BioC 3.4: CHECK report for phyloseq on morelia

Package: phyloseq

Version: 1.19.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings phyloseq_1.19.1.tar.gz

StartedAt: 2017-04-15 06:12:28 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 06:17:31 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 302.7 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 phyloseq_1.19.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/phyloseq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.19.1’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.2Mb
* 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 dependencies in R code ... NOTE
':::' calls which should be '::':
  ‘ape:::node_depth_edgelength’ ‘ape:::node_height’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .C(ape:::node_depth_edgelength, ..., PACKAGE = "ape")
  .C(ape:::node_height, ..., PACKAGE = "ape")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
DPCoA: no visible global function definition for ‘as.dist’
chunkReOrder: no visible global function definition for ‘tail’
chunkReOrder: no visible global function definition for ‘head’
export_env_file: no visible global function definition for
  ‘write.table’
export_mothur_dist: no visible global function definition for ‘as.dist’
export_mothur_dist: no visible global function definition for
  ‘write.table’
fastUniFrac: no visible global function definition for ‘combn’
fastUniFrac: no visible global function definition for ‘as.dist’
import_RDP_otu: no visible global function definition for ‘read.table’
import_env_file: no visible global function definition for ‘read.table’
import_mothur_constaxonomy: no visible global function definition for
  ‘read.table’
import_mothur_dist: no visible global function definition for ‘as.dist’
import_mothur_groups: no visible global function definition for
  ‘read.table’
import_mothur_shared: no visible global function definition for
  ‘read.table’
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_qiime_sample_data: no visible global function definition for
  ‘read.table’
import_uparse: no visible global function definition for ‘:=’
import_uparse: no visible binding for global variable ‘count’
import_uparse: no visible binding for global variable ‘queryString’
import_uparse: no visible binding for global variable ‘queryID’
import_uparse: no visible binding for global variable ‘Classification’
import_uparse: no visible global function definition for
  ‘dcast.data.table’
import_uparse: no visible binding for global variable ‘OTULabel’
import_usearch_uc: no visible global function definition for ‘:=’
import_usearch_uc: no visible binding for global variable ‘read’
microbio_me_qiime: no visible global function definition for
  ‘download.file’
microbio_me_qiime: no visible global function definition for ‘unzip’
microbio_me_qiime: no visible global function definition for ‘untar’
nodeplotboot : <anonymous>: no visible global function definition for
  ‘complete.cases’
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’
ordinate: no visible global function definition for ‘as.formula’
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 global function definition for
  ‘capture.output’
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_net : vertex_layout: no visible binding for global variable ‘x’
plot_net : link_layout: no visible binding for global variable ‘x’
plot_net : link_layout: no visible binding for global variable ‘y’
plot_net: no visible binding for global variable ‘x’
plot_net: no visible binding for global variable ‘y’
plot_net: no visible binding for global variable ‘xend’
plot_net: no visible binding for global variable ‘yend’
