Package: phyloseq

Version: 1.3.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.3.0.tar.gz

StartedAt: 2013-01-16 05:12:51 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 05:19:04 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 373.6 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/phyloseq.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.3.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘phyloseq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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     44.226  0.072  44.298
plot_tree           27.762  0.032  27.797
plot_heatmap        20.453  0.032  20.488
plot_ordination     19.681  0.108  19.790
plot-taxa-bar       17.410  0.000  17.410
plot_richness       14.208  0.040  14.249
data-soilrep         9.872  0.108   9.978
data-GlobalPatterns  8.992  0.080   9.068
make_network         5.544  0.004   5.550
data-enterotype      5.141  0.024   5.170
* 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
  ‘/loc/home/biocbuild/bbs-2.12-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) :
  the specification for S3 class “AsIs” 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) :
  the 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) :
  the 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) :
  the 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) :
  the 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) :
  the specification for S3 class “AsIs” 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) :
  the 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) :
  the 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) :
  the 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) :
  the 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	0.012	0.000	0.014
JSD	0.008	0.000	0.010
UniFrac-methods	0.028	0.000	0.028
access	0.012	0.000	0.010
assign-otu_table	0.012	0.000	0.015
assign-phy_tree	0.016	0.000	0.015
assign-sample_data	0.012	0.000	0.014
assign-tax_table	0.016	0.000	0.015
assign-taxa_are_rows	0.008	0.000	0.009
cca-rda-phyloseq-methods	0.016	0.000	0.018
data-GlobalPatterns	8.992	0.080	9.068
data-enterotype	5.141	0.024	5.170
data-esophagus	1.656	0.008	1.660
data-soilrep	9.872	0.108	9.978
distance	1.680	0.036	1.975
edgelist2clique	0.008	0.000	0.010
envHash2otu_table	0.012	0.000	0.011
estimate_richness	1.241	0.036	1.278
export_env_file	0.008	0.000	0.010
export_mothur_dist	0.012	0.000	0.010
filter_taxa	4.664	0.024	4.690
filterfun_sample	0.012	0.000	0.011
genefilter_sample-methods	0.012	0.000	0.010
get.component.classes	0.008	0.000	0.007
get_sample-methods	0.008	0.004	0.015
get_taxa-methods	0.016	0.000	0.015
get_taxa_unique	0.244	0.004	0.246
get_variable	0.192	0.004	0.193
getslots.phyloseq	0.224	0.008	0.233
import	0.012	0.000	0.014
import_RDP_otu	2.728	0.020	2.747
import_biom	0.008	0.000	0.008
import_env_file	0.000	0.000	0.002
import_mothur	0.008	0.000	0.005
import_mothur_dist	0.004	0.000	0.003
import_pyrotagger_tab	0.000	0.000	0.002
import_qiime	0.004	0.000	0.002
import_qiime_otu_tax	0.008	0.000	0.007
import_qiime_sample_data	0.032	0.000	0.034
intersect_species	0.004	0.000	0.003
make_network	5.544	0.004	5.550
merge_phyloseq	0.008	0.000	0.010
merge_phyloseq_pair-methods	0.016	0.000	0.016
merge_samples-methods	0.004	0.004	0.009
merge_taxa-methods	0.008	0.000	0.008
mt-methods	0.012	0.000	0.010
nsamples-methods	0.008	0.000	0.009
ntaxa-methods	0.008	0.000	0.009
ordinate	0.016	0.000	0.013
otu_table-methods	0.004	0.000	0.007
phy_tree-methods	0.200	0.000	0.196
phyloseq	0.02	0.00	0.02
plot-taxa-bar	17.41	0.00	17.41
plot_heatmap	20.453	0.032	20.488
plot_network	3.960	0.004	3.964
plot_ordination	19.681	0.108	19.790
plot_phyloseq-methods	4.073	0.004	4.078
plot_richness	14.208	0.040	14.249
plot_tree	27.762	0.032	27.797
prune_samples-methods	1.572	0.012	1.583
prune_taxa-methods	0.016	0.000	0.019
rank_names	0.040	0.004	0.041
rarefy_even_depth	4.849	0.032	4.880
read_tree	0.192	0.000	0.196
reconcile_categories	0.020	0.000	0.021
reconcile_samples	0.020	0.000	0.021
reconcile_species-methods	0.02	0.00	0.02
rm_outlierf	0.024	0.000	0.022
sample_data-methods	0.020	0.000	0.019
sample_names-methods	0.020	0.000	0.019
sample_sums	0.048	0.004	0.052
sample_variables	0.056	0.000	0.057
show-methods	0.004	0.000	0.003
splat.phyloseq.objects	0.020	0.000	0.021
subset_ord_plot	44.226	0.072	44.298
subset_samples-methods	0.004	0.000	0.003
subset_taxa-methods	0.004	0.000	0.003
tax_glom	0.020	0.000	0.019
tax_table-methods	0.004	0.000	0.003
taxa_names-methods	0.004	0.000	0.004
taxa_sums	0.048	0.004	0.054
threshrank	3.313	0.648	3.958
threshrankfun	3.172	0.716	3.891
tip_glom-methods	0.020	0.000	0.018
topf	0.004	0.000	0.005
topk	0.004	0.000	0.004
topp	0.004	0.000	0.005
transformcounts	4.440	0.428	4.866
transpose-methods	0.752	0.444	1.195
tree.get.tags	0.012	0.000	0.014
tree.has.tags	0.004	0.000	0.004