BioC 2.12: CHECK report for phyloseq on pelham

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: 2013-03-24 08:44:11 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 08:53:56 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 584.9 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 beta (2013-03-21 r62346)
* 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 '1.3.23'
* 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 ... [24s/26s] 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/271s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plot_scree            50.150  6.313  56.674
plot_ordination       26.325  3.287  29.761
plot_tree             26.290  0.620  26.979
data-soilrep          14.885  1.535  16.673
data-GlobalPatterns   13.710  1.767  15.621
plot_richness         12.628  2.398  15.064
nodeplotblank         10.251  0.275  10.565
data-enterotype        7.257  0.293   7.594
merge_samples-methods  6.514  0.594   7.131
make_network           6.371  0.208   6.592
threshrank             4.528  2.015   6.577
rarefy_even_depth      5.646  0.454   6.119
plot_network           5.874  0.133   6.031
plot_phyloseq-methods  5.635  0.135   5.793
plot_bar               5.207  0.380   5.612
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'testthat-phyloseq.R' [65s/66s]
 [66s/67s] 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	0.016	0.003	0.019
JSD	0.013	0.004	0.017
UniFrac-methods	0.038	0.008	0.047
access	0.013	0.003	0.016
assign-otu_table	0.019	0.004	0.023
assign-phy_tree	0.020	0.003	0.023
assign-sample_data	0.016	0.003	0.019
assign-sample_names	0.080	0.016	0.097
assign-tax_table	0.020	0.003	0.023
assign-taxa_are_rows	0.012	0.002	0.014
assign-taxa_names	0.038	0.011	0.050
build_tax_table	0.066	0.002	0.069
cca-rda-phyloseq-methods	0.023	0.001	0.029
data-GlobalPatterns	13.710	1.767	15.621
data-enterotype	7.257	0.293	7.594
data-esophagus	2.674	0.089	2.775
data-soilrep	14.885	1.535	16.673
distance	2.378	0.051	2.618
edgelist2clique	0.011	0.006	0.017
envHash2otu_table	0.004	0.006	0.010
estimate_richness	1.747	0.258	2.010
export_env_file	0.003	0.003	0.006
export_mothur_dist	0.003	0.005	0.008
filter_taxa	1.757	0.184	1.955
filterfun_sample	0.046	0.012	0.059
genefilter_sample-methods	0.015	0.011	0.027
get.component.classes	0.003	0.005	0.008
get_sample-methods	0.008	0.007	0.015
get_taxa-methods	0.020	0.012	0.032
get_taxa_unique	0.366	0.066	0.432
get_variable	0.293	0.040	0.333
getslots.phyloseq	0.312	0.053	0.365
import	0.003	0.003	0.005
import_RDP_otu	1.324	0.071	1.404
import_biom	0.191	0.049	0.251
import_env_file	0.003	0.003	0.005
import_mothur	0.005	0.008	0.014
import_mothur_dist	0.003	0.006	0.009
import_pyrotagger_tab	0.003	0.004	0.007
import_qiime	1.275	0.047	1.329
import_qiime_otu_tax	1.055	0.093	1.188
import_qiime_sample_data	0.037	0.007	0.045
index_reorder	0.003	0.004	0.006
intersect_taxa	0.009	0.008	0.017
make_network	6.371	0.208	6.592
merge_phyloseq	0.010	0.006	0.016
merge_phyloseq_pair-methods	0.020	0.011	0.031
merge_samples-methods	6.514	0.594	7.131
merge_taxa-methods	2.434	0.081	2.544
mt-methods	0.004	0.007	0.012
nodeplotblank	10.251	0.275	10.565
nodeplotboot	0.004	0.006	0.011
nodeplotdefault	0.014	0.007	0.021
nsamples-methods	0.004	0.006	0.011
ntaxa-methods	0.004	0.006	0.010
ordinate	0.021	0.022	0.043
otu_table-methods	0.013	0.009	0.024
parseTaxonomy-functions	0.007	0.008	0.015
phy_tree-methods	0.284	0.039	0.324
phyloseq	0.071	0.037	0.109
plot-taxa-bar	3.770	0.371	4.173
plot_bar	5.207	0.380	5.612
plot_heatmap	4.354	0.407	4.804
plot_network	5.874	0.133	6.031
plot_ordination	26.325	3.287	29.761
plot_phyloseq-methods	5.635	0.135	5.793
plot_richness	12.628	2.398	15.064
plot_scree	50.150	6.313	56.674
plot_tree	26.290	0.620	26.979
prune_samples-methods	1.504	0.365	1.872
prune_taxa-methods	0.110	0.053	0.165
psmelt	2.106	0.370	2.489
rank_names	0.037	0.019	0.057
rarefy_even_depth	5.646	0.454	6.119
read_tree	0.271	0.013	0.283
reconcile_categories	0.006	0.010	0.016
refseq-methods	0.274	0.033	0.307
rm_outlierf	0.043	0.016	0.060
sample_data-methods	0.013	0.008	0.021
sample_names-methods	0.003	0.006	0.009
sample_sums	0.058	0.025	0.083
sample_variables	0.051	0.017	0.068
show-methods	0.003	0.006	0.009
splat.phyloseq.objects	0.015	0.008	0.022
subset_ord_plot	0.003	0.005	0.007
subset_samples-methods	0.003	0.002	0.005
subset_taxa-methods	0.003	0.004	0.007
tax_glom	0.005	0.007	0.012
tax_table-methods	0.014	0.007	0.022
taxa_names-methods	0.005	0.009	0.013
taxa_sums	0.048	0.028	0.076
threshrank	4.528	2.015	6.577
threshrankfun	0.137	0.053	0.190
tip_glom-methods	0.006	0.012	0.019
topf	0.032	0.010	0.042
topk	0.029	0.006	0.035
topp	0.040	0.011	0.051
transformcounts	0.217	0.064	0.281
transpose-methods	1.157	1.120	2.280
tree.get.tags	0.002	0.004	0.009
tree.has.tags	0.003	0.005	0.008

Summary

Command output