Package: phyloseq

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phyloseq_1.2.1.tar.gz

StartedAt: 2013-03-25 00:48:19 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:54:24 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 365.2 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/phyloseq.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.2.1'
* 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 whether package 'phyloseq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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'
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 'value'
plot_richness: no visible binding for global variable 'se'
plot_richness_estimates: no visible binding for global variable 'value'
plot_richness_estimates: no visible binding for global variable 'se'
plot_taxa_bar: no visible binding for global variable 'Abundance'
plot_tree_only: no visible binding for global variable 'type'
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 'type'
plot_tree_sampledodge: no visible binding for global variable 'x'
plot_tree_sampledodge: no visible binding for global variable 'y'
plot_tree_sampledodge: no visible binding for global variable 'xend'
plot_tree_sampledodge: 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.adj'
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 ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
subset_ord_plot 30.336  1.773  32.842
plot_tree       27.515  0.439  28.355
plot_heatmap    19.648  1.313  21.334
plot-taxa-bar   15.371  0.444  16.125
plot_richness   11.580  2.508  14.453
plot_ordination 11.205  1.791  13.632
data-soilrep    10.136  1.856  12.377
transformcounts  4.654  1.515   6.414
data-enterotype  5.226  0.377   5.905
make_network     5.209  0.277   5.587
threshrank       3.274  1.685   5.035
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'testthat-phyloseq.R'
 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-2.11-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) :
  A specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "pipe" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "textConnection" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO' 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) :
  A specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "pipe" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "textConnection" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO' and is not turning on duplicate class definitions for this class

* DONE (phyloseq)

name	user	system	elapsed
DPCoA	0	0	0
JSD	0.000	0.000	0.001
UniFrac-methods	0.001	0.001	0.001
access	0.001	0.000	0.000
assign-otu_table	0	0	0
assign-phy_tree	0.000	0.001	0.000
assign-sample_data	0	0	0
assign-tax_table	0.000	0.000	0.001
assign-taxa_are_rows	0	0	0
cca-rda-phyloseq-methods	0.000	0.000	0.001
data-GlobalPatterns	3.120	0.399	3.730
data-enterotype	5.226	0.377	5.905
data-esophagus	1.957	0.022	1.985
data-soilrep	10.136	1.856	12.377
distance	1.737	0.042	2.055
edgelist2clique	0.000	0.001	0.000
envHash2otu_table	0	0	0
estimate_richness	0.990	0.395	1.419
export_env_file	0.000	0.001	0.000
export_mothur_dist	0	0	0
filter_taxa	4.556	0.286	4.887
filterfun_sample	0.000	0.000	0.001
genefilter_sample-methods	0	0	0
get.component.classes	0.001	0.000	0.000
get_sample-methods	0.004	0.002	0.005
get_taxa-methods	0.004	0.001	0.004
get_taxa_unique	0.320	0.039	0.365
get_variable	0.275	0.030	0.319
getslots.phyloseq	0.262	0.031	0.299
import	0.001	0.000	0.000
import_RDP_otu	1.177	0.050	1.245
import_biom	0.000	0.001	0.000
import_env_file	0	0	0
import_mothur	0	0	0
import_mothur_dist	0.000	0.001	0.000
import_pyrotagger_tab	0	0	0
import_qiime	0	0	0
import_qiime_otu_tax	0	0	0
import_qiime_sample_data	0.032	0.004	0.036
intersect_species	0.001	0.000	0.001
make_network	5.209	0.277	5.587
merge_phyloseq	0.000	0.000	0.001
merge_phyloseq_pair-methods	0.000	0.000	0.001
merge_samples-methods	0	0	0
merge_taxa-methods	0.001	0.000	0.000
mt-methods	0	0	0
nsamples-methods	0	0	0
ntaxa-methods	0	0	0
ordinate	0.001	0.000	0.000
otu_table-methods	0.001	0.000	0.000
phy_tree-methods	0.266	0.027	0.302
phyloseq	0.001	0.000	0.000
plot-taxa-bar	15.371	0.444	16.125
plot_heatmap	19.648	1.313	21.334
plot_network	4.122	0.174	4.381
plot_ordination	11.205	1.791	13.632
plot_phyloseq-methods	4.230	0.017	4.273
plot_richness	11.580	2.508	14.453
plot_tree	27.515	0.439	28.355
prune_samples-methods	1.622	0.330	2.009
prune_taxa-methods	0	0	0
rank_names	0.031	0.004	0.035
rarefy_even_depth	4.161	0.361	4.565
read_tree	0.193	0.008	0.218
reconcile_categories	0	0	0
reconcile_samples	0	0	0
reconcile_species-methods	0.001	0.000	0.000
rm_outlierf	0.000	0.000	0.001
sample_data-methods	0	0	0
sample_names-methods	0.000	0.000	0.001
sample_sums	0.035	0.008	0.047
sample_variables	0.031	0.006	0.038
show-methods	0	0	0
splat.phyloseq.objects	0	0	0
subset_ord_plot	30.336	1.773	32.842
subset_samples-methods	0	0	0
subset_taxa-methods	0	0	0
tax_glom	0.000	0.001	0.000
tax_table-methods	0	0	0
taxa_names-methods	0	0	0
taxa_sums	0.037	0.011	0.047
threshrank	3.274	1.685	5.035
threshrankfun	3.034	1.687	4.779
tip_glom-methods	0.000	0.000	0.001
topf	0.000	0.001	0.001
topk	0	0	0
topp	0	0	0
transformcounts	4.654	1.515	6.414
transpose-methods	0.923	0.859	1.808
tree.get.tags	0	0	0
tree.has.tags	0	0	0