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 ‘axis’
plot_scree: no visible binding for global variable ‘eigenvalue’
plot_tree: no visible binding for global variable ‘xleft’
plot_tree: no visible binding for global variable ‘xright’
plot_tree: no visible binding for global variable ‘y’
plot_tree: no visible binding for global variable ‘x’
plot_tree: no visible binding for global variable ‘vmin’
plot_tree: no visible binding for global variable ‘vmax’
plot_tree: no visible binding for global variable ‘OTU’
plot_tree: no visible binding for global variable ‘label’
plot_tree: no visible binding for global variable ‘Abundance’
plot_tree: no visible binding for global variable ‘Sample’
plot_tree: no visible global function definition for ‘:=’
plot_tree: no visible binding for global variable ‘h.adj.index’
plot_tree: no visible binding for global variable ‘xdodge’
plot_tree: no visible binding for global variable ‘xfartiplab’
plot_tree: no visible binding for global variable ‘.SD’
rp.joint.fill: no visible global function definition for ‘relevel’
tip_glom: no visible global function definition for ‘as.dist’
tip_glom: no visible global function definition for ‘cutree’
tip_glom: no visible global function definition for ‘as.hclust’
tree_layout: no visible global function definition for ‘:=’
tree_layout: no visible binding for global variable ‘OTU’
tree_layout: no visible binding for global variable ‘V2’
tree_layout: no visible binding for global variable ‘xleft’
tree_layout: no visible binding for global variable ‘V1’
tree_layout: no visible binding for global variable ‘xright’
tree_layout: no visible binding for global variable ‘y’
tree_layout: no visible binding for global variable ‘x’
tree_layout: no visible binding for global variable ‘label’
tree_layout: no visible global function definition for ‘J’
tree_layout: no visible binding for global variable ‘vmin’
tree_layout: no visible binding for global variable ‘vmax’
JSD,matrix: no visible global function definition for ‘combn’
JSD,matrix: no visible binding for global variable ‘i’
JSD,matrix: no visible global function definition for ‘as.dist’
capscale.phyloseq,phyloseq-formula-character: no visible global
  function definition for ‘as.formula’
capscale.phyloseq,phyloseq-formula-dist: no visible global function
  definition for ‘as.formula’
cca.phyloseq,phyloseq-formula: no visible global function definition
  for ‘as.formula’
distance,phyloseq-character: no visible global function definition for
  ‘as.dist’
merge_phyloseq_pair,sample_data-sample_data : <anonymous>: no visible
  binding for global variable ‘X0’
merge_samples,sample_data: no visible global function definition for
  ‘aggregate’
plot_phyloseq,phyloseq: no visible binding for global variable
  ‘esophagus’
Undefined global functions or variables:
  #OTU ID .SD := Abundance Classification Consensus Lineage J OTU
  OTULabel SE.sim Sample V1 V2 X0 aggregate as.dist as.formula
  as.hclust axis capture.output combn complete.cases count cutree
  dcast.data.table download.file eigenvalue esophagus gap h.adj.index
  head i k label queryID queryString read read.table relevel se tail
  untar unzip value vmax vmin write.table x xdodge xend xfartiplab
  xleft xright y yend
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "aggregate", "as.dist", "as.formula", "as.hclust",
             "complete.cases", "cutree", "relevel")
  importFrom("utils", "capture.output", "combn", "download.file", "head",
             "read.table", "tail", "untar", "unzip", "write.table")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot_richness 4.730  0.392   5.128
plot_heatmap  4.751  0.246   5.001
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/phyloseq.Rcheck/00check.log’
