Package: phyloseq

Version: 1.2.1

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.2.1.tar.gz

StartedAt: 2013-03-25 03:42:48 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:49:43 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 414.5 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/phyloseq.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... 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 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
subset_ord_plot     37.471  0.104  39.710
plot_tree           25.762  0.204  29.050
plot_heatmap        18.773  0.148  19.682
plot-taxa-bar       14.537  0.048  20.574
plot_ordination     14.312  0.140  15.373
plot_richness       12.320  0.088  19.101
data-soilrep        10.284  0.136  13.120
data-GlobalPatterns  6.876  0.040   7.159
data-enterotype      5.296  0.024   5.364
make_network         5.108  0.040   5.814
filter_taxa          4.409  0.084   5.074
transformcounts      3.712  0.488  10.470
threshrankfun        3.040  0.648  19.478
* 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 were 2 notes.
See
  ‘/loc/home/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	0	0
UniFrac-methods	0	0	0
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0	0	0
assign-sample_data	0	0	0
assign-tax_table	0	0	0
assign-taxa_are_rows	0	0	0
cca-rda-phyloseq-methods	0.000	0.000	0.001
data-GlobalPatterns	6.876	0.040	7.159
data-enterotype	5.296	0.024	5.364
data-esophagus	1.873	0.012	2.282
data-soilrep	10.284	0.136	13.120
distance	1.568	0.044	2.970
edgelist2clique	0.000	0.000	0.001
envHash2otu_table	0	0	0
estimate_richness	1.104	0.036	1.288
export_env_file	0	0	0
export_mothur_dist	0	0	0
filter_taxa	4.409	0.084	5.074
filterfun_sample	0	0	0
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0.004	0.000	0.005
get_taxa-methods	0.004	0.000	0.005
get_taxa_unique	0.228	0.012	0.353
get_variable	0.200	0.004	0.236
getslots.phyloseq	0.192	0.016	0.228
import	0	0	0
import_RDP_otu	2.680	0.032	2.959
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
import_qiime_otu_tax	0.000	0.000	0.001
import_qiime_sample_data	0.028	0.004	0.032
intersect_species	0	0	0
make_network	5.108	0.040	5.814
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	0.000	0.004	0.000
merge_taxa-methods	0	0	0
mt-methods	0.000	0.000	0.001
nsamples-methods	0	0	0
ntaxa-methods	0	0	0
ordinate	0.004	0.000	0.000
otu_table-methods	0	0	0
phy_tree-methods	0.192	0.016	0.264
phyloseq	0	0	0
plot-taxa-bar	14.537	0.048	20.574
plot_heatmap	18.773	0.148	19.682
plot_network	4.357	0.068	4.701
plot_ordination	14.312	0.140	15.373
plot_phyloseq-methods	3.965	0.016	4.190
plot_richness	12.320	0.088	19.101
plot_tree	25.762	0.204	29.050
prune_samples-methods	1.848	0.024	2.067
prune_taxa-methods	0	0	0
rank_names	0.028	0.000	0.116
rarefy_even_depth	4.544	0.024	4.845
read_tree	0.160	0.004	0.182
reconcile_categories	0	0	0
reconcile_samples	0	0	0
reconcile_species-methods	0	0	0
rm_outlierf	0.004	0.000	0.000
sample_data-methods	0	0	0
sample_names-methods	0	0	0
sample_sums	0.020	0.012	0.032
sample_variables	0.024	0.000	0.025
show-methods	0	0	0
splat.phyloseq.objects	0	0	0
subset_ord_plot	37.471	0.104	39.710
subset_samples-methods	0	0	0
subset_taxa-methods	0	0	0
tax_glom	0.000	0.000	0.001
tax_table-methods	0	0	0
taxa_names-methods	0	0	0
taxa_sums	0.028	0.008	0.044
threshrank	3.144	0.652	4.857
threshrankfun	3.040	0.648	19.478
tip_glom-methods	0	0	0
topf	0	0	0
topk	0	0	0
topp	0	0	0
transformcounts	3.712	0.488	10.470
transpose-methods	0.785	0.436	1.387
tree.get.tags	0	0	0
tree.has.tags	0.000	0.000	0.001