BioC 3.1: CHECK report for phyloseq on moscato2

Package: phyloseq

Version: 1.12.2

Command: rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.12.2.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.12.2.tar.gz

StartedAt: 2015-10-09 04:47:54 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:59:11 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 677.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: phyloseq.Rcheck

Warnings: 1

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###
### Running command:
###
###   rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.12.2.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.12.2.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/phyloseq.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phyloseq/DESCRIPTION' ... OK
* this is package 'phyloseq' version '1.12.2'
* 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 whether package 'phyloseq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
':::' calls which should be '::':
  'ape:::node_depth_edgelength' 'ape:::node_height'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'JSD.pair'
* 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
JSD: 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'
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_net : vertex_layout: no visible binding for global variable
  'vertex'
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 : links_to_ggplot: no visible binding for global variable 'x'
plot_net : links_to_ggplot: no visible binding for global variable 'y'
plot_net : links_to_ggplot: no visible binding for global variable
  'xend'
plot_net : links_to_ggplot: 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 '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'
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'
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 ... WARNING
Undocumented S4 classes:
  'dist'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ...
** running examples for arch 'i386' ... [83s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_net      6.66   0.02    6.68
plot_richness 5.34   0.02    5.35
** running examples for arch 'x64' ... [93s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_net      7.33   0.00    7.58
plot_clusgap  5.48   0.07    5.54
make_network  5.27   0.02    5.28
plot_richness 5.18   0.08    5.26
plot_heatmap  5.15   0.06    5.21
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat-phyloseq.R' [84s]
 [84s] OK
** running tests for arch 'x64' ...
  Running 'testthat-phyloseq.R' [89s]
 [89s] 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: 1 WARNING, 4 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/phyloseq.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'phyloseq' ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** 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 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'phyloseq' ...
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'phyloseq' as phyloseq_1.12.2.zip
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	3.59	0.02	3.62
JSD	0	0	0
UniFrac-methods	0.12	0.00	0.13
access	0	0	0
assign-otu_table	0.02	0.00	0.01
assign-phy_tree	0.03	0.00	0.03
assign-sample_data	0.69	0.00	0.69
assign-sample_names	0.01	0.00	0.02
assign-tax_table	0	0	0
assign-taxa_are_rows	0	0	0
assign-taxa_names	0.02	0.00	0.01
build_tax_table	0.01	0.00	0.02
capscale-phyloseq-methods	0.72	0.01	0.73
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	2.09	0.00	2.09
data-enterotype	2.14	0.02	2.15
data-esophagus	0.98	0.00	0.98
data-soilrep	1.95	0.05	2.00
distance	0.30	0.02	1.56
envHash2otu_table	0	0	0
estimate_richness	0.04	0.00	0.03
export_env_file	0	0	0
export_mothur_dist	0.14	0.00	0.14
extract-methods	0	0	0
filter_taxa	0.23	0.01	0.25
filterfun_sample	0.01	0.00	0.02
gapstat_ord	2.09	0.05	2.13
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0	0	0
get_taxa-methods	0	0	0
get_taxa_unique	0.25	0.03	0.28
get_variable	0.5	0.0	0.5
getslots.phyloseq	0.22	0.00	0.22
import	0.01	0.00	0.01
import_RDP_otu	2	0	2
import_biom	0.17	0.00	0.19
import_env_file	0	0	0
import_mothur	0	0	0
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	0.74	0.00	0.73
import_qiime_otu_tax	0.57	0.01	0.59
import_qiime_sample_data	0.02	0.00	0.02
import_usearch_uc	0.03	0.00	0.09
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	3.53	0.03	3.56
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	1.01	0.03	1.05
merge_taxa-methods	0.06	0.00	0.06
microbio_me_qiime	0.61	0.00	0.68
mt-methods	4.2	0.0	4.2
nodeplotblank	0.31	0.00	0.31
nodeplotboot	0	0	0
nodeplotdefault	0	0	0
nsamples-methods	0.01	0.02	0.03
ntaxa-methods	0	0	0
ordinate	0.02	0.00	0.02
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.22	0.00	0.21
phyloseq	0.01	0.00	0.02
phyloseq_to_deseq2	1.30	0.08	1.38
plot_bar	2.88	0.03	2.91
plot_clusgap	4.78	0.03	4.81
plot_heatmap	4.38	0.00	4.38
plot_net	6.66	0.02	6.68
plot_network	2.88	0.00	2.88
plot_ordination	0.71	0.01	0.72
plot_phyloseq-methods	0.23	0.00	0.23
plot_richness	5.34	0.02	5.35
plot_scree	1.87	0.01	1.89
plot_tree	0.58	0.00	0.58
prune_samples-methods	0.56	0.00	0.56
prune_taxa-methods	0.03	0.00	0.03
psmelt	1.14	0.00	1.14
rank_names	0.02	0.00	0.01
rarefy_even_depth	0.08	0.00	0.08
read_tree	0.13	0.00	0.12
read_tree_greengenes	0.04	0.00	0.05
reconcile_categories	0	0	0
refseq-methods	0.22	0.00	0.22
rm_outlierf	0.02	0.00	0.01
sample_data-methods	0.04	0.00	0.05
sample_names-methods	0	0	0
sample_sums	0.04	0.02	0.04
sample_variables	0.03	0.00	0.04
show-methods	0	0	0
splat.phyloseq.objects	0	0	0
subset_ord_plot	0	0	0
subset_samples-methods	0	0	0
subset_taxa-methods	0	0	0
tax_glom	0	0	0
tax_table-methods	0	0	0
taxa_names-methods	0.03	0.00	0.03
taxa_sums	0.03	0.00	0.03
threshrank	3.84	0.17	4.01
threshrankfun	0.05	0.00	0.05
tip_glom	0.69	0.00	0.69
topf	0.01	0.00	0.01
topk	0.02	0.00	0.02
topp	0.01	0.00	0.01
transformcounts	0.1	0.0	0.1
transpose-methods	1.27	0.13	1.40
tree_layout	0.55	0.00	0.55

