Package: phyloseq

Version: 1.0.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.0.0.tar.gz

StartedAt: 2012-04-01 02:41:40 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 02:43:36 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 116.4 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/phyloseq.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phyloseq/DESCRIPTION' ... OK
* this is package 'phyloseq' version '1.0.0'
* 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'
export_env_file: no visible global function definition for 'ps'
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'
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_richness_estimates: no visible binding for global variable 'value'
plot_richness_estimates: no visible binding for global variable 'se'
plot_sample_network: no visible binding for global variable 'x'
plot_sample_network: no visible binding for global variable 'y'
plot_taxa_bar: no visible binding for global variable 'Abundance'
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 installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'naturemag.bst'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* 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 3 notes.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-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	0	0
JSD	0	0	0
UniFrac-methods	0	0	0
access	0	0	0
assign-otuTable	0	0	0
assign-sampleData	0	0	0
assign-speciesarerows	0	0	0
assign-taxTab	0.000	0.000	0.001
assign-tre	0	0	0
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	0.000	0.000	0.001
data-enterotype	0.000	0.000	0.001
data-esophagus	0	0	0
data-soilrep	8.268	0.072	8.367
distance	1.388	0.016	1.472
edgelist2clique	0	0	0
envHash2otuTable	0.000	0.000	0.001
estimate_richness	0.828	0.040	0.885
export_env_file	0	0	0
export_mothur_dist	0.000	0.000	0.001
filter_taxa	0	0	0
filterfunSample	0	0	0
genefilterSample-methods	0.000	0.000	0.001
get.component.classes	0	0	0
getSamples-methods	0.004	0.000	0.028
getSpecies-methods	0.008	0.000	0.030
getTaxa	0.240	0.012	0.294
getVariable	0.184	0.004	0.239
getslots.phyloseq	0.188	0.004	0.227
import	0	0	0
import_biom	0	0	0
import_env_file	0	0	0
import_mothur	0	0	0
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	0	0	0
intersect_species	0	0	0
make_sample_network	3.885	0.020	3.955
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	0	0
nsamples-methods	0	0	0
nspecies-methods	0	0	0
ordinate	0.000	0.004	0.000
otuTable-methods	0	0	0
phyloseq	0	0	0
plot-taxa-bar	0	0	0
plot_ordination	0.000	0.000	0.001
plot_phyloseq-methods	0	0	0
plot_richness_estimates	0	0	0
plot_sample_network	3.372	0.000	3.394
plot_tree_phyloseq	0	0	0
prune_samples-methods	0	0	0
prune_species-methods	0	0	0
rank.names	0.036	0.000	0.055
reconcile_categories	0	0	0
reconcile_samples	0	0	0
reconcile_species-methods	0	0	0
rm_outlierf	0	0	0
sample.names-methods	0	0	0
sample.variables	0.028	0.000	0.049
sampleData-methods	0	0	0
sampleSums	0.036	0.008	0.095
show-methods	0	0	0
species.names-methods	0	0	0
speciesSums	0.040	0.004	0.083
splat.phyloseq.objects	0	0	0
subset_ord_plot	0	0	0
subset_samples-methods	0.000	0.000	0.001
subset_species-methods	0	0	0
taxTab-methods	0	0	0
taxglom-methods	0.000	0.000	0.001
threshrank	2.660	0.428	3.112
threshrankfun	2.296	0.392	2.710
tip-annotate	0	0	0
tipglom-methods	0	0	0
topf	0	0	0
topk	0	0	0
topp	0	0	0
transformcounts	2.480	0.284	2.786
transpose-methods	0.720	0.300	1.041
tre-methods	0	0	0