for details.

* installing *source* package ‘phyloseq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	2.853	0.137	3.127
JSD	0.000	0.000	0.001
UniFrac-methods	0.098	0.004	0.101
access	0.001	0.000	0.001
assign-otu_table	0.000	0.000	0.001
assign-phy_tree	0.031	0.002	0.032
assign-sample_data	0.309	0.015	0.325
assign-sample_names	0.006	0.005	0.011
assign-tax_table	0	0	0
assign-taxa_are_rows	0.002	0.005	0.007
assign-taxa_names	0.005	0.005	0.011
build_tax_table	0.009	0.000	0.009
capscale-phyloseq-methods	0.742	0.063	0.884
cca-rda-phyloseq-methods	0.001	0.000	0.001
chunkReOrder	0	0	0
data-GlobalPatterns	1.148	0.063	1.547
data-enterotype	1.710	0.020	1.732
data-esophagus	0.752	0.011	0.763
data-soilrep	1.674	0.106	1.799
distance	0.206	0.032	1.420
distanceMethodList	0.001	0.000	0.000
envHash2otu_table	0.001	0.001	0.001
estimate_richness	0.031	0.005	0.036
export_env_file	0.001	0.000	0.001
export_mothur_dist	0.096	0.020	0.116
extract-methods	0.009	0.004	0.013
filter_taxa	1.121	0.024	1.146
filterfun_sample	0.024	0.000	0.024
gapstat_ord	2.095	0.065	2.167
genefilter_sample-methods	0.001	0.000	0.001
get.component.classes	0	0	0
get_sample-methods	0.004	0.007	0.010
get_taxa-methods	0.004	0.006	0.010
get_taxa_unique	0.227	0.024	0.252
get_variable	0.220	0.010	0.231
getslots.phyloseq	0.216	0.018	0.235
import	0.001	0.000	0.001
import_RDP_otu	1.031	0.037	1.070
import_biom	0.248	0.010	0.260
import_env_file	0.001	0.000	0.001
import_mothur	0.001	0.000	0.001
import_mothur_dist	0.001	0.000	0.000
import_pyrotagger_tab	0.001	0.000	0.001
import_qiime	0.653	0.003	0.657
import_qiime_otu_tax	0.557	0.042	0.599
import_qiime_sample_data	0.023	0.001	0.024
import_uparse	0.000	0.000	0.001
import_usearch_uc	0.019	0.004	0.023
index_reorder	0	0	0
intersect_taxa	0.001	0.000	0.001
make_network	2.524	0.075	2.602
merge_phyloseq	0.001	0.001	0.001
merge_phyloseq_pair-methods	0.001	0.000	0.001
merge_samples-methods	0.690	0.133	0.823
merge_taxa-methods	0.051	0.001	0.052
microbio_me_qiime	0.639	0.015	0.690
mt-methods	1.199	0.019	1.219
nodeplotblank	0.334	0.003	0.372
nodeplotboot	0.002	0.000	0.003
nodeplotdefault	0.001	0.000	0.002
nsamples-methods	0.023	0.002	0.026
ntaxa-methods	0.003	0.001	0.004
ordinate	0	0	0
otu_table-methods	0.000	0.000	0.001
parseTaxonomy-functions	0.002	0.001	0.001
phy_tree-methods	0.201	0.010	0.212
phyloseq	0.032	0.005	0.037
phyloseq_to_deseq2	2.235	0.100	2.338
phyloseq_to_metagenomeSeq	1.008	0.084	1.091
plot_bar	2.564	0.116	2.681
plot_clusgap	3.608	0.139	3.772
plot_heatmap	4.751	0.246	5.001
plot_net	3.393	0.131	3.542
plot_network	2.206	0.029	2.239
plot_ordination	0.633	0.060	0.713
plot_phyloseq-methods	0.290	0.007	0.297
plot_richness	4.730	0.392	5.128
plot_scree	1.876	0.072	1.951
plot_tree	0.579	0.009	0.588
prune_samples-methods	0.401	0.072	0.472
prune_taxa-methods	0.029	0.004	0.033
psmelt	1.208	0.094	1.303
rank_names	0.026	0.008	0.034
rarefy_even_depth	0.077	0.007	0.085
read_tree	0.093	0.001	0.095
read_tree_greengenes	0.037	0.002	0.040
reconcile_categories	0.001	0.000	0.000
refseq-methods	0.191	0.011	0.203
rm_outlierf	0.032	0.000	0.033
sample_data-methods	0.056	0.009	0.066
sample_names-methods	0.003	0.006	0.009
sample_sums	0.034	0.015	0.049
sample_variables	0.028	0.007	0.035
show-methods	0.001	0.000	0.000
splat.phyloseq.objects	0	0	0
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	0.000	0.001
tax_table-methods	0.001	0.000	0.001
taxa_names-methods	0.026	0.008	0.033
taxa_sums	0.028	0.013	0.041
threshrank	2.401	0.853	3.255
threshrankfun	0.043	0.004	0.047
tip_glom	0.620	0.007	0.628
topf	0.012	0.000	0.012
topk	0.012	0.001	0.012
topp	0.012	0.000	0.012
transformcounts	0.079	0.004	0.083
transpose-methods	0.794	0.492	1.285
tree_layout	0.719	0.011	0.772