name	user	system	elapsed
DPCoA	4.35	0.05	4.40
JSD	0	0	0
UniFrac-methods	0.13	0.00	0.14
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.05	0.00	0.05
assign-sample_data	0.50	0.02	0.51
assign-sample_names	0	0	0
assign-tax_table	0.01	0.00	0.02
assign-taxa_are_rows	0	0	0
assign-taxa_names	0	0	0
build_tax_table	0	0	0
capscale-phyloseq-methods	0.81	0.00	0.81
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	1.81	0.00	1.81
data-enterotype	2.90	0.01	2.91
data-esophagus	0.91	0.00	0.91
data-soilrep	2.29	0.05	2.34
distance	0.22	0.03	0.25
envHash2otu_table	0	0	0
estimate_richness	0.03	0.00	0.03
export_env_file	0	0	0
export_mothur_dist	0.09	0.00	0.09
extract-methods	0	0	0
filter_taxa	0.63	0.02	0.64
filterfun_sample	0.03	0.00	0.03
gapstat_ord	2.53	0.03	2.56
genefilter_sample-methods	0.01	0.00	0.02
get.component.classes	0	0	0
get_sample-methods	0	0	0
get_taxa-methods	0.02	0.00	0.01
get_taxa_unique	0.25	0.01	0.27
get_variable	0.17	0.02	0.19
getslots.phyloseq	0.25	0.00	0.25
import	0	0	0
import_RDP_otu	1.36	0.00	1.36
import_biom	0.19	0.00	1.54
import_env_file	0	0	0
import_mothur	0	0	0
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	0.82	0.00	0.83
import_qiime_otu_tax	0.74	0.03	0.76
import_qiime_sample_data	0.01	0.00	0.02
import_usearch_uc	0.02	0.00	0.05
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	5.27	0.02	5.28
merge_phyloseq	0.02	0.00	0.02
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	1.59	0.06	1.65
merge_taxa-methods	0.06	0.01	0.08
microbio_me_qiime	0.73	0.02	1.39
mt-methods	2.17	0.01	2.18
nodeplotblank	0.39	0.00	0.39
nodeplotboot	0	0	0
nodeplotdefault	0	0	0
nsamples-methods	0.05	0.00	0.05
ntaxa-methods	0	0	0
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.3	0.0	0.3
phyloseq	0.05	0.00	0.05
phyloseq_to_deseq2	0.96	0.08	1.04
plot_bar	2.81	0.03	2.84
plot_clusgap	5.48	0.07	5.54
plot_heatmap	5.15	0.06	5.21
plot_net	7.33	0.00	7.58
plot_network	3.91	0.00	3.92
plot_ordination	0.77	0.01	0.78
plot_phyloseq-methods	0.28	0.00	0.28
plot_richness	5.18	0.08	5.26
plot_scree	2.05	0.00	2.05
plot_tree	0.67	0.00	0.67
prune_samples-methods	0.71	0.00	0.70
prune_taxa-methods	0.03	0.00	0.04
psmelt	0.93	0.02	0.95
rank_names	0.03	0.00	0.03
rarefy_even_depth	0.11	0.00	0.11
read_tree	0.18	0.00	0.17
read_tree_greengenes	0.06	0.01	0.08
reconcile_categories	0	0	0
refseq-methods	0.25	0.02	0.26
rm_outlierf	0.01	0.00	0.02
sample_data-methods	0.08	0.00	0.08
sample_names-methods	0.01	0.00	0.02
sample_sums	0.05	0.00	0.04
sample_variables	0.05	0.00	0.05
show-methods	0	0	0
splat.phyloseq.objects	0	0	0
subset_ord_plot	0	0	0
subset_samples-methods	0	0	0
subset_taxa-methods	0	0	0
tax_glom	0	0	0
tax_table-methods	0	0	0
taxa_names-methods	0.05	0.00	0.04
taxa_sums	0.05	0.00	0.05
threshrank	3.73	0.39	4.11
threshrankfun	0.11	0.00	0.11
tip_glom	1.31	0.00	1.31
topf	0.05	0.00	0.05
topk	0.03	0.00	0.03
topp	0.01	0.00	0.02
transformcounts	0.19	0.00	0.19
transpose-methods	0.88	0.31	1.20
tree_layout	0.77	0.02	0.78