BioC 2.13: CHECK report for phyloseq on perceval

Package: phyloseq

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phyloseq_1.6.1.tar.gz

StartedAt: 2014-04-05 03:21:00 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:35:06 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 846.0 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/phyloseq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.6.1’
* 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 ... [36s/39s] 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘ade4’ ‘methods’ ‘picante’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘internal2tips.self’ ‘JSD.pair’ ‘ufnum’ ‘UFwi’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fastUniFrac: no visible binding for global variable ‘i’
import_qiime_otu_tax: no visible binding for global variable ‘i’
JSD: 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’
plot_clusgap: no visible binding for global variable ‘k’
plot_clusgap: no visible binding for global variable ‘gap’
plot_clusgap: no visible binding for global variable ‘SE.sim’
plot_heatmap: no visible binding for global variable ‘Sample’
plot_heatmap: no visible binding for global variable ‘OTU’
plot_heatmap: no visible binding for global variable ‘Abundance’
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_scree: no visible binding for global variable ‘eigenvalue’
plot_tree: no visible binding for global variable ‘type’
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 ‘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’
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 ... NOTE
  Note: the specification for S3 class "AsIs" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO': not turning on duplicate class definitions for this class.
  Note: the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO': not turning on duplicate class definitions for this class.
  Note: the specification for S3 class "file" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO': not turning on duplicate class definitions for this class.
  Note: the specification for S3 class "pipe" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO': not turning on duplicate class definitions for this class.
  Note: the specification for S3 class "textConnection" in package 'BiocGenerics' seems equivalent to one from package 'RJSONIO': not turning on duplicate class definitions for this class.
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [381s/392s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
rarefy_even_depth   137.853 26.161 166.595
plot_scree           31.769  2.983  36.266
plot_ordination      18.681  3.331  22.318
plot_tree            21.221  0.607  22.921
data-GlobalPatterns  12.227  1.573  14.968
plot_clusgap         10.644  0.468  11.306
gapstat_ord           8.323  0.475   8.928
nodeplotblank         8.293  0.267   8.955
estimate_richness     6.704  1.209   8.324
threshrank            4.234  1.906   6.236
plot_richness         5.073  1.044   6.331
data-enterotype       5.517  0.225   6.146
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [76s/77s]
 [76s/77s] OK
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/phyloseq.Rcheck/00check.log’
for details.

* installing *source* package ‘phyloseq’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “file” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “pipe” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “textConnection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “file” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “pipe” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “textConnection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	0.007	0.004	0.011
JSD	0.008	0.003	0.014
UniFrac-methods	0.023	0.012	0.037
access	0.011	0.004	0.016
assign-otu_table	0.013	0.004	0.017
assign-phy_tree	0.011	0.007	0.018
assign-sample_data	0.014	0.006	0.022
assign-sample_names	0.033	0.013	0.065
assign-tax_table	0.015	0.006	0.021
assign-taxa_are_rows	0.006	0.003	0.010
assign-taxa_names	0.033	0.013	0.047
build_tax_table	0.064	0.007	0.075
cca-rda-phyloseq-methods	0.013	0.005	0.022
data-GlobalPatterns	12.227	1.573	14.968
data-enterotype	5.517	0.225	6.146
data-esophagus	2.146	0.054	2.299
data-soilrep	3.055	0.355	3.571
distance	1.762	0.045	2.356
edgelist2clique	0.002	0.004	0.005
envHash2otu_table	0.003	0.005	0.009
estimate_richness	6.704	1.209	8.324
export_env_file	0.002	0.003	0.005
export_mothur_dist	0.002	0.003	0.005
extract-methods	0.022	0.010	0.052
filter_taxa	1.566	0.121	1.775
filterfun_sample	0.030	0.006	0.044
gapstat_ord	8.323	0.475	8.928
genefilter_sample-methods	0.003	0.005	0.008
get.component.classes	0.002	0.004	0.005
get_sample-methods	0.006	0.007	0.013
get_taxa-methods	0.006	0.007	0.014
get_taxa_unique	0.290	0.048	0.345
get_variable	0.234	0.028	0.264
getslots.phyloseq	0.244	0.053	0.306
import	0.002	0.002	0.004
import_RDP_otu	1.514	0.086	1.626
import_biom	0.253	0.051	0.315
import_env_file	0.001	0.003	0.005
import_mothur	0.014	0.013	0.026
import_mothur_dist	0.002	0.004	0.006
import_pyrotagger_tab	0.001	0.004	0.005
import_qiime	1.711	0.040	1.826
import_qiime_otu_tax	1.530	0.085	1.726
import_qiime_sample_data	0.034	0.006	0.041
index_reorder	0.002	0.003	0.006
intersect_taxa	0.009	0.009	0.018
make_network	4.688	0.202	4.995
merge_phyloseq	0.003	0.006	0.009
merge_phyloseq_pair-methods	0.004	0.008	0.013
merge_samples-methods	3.947	0.568	4.626
merge_taxa-methods	1.969	0.074	2.134
microbio_me_qiime	1.147	0.125	1.461
mt-methods	0.018	0.008	0.027
nodeplotblank	8.293	0.267	8.955
nodeplotboot	0.004	0.004	0.008
nodeplotdefault	0.002	0.003	0.005
nsamples-methods	0.009	0.008	0.016
ntaxa-methods	0.002	0.004	0.007
ordinate	0.011	0.014	0.025
otu_table-methods	0.002	0.004	0.005
parseTaxonomy-functions	0.010	0.010	0.021
phy_tree-methods	0.202	0.026	0.227
phyloseq	0.035	0.017	0.052
plot_bar	3.901	0.330	4.280
plot_clusgap	10.644	0.468	11.306
plot_heatmap	2.841	0.347	3.245
plot_network	3.985	0.112	4.151
plot_ordination	18.681	3.331	22.318
plot_phyloseq-methods	4.195	0.128	4.362
plot_richness	5.073	1.044	6.331
plot_scree	31.769	2.983	36.266
plot_tree	21.221	0.607	22.921
prune_samples-methods	1.086	0.348	1.464
prune_taxa-methods	0.081	0.028	0.110
psmelt	2.301	0.331	2.679
rank_names	0.029	0.012	0.040
rarefy_even_depth	137.853	26.161	166.595
read_tree	0.190	0.009	0.199
read_tree_greengenes	0.076	0.014	0.108
reconcile_categories	0.016	0.009	0.025
refseq-methods	0.210	0.028	0.244
rm_outlierf	0.047	0.018	0.066
sample_data-methods	0.015	0.009	0.024
sample_names-methods	0.002	0.005	0.007
sample_sums	0.051	0.024	0.076
sample_variables	0.027	0.011	0.040
show-methods	0.002	0.004	0.006
splat.phyloseq.objects	0.002	0.004	0.006
subset_ord_plot	0.002	0.003	0.005
subset_samples-methods	0.001	0.003	0.006
subset_taxa-methods	0.002	0.002	0.004
tax_glom	0.003	0.006	0.009
tax_table-methods	0.003	0.005	0.007
taxa_names-methods	0.020	0.012	0.033
taxa_sums	0.049	0.033	0.085
threshrank	4.234	1.906	6.236
threshrankfun	0.096	0.046	0.142
tip_glom-methods	0.004	0.008	0.013
topf	0.038	0.015	0.054
topk	0.026	0.007	0.034
topp	0.025	0.008	0.033
transformcounts	0.169	0.054	0.225
transpose-methods	1.201	1.091	2.334
tree.get.tags	0.003	0.004	0.007
tree.has.tags	0.013	0.014	0.028