BioC 3.0: CHECK report for phyloseq on moscato1

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###
### Running command:
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###   rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.10.0.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.10.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/phyloseq.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phyloseq/DESCRIPTION' ... OK
* this is package 'phyloseq' version '1.10.0'
* 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 ... 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
* 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 ... 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 ...
** running examples for arch 'i386' ... [94s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_net      7.89   0.02    7.91
plot_richness 6.27   0.05    6.32
plot_clusgap  5.13   0.03    5.18
** running examples for arch 'x64' ... [98s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_net      7.24   0.00    7.56
plot_clusgap  6.24   0.04    6.29
plot_richness 6.10   0.05    6.70
plot_heatmap  5.60   0.05    5.65
make_network  5.02   0.03    5.48
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat-phyloseq.R' [100s]
 [100s] OK
** running tests for arch 'x64' ...
  Running 'testthat-phyloseq.R' [117s]
 [118s] 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-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 '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.

install for x64

* installing *source* package 'phyloseq' ...
** 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.
* MD5 sums
packaged installation of 'phyloseq' as phyloseq_1.10.0.zip
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	3.65	0.03	3.71
JSD	0	0	0
UniFrac-methods	0.14	0.00	0.15
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.03	0.00	0.04
assign-sample_data	0.69	0.00	0.68
assign-sample_names	0.02	0.00	0.02
assign-tax_table	0	0	0
assign-taxa_are_rows	0	0	0
assign-taxa_names	0.01	0.00	0.01
build_tax_table	0.02	0.00	0.02
capscale-phyloseq-methods	1.11	0.02	1.12
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	2.07	0.05	2.12
data-enterotype	2.53	0.01	2.55
data-esophagus	0.78	0.00	0.78
data-soilrep	2.57	0.02	2.59
distance	0.49	0.08	2.31
envHash2otu_table	0	0	0
estimate_richness	0.03	0.00	0.03
export_env_file	0	0	0
export_mothur_dist	0.06	0.00	0.06
extract-methods	0.01	0.00	0.01
filter_taxa	0.43	0.01	0.86
filterfun_sample	0.02	0.00	0.01
gapstat_ord	2.2	0.0	2.2
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0.01	0.00	0.02
get_taxa-methods	0	0	0
get_taxa_unique	0.53	0.00	0.53
get_variable	0.22	0.00	0.22
getslots.phyloseq	0.20	0.02	0.22
import	0	0	0
import_RDP_otu	2.05	0.00	2.04
import_biom	0.26	0.00	0.36
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	0.64	0.01	0.65
import_qiime_otu_tax	0.42	0.00	0.42
import_qiime_sample_data	0.02	0.00	0.01
import_usearch_uc	0.02	0.00	0.05
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	3.98	0.02	4.00
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	1.16	0.04	1.20
merge_taxa-methods	0.06	0.00	0.07
microbio_me_qiime	1.00	0.02	1.22
mt-methods	4.36	0.00	4.37
nodeplotblank	0.36	0.02	0.37
nodeplotboot	0	0	0
nodeplotdefault	0	0	0
nsamples-methods	0.03	0.00	0.03
ntaxa-methods	0	0	0
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.20	0.01	0.22
phyloseq	0.02	0.00	0.01
phyloseq_to_deseq2	1.42	0.02	1.44
plot_bar	2.57	0.00	2.57
plot_clusgap	5.13	0.03	5.18
plot_heatmap	4.86	0.01	4.87
plot_net	7.89	0.02	7.91
plot_network	3.20	0.00	3.34
plot_ordination	0.79	0.00	0.79
plot_phyloseq-methods	0.28	0.00	0.28
plot_richness	6.27	0.05	6.32
plot_scree	1.81	0.01	1.83
plot_tree	0.71	0.02	0.71
prune_samples-methods	0.59	0.03	0.63
prune_taxa-methods	0.03	0.00	0.03
psmelt	1.26	0.01	1.28
rank_names	0.02	0.00	0.02
rarefy_even_depth	0.06	0.00	0.07
read_tree	0.12	0.00	0.13
read_tree_greengenes	0.05	0.00	0.04
reconcile_categories	0	0	0
refseq-methods	0.22	0.00	0.22
rm_outlierf	0.01	0.00	0.02
sample_data-methods	0.07	0.00	0.06
sample_names-methods	0	0	0
sample_sums	0.04	0.00	0.05
sample_variables	0.02	0.00	0.01
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	0.04	0.00	0.03
taxa_sums	0.03	0.00	0.03
threshrank	3.37	0.36	3.90
threshrankfun	0.04	0.00	0.05
tip_glom	0.78	0.00	0.79
topf	0.02	0.00	0.02
topk	0.01	0.00	0.01
topp	0.02	0.00	0.02
transformcounts	0.09	0.00	0.09
transpose-methods	1.27	0.17	1.44
tree_layout	0.62	0.00	0.62

