Package: phyloseq

Version: 1.3.23

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.3.23.tar.gz

StartedAt: 2013-03-25 03:43:41 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:54:52 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 670.5 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/phyloseq.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.3.23’
* 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 ... [30s/31s] 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’
nodeplotboot : <anonymous>: no visible binding for global variable ‘x’
nodeplotboot : <anonymous>: no visible binding for global variable ‘y’
nodeplotdefault : <anonymous>: no visible binding for global variable
  ‘x’
nodeplotdefault : <anonymous>: no visible binding for global variable
  ‘y’
nodeplotdefault : <anonymous>: no visible binding for global variable
  ‘label’
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 ‘variable’
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
  ‘variable’
plot_richness_estimates: no visible binding for global variable ‘value’
plot_richness_estimates: no visible binding for global variable ‘se’
plot_scree: no visible binding for global variable ‘eigenvalue’
plot_taxa_bar: no visible binding for global variable ‘Abundance’
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 ‘value’
plot_tree_sampledodge: no visible binding for global variable ‘x’
plot_tree_sampledodge: no visible binding for global variable ‘x.adj’
plot_tree_sampledodge: no visible binding for global variable ‘y’
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 ... [264s/276s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plot_scree            49.267  0.100  51.254
plot_ordination       29.438  0.232  30.143
plot_tree             26.698  0.028  26.985
data-soilrep          18.041  0.224  19.413
data-GlobalPatterns   15.825  0.132  19.181
plot_richness         12.817  0.116  13.810
nodeplotblank         10.184  0.036  10.339
data-enterotype        7.429  0.040   7.548
merge_samples-methods  7.073  0.072   7.207
make_network           6.568  0.028   7.271
plot-taxa-bar          6.541  0.040   6.738
threshrank             5.429  0.868   6.322
rarefy_even_depth      6.232  0.040   6.332
plot_phyloseq-methods  5.828  0.004   5.970
plot_bar               5.216  0.048   5.299
plot_heatmap           5.025  0.080   5.418
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [75s/78s]
 [75s/78s] 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
  ‘/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 ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’ 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 ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	0.012	0.016	0.031
JSD	0.028	0.000	0.027
UniFrac-methods	0.048	0.000	0.047
access	0.020	0.000	0.019
assign-otu_table	0.024	0.004	0.027
assign-phy_tree	0.008	0.008	0.018
assign-sample_data	0.016	0.012	0.025
assign-sample_names	0.076	0.012	0.088
assign-tax_table	0.024	0.000	0.024
assign-taxa_are_rows	0.012	0.000	0.012
assign-taxa_names	0.056	0.004	0.061
build_tax_table	0.08	0.00	0.08
cca-rda-phyloseq-methods	0.028	0.004	0.030
data-GlobalPatterns	15.825	0.132	19.181
data-enterotype	7.429	0.040	7.548
data-esophagus	2.536	0.004	2.923
data-soilrep	18.041	0.224	19.413
distance	2.460	0.036	3.000
edgelist2clique	0.020	0.000	0.018
envHash2otu_table	0.008	0.000	0.025
estimate_richness	2.124	0.112	2.294
export_env_file	0.004	0.000	0.006
export_mothur_dist	0.008	0.000	0.008
filter_taxa	2.168	0.032	2.206
filterfun_sample	0.048	0.000	0.050
genefilter_sample-methods	0.004	0.000	0.008
get.component.classes	0.004	0.000	0.005
get_sample-methods	0.02	0.00	0.02
get_taxa-methods	0.012	0.000	0.014
get_taxa_unique	0.296	0.032	0.327
get_variable	0.220	0.020	0.242
getslots.phyloseq	0.316	0.020	0.339
import	0.004	0.000	0.005
import_RDP_otu	2.069	0.004	2.083
import_biom	0.180	0.000	0.575
import_env_file	0.004	0.000	0.004
import_mothur	0.016	0.000	0.016
import_mothur_dist	0.016	0.000	0.021
import_pyrotagger_tab	0.008	0.000	0.005
import_qiime	1.784	0.004	2.169
import_qiime_otu_tax	1.624	0.028	1.658
import_qiime_sample_data	0.048	0.004	0.052
index_reorder	0.016	0.000	0.016
intersect_taxa	0.008	0.000	0.008
make_network	6.568	0.028	7.271
merge_phyloseq	0.02	0.00	0.02
merge_phyloseq_pair-methods	0.020	0.000	0.021
merge_samples-methods	7.073	0.072	7.207
merge_taxa-methods	2.568	0.016	2.594
mt-methods	0.020	0.004	0.026
nodeplotblank	10.184	0.036	10.339
nodeplotboot	0.032	0.000	0.031
nodeplotdefault	0.008	0.000	0.007
nsamples-methods	0.012	0.000	0.009
ntaxa-methods	0.020	0.000	0.019
ordinate	0.028	0.000	0.028
otu_table-methods	0.008	0.000	0.007
parseTaxonomy-functions	0.012	0.000	0.010
phy_tree-methods	0.224	0.012	0.364
phyloseq	0.084	0.004	0.136
plot-taxa-bar	6.541	0.040	6.738
plot_bar	5.216	0.048	5.299
plot_heatmap	5.025	0.080	5.418
plot_network	4.848	0.048	4.919
plot_ordination	29.438	0.232	30.143
plot_phyloseq-methods	5.828	0.004	5.970
plot_richness	12.817	0.116	13.810
plot_scree	49.267	0.100	51.254
plot_tree	26.698	0.028	26.985
prune_samples-methods	1.364	0.048	1.410
prune_taxa-methods	0.096	0.008	0.103
psmelt	2.192	0.020	2.212
rank_names	0.048	0.004	0.053
rarefy_even_depth	6.232	0.040	6.332
read_tree	0.236	0.000	0.238
reconcile_categories	0.004	0.004	0.006
refseq-methods	0.200	0.012	0.209
rm_outlierf	0.052	0.000	0.053
sample_data-methods	0.020	0.000	0.021
sample_names-methods	0.000	0.004	0.006
sample_sums	0.052	0.004	0.057
sample_variables	0.048	0.000	0.047
show-methods	0.008	0.000	0.006
splat.phyloseq.objects	0.024	0.000	0.020
subset_ord_plot	0.008	0.000	0.005
subset_samples-methods	0.004	0.000	0.004
subset_taxa-methods	0.004	0.000	0.005
tax_glom	0.012	0.000	0.011
tax_table-methods	0.020	0.000	0.022
taxa_names-methods	0.024	0.000	0.023
taxa_sums	0.040	0.012	0.048
threshrank	5.429	0.868	6.322
threshrankfun	0.212	0.008	0.219
tip_glom-methods	0.024	0.000	0.025
topf	0.052	0.000	0.053
topk	0.052	0.000	0.050
topp	0.048	0.000	0.052
transformcounts	0.324	0.004	0.328
transpose-methods	1.608	0.596	2.265
tree.get.tags	0.008	0.000	0.009
tree.has.tags	0.036	0.000	0.034