Package: phyloseq

Version: 1.0.3

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phyloseq_1.0.3.tar.gz

StartedAt: 2012-09-24 01:16:00 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 01:18:52 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 171.8 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/phyloseq.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.0.3'
* 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 sizes of PDF files under 'inst/doc' ... 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
  '/Users/biocbuild/bbs-2.10-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	0.001	0.000	0.000
UniFrac-methods	0.001	0.001	0.001
access	0	0	0
assign-otuTable	0.000	0.001	0.001
assign-sampleData	0	0	0
assign-speciesarerows	0	0	0
assign-taxTab	0.000	0.001	0.000
assign-tre	0	0	0
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	0.001	0.000	0.001
data-enterotype	0.000	0.000	0.001
data-esophagus	0	0	0
data-soilrep	12.819	1.414	14.262
distance	1.982	0.031	2.195
edgelist2clique	0	0	0
envHash2otuTable	0.000	0.001	0.000
estimate_richness	1.192	0.325	1.522
export_env_file	0	0	0
export_mothur_dist	0	0	0
filter_taxa	0.001	0.001	0.000
filterfunSample	0.001	0.000	0.001
genefilterSample-methods	0	0	0
get.component.classes	0.000	0.001	0.000
getSamples-methods	0.006	0.001	0.007
getSpecies-methods	0.006	0.002	0.008
getTaxa	0.399	0.036	0.435
getVariable	0.276	0.022	0.297
getslots.phyloseq	0.277	0.021	0.299
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	0.000	0.000	0.001
intersect_species	0	0	0
make_sample_network	5.427	0.194	5.636
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0.001	0.000	0.000
merge_samples-methods	0.000	0.000	0.001
merge_species-methods	0.000	0.001	0.000
mt-methods	0.000	0.000	0.001
nsamples-methods	0.000	0.001	0.000
nspecies-methods	0.001	0.000	0.000
ordinate	0	0	0
otuTable-methods	0	0	0
phyloseq	0.000	0.000	0.001
plot-taxa-bar	0	0	0
plot_ordination	0.000	0.000	0.001
plot_phyloseq-methods	0.001	0.000	0.000
plot_richness_estimates	0	0	0
plot_sample_network	6.677	0.153	6.837
plot_tree_phyloseq	0	0	0
prune_samples-methods	0	0	0
prune_species-methods	0	0	0
rank.names	0.035	0.003	0.039
reconcile_categories	0	0	0
reconcile_samples	0	0	0
reconcile_species-methods	0.000	0.001	0.001
rm_outlierf	0.001	0.000	0.001
sample.names-methods	0	0	0
sample.variables	0.036	0.004	0.041
sampleData-methods	0.000	0.000	0.001
sampleSums	0.045	0.008	0.053
show-methods	0	0	0
species.names-methods	0.000	0.000	0.001
speciesSums	0.058	0.015	0.072
splat.phyloseq.objects	0	0	0
subset_ord_plot	0.000	0.001	0.000
subset_samples-methods	0	0	0
subset_species-methods	0	0	0
taxTab-methods	0.001	0.001	0.000
taxglom-methods	0.000	0.000	0.001
threshrank	4.189	1.797	5.996
threshrankfun	3.791	1.732	5.544
tip-annotate	0.000	0.001	0.000
tipglom-methods	0	0	0
topf	0	0	0
topk	0	0	0
topp	0	0	0
transformcounts	3.739	1.438	5.200
transpose-methods	0.899	0.760	1.662
tre-methods	0.000	0.000	0.001