name	user	system	elapsed
DPCoA	3.59	0.02	3.60
JSD	0	0	0
UniFrac-methods	0.14	0.01	0.16
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.05	0.00	0.05
assign-sample_data	0.85	0.00	0.86
assign-sample_names	0.02	0.00	0.01
assign-tax_table	0	0	0
assign-taxa_are_rows	0.00	0.02	0.02
assign-taxa_names	0	0	0
build_tax_table	0.02	0.00	0.01
capscale-phyloseq-methods	1.35	0.06	1.42
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	2.27	0.03	2.29
data-enterotype	2.82	0.00	2.83
data-esophagus	0.87	0.00	0.87
data-soilrep	1.89	0.00	1.89
distance	0.50	0.06	0.64
envHash2otu_table	0	0	0
estimate_richness	0.01	0.02	0.03
export_env_file	0	0	0
export_mothur_dist	0.05	0.00	0.04
extract-methods	0.01	0.00	0.02
filter_taxa	0.59	0.00	0.60
filterfun_sample	0.03	0.00	0.03
gapstat_ord	2.36	0.03	2.38
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0.01	0.00	0.02
get_taxa-methods	0	0	0
get_taxa_unique	0.25	0.00	0.25
get_variable	0.17	0.02	0.19
getslots.phyloseq	0.19	0.00	0.18
import	0	0	0
import_RDP_otu	1.74	0.00	1.75
import_biom	0.66	0.00	0.92
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	0.64	0.02	0.66
import_qiime_otu_tax	0.64	0.00	0.64
import_qiime_sample_data	0.01	0.00	0.01
import_usearch_uc	0.02	0.01	0.03
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	5.02	0.03	5.48
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	2.12	0.05	2.16
merge_taxa-methods	0.09	0.00	0.09
microbio_me_qiime	0.72	0.03	2.06
mt-methods	1.93	0.00	1.97
nodeplotblank	0.42	0.00	0.42
nodeplotboot	0	0	0
nodeplotdefault	0	0	0
nsamples-methods	0.03	0.00	0.03
ntaxa-methods	0	0	0
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.19	0.00	0.18
phyloseq	0.03	0.00	0.03
phyloseq_to_deseq2	0.76	0.10	0.86
plot_bar	2.90	0.03	2.93
plot_clusgap	6.24	0.04	6.29
plot_heatmap	5.60	0.05	5.65
plot_net	7.24	0.00	7.56
plot_network	4.25	0.00	4.24
plot_ordination	0.93	0.00	0.94
plot_phyloseq-methods	0.33	0.00	0.32
plot_richness	6.10	0.05	6.70
plot_scree	2.09	0.00	2.09
plot_tree	0.80	0.00	0.79
prune_samples-methods	0.75	0.01	0.77
prune_taxa-methods	0.04	0.00	0.04
psmelt	1.48	0.00	1.49
rank_names	0.04	0.00	0.03
rarefy_even_depth	0.07	0.00	0.07
read_tree	0.14	0.00	0.15
read_tree_greengenes	0.05	0.00	0.04
reconcile_categories	0	0	0
refseq-methods	0.19	0.00	0.19
rm_outlierf	0.03	0.00	0.03
sample_data-methods	0.05	0.00	0.05
sample_names-methods	0.01	0.00	0.01
sample_sums	0.02	0.02	0.03
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	0.02	0.00	0.02
taxa_sums	0.03	0.00	0.03
threshrank	2.95	0.28	3.23
threshrankfun	0.04	0.00	0.05
tip_glom	0.86	0.00	0.88
topf	0.01	0.00	0.01
topk	0.01	0.00	0.02
topp	0.02	0.02	0.03
transformcounts	0.09	0.00	0.09
transpose-methods	0.81	0.15	0.97
tree_layout	0.72	0.00	0.71

BioC 3.0: CHECK report for phyloseq on moscato1

Summary

Command output