BioC 2.12: CHECK report for phyloseq on petty

Package: phyloseq

Version: 1.3.23

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phyloseq_1.3.23.tar.gz

StartedAt: 2013-03-25 04:01:59 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:09:19 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 440.2 seconds

RetCode: 0

Status: OK

CheckDir: phyloseq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/phyloseq.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'phyloseq/DESCRIPTION' ... OK
* this is package 'phyloseq' version '1.3.23'
* 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/21s] 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 ... [169s/169s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plot_tree             30.820  0.103  30.931
plot_ordination       14.963  1.802  16.801
data-soilrep           9.120  1.299  10.466
nodeplotblank         10.039  0.042  10.083
plot_scree             7.576  1.298   8.894
plot_richness          6.528  0.924   7.468
make_network           5.519  0.203   5.731
data-enterotype        5.399  0.295   5.707
threshrank             3.736  1.747   5.503
plot_phyloseq-methods  5.082  0.030   5.113
data-GlobalPatterns    4.643  0.380   5.041
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'testthat-phyloseq.R' [44s/45s]
 [45s/45s] 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
   'phyloseq_analysis.Rnw' 
   'phyloseq_basics.Rnw' 
** 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	0.012	0.009	0.021
JSD	0.008	0.006	0.014
UniFrac-methods	0.019	0.016	0.036
access	0.008	0.006	0.016
assign-otu_table	0.009	0.008	0.018
assign-phy_tree	0.012	0.009	0.022
assign-sample_data	0.011	0.009	0.021
assign-sample_names	0.050	0.017	0.068
assign-tax_table	0.015	0.011	0.027
assign-taxa_are_rows	0.007	0.006	0.013
assign-taxa_names	0.031	0.017	0.048
build_tax_table	0.044	0.012	0.055
cca-rda-phyloseq-methods	0.009	0.007	0.016
data-GlobalPatterns	4.643	0.380	5.041
data-enterotype	5.399	0.295	5.707
data-esophagus	2.189	0.051	2.245
data-soilrep	9.120	1.299	10.466
distance	1.797	0.047	1.994
edgelist2clique	0.002	0.004	0.006
envHash2otu_table	0.008	0.008	0.015
estimate_richness	1.306	0.373	1.692
export_env_file	0.002	0.004	0.006
export_mothur_dist	0.007	0.008	0.015
filter_taxa	1.546	0.192	1.748
filterfun_sample	0.04	0.01	0.05
genefilter_sample-methods	0.004	0.009	0.015
get.component.classes	0.005	0.009	0.014
get_sample-methods	0.009	0.009	0.017
get_taxa-methods	0.009	0.010	0.018
get_taxa_unique	0.350	0.046	0.402
get_variable	0.316	0.031	0.353
getslots.phyloseq	0.334	0.040	0.376
import	0.003	0.004	0.007
import_RDP_otu	0.648	0.036	0.688
import_biom	0.160	0.055	0.216
import_env_file	0.002	0.004	0.006
import_mothur	0.012	0.013	0.026
import_mothur_dist	0.004	0.005	0.008
import_pyrotagger_tab	0.003	0.004	0.007
import_qiime	0.849	0.056	0.906
import_qiime_otu_tax	0.681	0.074	0.755
import_qiime_sample_data	0.031	0.009	0.040
index_reorder	0.002	0.004	0.007
intersect_taxa	0.002	0.004	0.006
make_network	5.519	0.203	5.731
merge_phyloseq	0.006	0.009	0.015
merge_phyloseq_pair-methods	0.014	0.018	0.032
merge_samples-methods	3.714	0.592	4.327
merge_taxa-methods	2.300	0.075	2.395
mt-methods	0.012	0.011	0.023
nodeplotblank	10.039	0.042	10.083
nodeplotboot	0.004	0.006	0.010
nodeplotdefault	0.004	0.007	0.011
nsamples-methods	0.01	0.01	0.02
ntaxa-methods	0.010	0.010	0.019
ordinate	0.016	0.019	0.035
otu_table-methods	0.011	0.009	0.019
parseTaxonomy-functions	0.017	0.013	0.032
phy_tree-methods	0.416	0.033	0.451
phyloseq	0.056	0.030	0.090
plot-taxa-bar	3.386	0.340	3.734
plot_bar	3.489	0.313	3.811
plot_heatmap	4.064	0.453	4.550
plot_network	4.706	0.140	4.848
plot_ordination	14.963	1.802	16.801
plot_phyloseq-methods	5.082	0.030	5.113
plot_richness	6.528	0.924	7.468
plot_scree	7.576	1.298	8.894
plot_tree	30.820	0.103	30.931
prune_samples-methods	0.941	0.300	1.245
prune_taxa-methods	0.062	0.026	0.087
psmelt	1.734	0.359	2.105
rank_names	0.044	0.012	0.057
rarefy_even_depth	4.417	0.353	4.778
read_tree	0.201	0.018	0.260
reconcile_categories	0.003	0.005	0.008
refseq-methods	0.270	0.024	0.298
rm_outlierf	0.026	0.010	0.036
sample_data-methods	0.002	0.005	0.007
sample_names-methods	0.002	0.005	0.008
sample_sums	0.045	0.013	0.059
sample_variables	0.057	0.016	0.074
show-methods	0.003	0.005	0.008
splat.phyloseq.objects	0.011	0.010	0.021
subset_ord_plot	0.002	0.004	0.007
subset_samples-methods	0.003	0.005	0.008
subset_taxa-methods	0.002	0.005	0.006
tax_glom	0.012	0.013	0.026
tax_table-methods	0.003	0.006	0.008
taxa_names-methods	0.012	0.013	0.025
taxa_sums	0.063	0.022	0.085
threshrank	3.736	1.747	5.503
threshrankfun	0.104	0.053	0.166
tip_glom-methods	0.009	0.013	0.023
topf	0.047	0.017	0.064
topk	0.037	0.013	0.050
topp	0.03	0.01	0.04
transformcounts	0.253	0.082	0.341
transpose-methods	1.407	1.079	2.500
tree.get.tags	0.009	0.012	0.021
tree.has.tags	0.003	0.008	0.012

Summary

Command output