
data-enterotype        7.459  0.328   7.886
make_network           7.533  0.212   7.809
threshrank             4.462  2.077   6.579
plot_network           6.126  0.159   6.351
rarefy_even_depth      5.848  0.426   6.360
plot-taxa-bar          5.430  0.343   5.889
merge_samples-methods  5.167  0.565   5.825
plot_phyloseq-methods  5.574  0.141   5.770
plot_bar               5.119  0.371   5.719
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'testthat-phyloseq.R' [63s/64s]
 [64s/65s] 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	0.017	0.004	0.020
JSD	0.011	0.002	0.012
UniFrac-methods	0.042	0.002	0.044
access	0.016	0.002	0.019
assign-otu_table	0.012	0.003	0.014
assign-phy_tree	0.014	0.003	0.018
assign-sample_data	0.015	0.003	0.020
assign-sample_names	0.064	0.012	0.078
assign-tax_table	0.022	0.002	0.025
assign-taxa_are_rows	0.012	0.001	0.014
assign-taxa_names	0.038	0.007	0.045
build_tax_table	0.070	0.002	0.072
cca-rda-phyloseq-methods	0.023	0.003	0.026
data-GlobalPatterns	13.925	1.779	15.973
data-enterotype	7.459	0.328	7.886
data-esophagus	2.607	0.067	2.694
data-soilrep	15.217	1.420	16.833
distance	2.347	0.059	2.670
edgelist2clique	0.013	0.007	0.022
envHash2otu_table	0.003	0.007	0.011
estimate_richness	1.691	0.307	2.010
export_env_file	0.003	0.004	0.007
export_mothur_dist	0.002	0.004	0.007
filter_taxa	1.794	0.146	1.954
filterfun_sample	0.111	0.021	0.132
genefilter_sample-methods	0.016	0.013	0.028
get.component.classes	0.003	0.005	0.008
get_sample-methods	0.021	0.016	0.038
get_taxa-methods	0.010	0.015	0.026
get_taxa_unique	0.356	0.062	0.420
get_variable	0.290	0.033	0.326
getslots.phyloseq	0.315	0.049	0.373
import	0.013	0.008	0.022
import_RDP_otu	1.356	0.074	1.446
import_biom	0.200	0.045	0.252
import_env_file	0.010	0.003	0.013
import_mothur	0.020	0.010	0.031
import_mothur_dist	0.010	0.005	0.016
import_pyrotagger_tab	0.010	0.003	0.013
import_qiime	1.209	0.041	1.255
import_qiime_otu_tax	1.099	0.098	1.209
import_qiime_sample_data	0.036	0.007	0.045
index_reorder	0.002	0.003	0.005
intersect_taxa	0.003	0.005	0.008
make_network	7.533	0.212	7.809
merge_phyloseq	0.011	0.014	0.026
merge_phyloseq_pair-methods	0.011	0.012	0.023
merge_samples-methods	5.167	0.565	5.825
merge_taxa-methods	2.754	0.095	2.942
mt-methods	0.004	0.007	0.010
nodeplotblank	9.633	0.246	10.108
nodeplotboot	0.004	0.006	0.009
nodeplotdefault	0.003	0.005	0.008
nsamples-methods	0.011	0.010	0.020
ntaxa-methods	0.004	0.006	0.010
ordinate	0.009	0.014	0.023
otu_table-methods	0.003	0.005	0.007
parseTaxonomy-functions	0.014	0.011	0.025
phy_tree-methods	0.317	0.045	0.366
phyloseq	0.063	0.029	0.091
plot-taxa-bar	5.430	0.343	5.889
plot_bar	5.119	0.371	5.719
plot_heatmap	3.952	0.400	4.396
plot_network	6.126	0.159	6.351
plot_ordination	27.423	3.491	31.179
plot_phyloseq-methods	5.574	0.141	5.770
plot_richness	12.772	2.460	15.367
plot_scree	49.504	6.137	56.034
plot_tree	25.101	0.588	25.888
prune_samples-methods	1.524	0.363	1.897
prune_taxa-methods	0.081	0.029	0.112
psmelt	2.435	0.362	2.814
rank_names	0.036	0.011	0.048
rarefy_even_depth	5.848	0.426	6.360
read_tree	0.249	0.010	0.261
reconcile_categories	0.003	0.006	0.010
refseq-methods	0.298	0.038	0.340
rm_outlierf	0.032	0.011	0.045
sample_data-methods	0.003	0.005	0.008
sample_names-methods	0.003	0.005	0.008
sample_sums	0.045	0.025	0.069
sample_variables	0.049	0.021	0.070
show-methods	0.002	0.005	0.008
splat.phyloseq.objects	0.013	0.009	0.022
subset_ord_plot	0.002	0.005	0.007
subset_samples-methods	0.002	0.004	0.007
subset_taxa-methods	0.002	0.003	0.006
tax_glom	0.016	0.013	0.029
tax_table-methods	0.003	0.005	0.008
taxa_names-methods	0.013	0.010	0.024
taxa_sums	0.046	0.026	0.073
threshrank	4.462	2.077	6.579
threshrankfun	0.133	0.062	0.200
tip_glom-methods	0.016	0.014	0.031
topf	0.057	0.016	0.074
topk	0.036	0.010	0.046
topp	0.040	0.012	0.053
transformcounts	0.216	0.069	0.287
transpose-methods	1.140	1.092	2.243
tree.get.tags	0.011	0.011	0.022
tree.has.tags	0.002	0.005	0.008

Summary

Command output