BioC 2.14: CHECK report for phyloseq on petty

Package: phyloseq

Version: 1.8.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phyloseq_1.8.2.tar.gz

StartedAt: 2014-10-07 23:27:25 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:41:47 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 861.6 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phyloseq_1.8.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/phyloseq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.8.2’
* 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 ... [52s/53s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
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 global function definition for ‘:=’
import_qiime_otu_tax: no visible binding for global variable ‘Consensus
  Lineage’
import_qiime_otu_tax: no visible binding for global variable ‘#OTU ID’
import_usearch_uc: no visible global function definition for ‘:=’
import_usearch_uc: no visible binding for global variable ‘read’
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 ... [175s/178s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
nodeplotblank         11.778  0.098  12.141
plot_heatmap          11.251  0.493  11.807
plot_clusgap           9.947  0.258  10.346
plot_richness          8.249  0.663   9.249
make_network           8.531  0.158   8.753
threshrank             5.484  1.655   7.161
DPCoA                  6.376  0.315   6.736
plot_phyloseq-methods  5.937  0.050   6.368
plot_tree              5.839  0.045   5.901
plot_network           5.611  0.071   5.694
gapstat_ord            5.431  0.097   5.553
plot_bar               4.758  0.214   5.071
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [138s/140s]
 [139s/141s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	6.376	0.315	6.736
JSD	0.001	0.000	0.002
UniFrac-methods	4.776	0.048	4.866
access	0.001	0.000	0.001
assign-otu_table	0.001	0.001	0.001
assign-phy_tree	0.080	0.005	0.093
assign-sample_data	0.794	0.026	0.830
assign-sample_names	0.021	0.007	0.028
assign-tax_table	0.002	0.000	0.002
assign-taxa_are_rows	0.005	0.006	0.012
assign-taxa_names	0.018	0.007	0.025
build_tax_table	0.029	0.001	0.030
capscale-phyloseq-methods	2.332	0.113	2.449
cca-rda-phyloseq-methods	0.001	0.000	0.001
data-GlobalPatterns	4.111	0.117	4.251
data-enterotype	4.533	0.046	4.598
data-esophagus	2.962	0.026	3.010
data-soilrep	3.617	0.247	3.896
distance	3.370	0.108	4.394
envHash2otu_table	0.001	0.000	0.002
estimate_richness	0.051	0.006	0.057
export_env_file	0.001	0.000	0.001
export_mothur_dist	0.167	0.034	0.201
extract-methods	0.022	0.004	0.026
filter_taxa	0.447	0.033	0.481
filterfun_sample	0.050	0.001	0.051
gapstat_ord	5.431	0.097	5.553
genefilter_sample-methods	0.002	0.000	0.002
get.component.classes	0.001	0.000	0.001
get_sample-methods	0.007	0.006	0.014
get_taxa-methods	0.007	0.006	0.013
get_taxa_unique	0.445	0.045	0.490
get_variable	0.324	0.016	0.340
getslots.phyloseq	0.340	0.026	0.366
import	0.001	0.000	0.001
import_RDP_otu	2.679	0.060	2.741
import_biom	0.366	0.004	0.383
import_env_file	0.001	0.000	0.001
import_mothur	0.002	0.000	0.002
import_mothur_dist	0.001	0.000	0.002
import_pyrotagger_tab	0.001	0.000	0.001
import_qiime	1.101	0.007	1.109
import_qiime_otu_tax	0.933	0.084	1.019
import_qiime_sample_data	0.051	0.003	0.055
import_usearch_uc	0.038	0.008	0.047
index_reorder	0.001	0.000	0.001
intersect_taxa	0.001	0.000	0.001
make_network	8.531	0.158	8.753
merge_phyloseq	0.001	0.001	0.002
merge_phyloseq_pair-methods	0.002	0.000	0.002
merge_samples-methods	2.123	0.337	2.464
merge_taxa-methods	0.110	0.005	0.114
microbio_me_qiime	1.262	0.041	1.397
mt-methods	0.002	0.000	0.002
nodeplotblank	11.778	0.098	12.141
nodeplotboot	0.004	0.001	0.004
nodeplotdefault	0.001	0.000	0.002
nsamples-methods	0.040	0.003	0.045
ntaxa-methods	0.005	0.004	0.009
ordinate	0.000	0.000	0.001
otu_table-methods	0.000	0.001	0.001
parseTaxonomy-functions	0.003	0.000	0.004
phy_tree-methods	0.338	0.024	0.363
phyloseq	0.049	0.010	0.059
phyloseq_to_deseq2	0.731	0.109	0.843
plot_bar	4.758	0.214	5.071
plot_clusgap	9.947	0.258	10.346
plot_heatmap	11.251	0.493	11.807
plot_network	5.611	0.071	5.694
plot_ordination	1.618	0.133	1.755
plot_phyloseq-methods	5.937	0.050	6.368
plot_richness	8.249	0.663	9.249
plot_scree	3.536	0.126	3.968
plot_tree	5.839	0.045	5.901
prune_samples-methods	1.300	0.181	1.486
prune_taxa-methods	0.066	0.008	0.075
psmelt	2.451	0.225	2.688
rank_names	0.042	0.013	0.054
rarefy_even_depth	0.186	0.008	0.194
read_tree	0.280	0.010	0.291
read_tree_greengenes	0.082	0.002	0.083
reconcile_categories	0.001	0.000	0.001
refseq-methods	0.331	0.025	0.359
rm_outlierf	0.038	0.000	0.039
sample_data-methods	0.091	0.017	0.109
sample_names-methods	0.005	0.012	0.017
sample_sums	0.051	0.032	0.084
sample_variables	0.038	0.016	0.053
show-methods	0.001	0.000	0.001
splat.phyloseq.objects	0.001	0.000	0.001
subset_ord_plot	0.001	0.000	0.001
subset_samples-methods	0.001	0.000	0.001
subset_taxa-methods	0.001	0.000	0.001
tax_glom	0.001	0.001	0.002
tax_table-methods	0.001	0.000	0.001
taxa_names-methods	0.049	0.015	0.063
taxa_sums	0.062	0.037	0.100
threshrank	5.484	1.655	7.161
threshrankfun	0.107	0.009	0.116
tip_glom	3.641	0.020	3.671
topf	0.038	0.001	0.039
topk	0.038	0.001	0.038
topp	0.042	0.001	0.042
transformcounts	0.218	0.009	0.227
transpose-methods	2.106	0.985	3.096
tree.get.tags	0.001	0.000	0.001
tree.has.tags	0.001	0.000	0.001