Package: phyloseq

Version: 1.1.18

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phyloseq_1.1.18.tar.gz

StartedAt: 2012-06-21 02:34:33 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 02:41:11 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 397.7 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 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.1.18'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doParallel'
* 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 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'
filter_taxa: no visible binding for global variable 'enterotype'
filter_taxa: no visible binding for global variable 'expr'
import_qiime: no visible binding for global variable 'trefile'
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_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'
* 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
* 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 were 2 notes.
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
** help
*** installing help indices
** building package indices
** installing vignettes
   'phyloseq_analysis.Rnw' 
   'phyloseq_basics.Rnw' 
** testing if installed package can be loaded

* DONE (phyloseq)

name	user	system	elapsed
DPCoA	0.001	0.000	0.000
JSD	0.000	0.000	0.001
UniFrac-methods	0.001	0.001	0.001
access	0	0	0
assign-otuTable	0.000	0.001	0.001
assign-sampleData	0.000	0.000	0.001
assign-speciesarerows	0	0	0
assign-taxTab	0.000	0.000	0.001
assign-tre	0	0	0
cca-rda-phyloseq-methods	0.000	0.000	0.001
data-GlobalPatterns	0.001	0.001	0.001
data-enterotype	0.001	0.000	0.001
data-esophagus	0.001	0.000	0.000
data-soilrep	14.865	2.022	17.182
distance	2.380	0.040	2.651
edgelist2clique	0.001	0.000	0.000
envHash2otuTable	0.000	0.000	0.001
estimate_richness	1.516	0.458	1.993
export_env_file	0.000	0.000	0.001
export_mothur_dist	0	0	0
filter_taxa	0.001	0.000	0.001
filterfunSample	0.001	0.000	0.000
genefilterSample-methods	0	0	0
get.component.classes	0	0	0
getSamples-methods	0.005	0.001	0.006
getSpecies-methods	0.005	0.002	0.006
getTaxa	0.438	0.042	0.483
getVariable	0.375	0.029	0.406
getslots.phyloseq	0.382	0.038	0.433
import	0	0	0
import_RDP_otu	0.785	0.058	1.309
import_biom	0	0	0
import_env_file	0	0	0
import_mothur	0.000	0.001	0.001
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	0	0	0
intersect_species	0	0	0
make_network	7.631	0.330	8.072
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0.000	0.000	0.001
merge_samples-methods	0	0	0
merge_species-methods	0	0	0
mt-methods	0.000	0.001	0.001
nsamples-methods	0	0	0
nspecies-methods	0	0	0
ordinate	0.000	0.000	0.001
otuTable-methods	0	0	0
phyloseq	0	0	0
plot-taxa-bar	20.688	0.527	21.408
plot_heatmap	26.575	1.531	28.472
plot_network	6.308	0.204	6.546
plot_ordination	18.765	3.507	22.682
plot_phyloseq-methods	5.641	0.025	6.050
plot_richness_estimates	16.298	2.717	19.430
plot_tree	38.343	0.501	39.209
prune_samples-methods	0	0	0
prune_species-methods	0.000	0.001	0.001
rank.names	0.043	0.005	0.049
reconcile_categories	0.000	0.000	0.001
reconcile_samples	0	0	0
reconcile_species-methods	0.000	0.001	0.000
rm_outlierf	0.001	0.000	0.001
sample.names-methods	0.000	0.001	0.000
sample.variables	0.042	0.005	0.047
sampleData-methods	0	0	0
sampleSums	0.047	0.008	0.056
show-methods	0.000	0.001	0.001
species.names-methods	0	0	0
speciesSums	0.052	0.014	0.066
splat.phyloseq.objects	0	0	0
subset_ord_plot	49.431	3.958	54.011
subset_samples-methods	0	0	0
subset_species-methods	0	0	0
taxTab-methods	0.000	0.001	0.000
taxglom-methods	0.000	0.000	0.001
threshrank	3.785	2.139	5.990
threshrankfun	3.758	2.143	6.177
tipglom-methods	0	0	0
topf	0.000	0.000	0.001
topk	0	0	0
topp	0.001	0.001	0.001
transformcounts	4.038	1.994	6.701
transpose-methods	1.399	1.143	2.578
tre-methods	0.001	0.000	0.000
tree.get.tags	0.001	0.001	0.000
tree.has.tags	0.001	0.000	0.001