BioC 3.2: CHECK report for phyloseq on moscato1

Package: phyloseq

Version: 1.13.2

Command: rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.13.2.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.13.2.tar.gz

StartedAt: 2015-08-20 08:36:01 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 08:50:02 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 841.2 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 && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.13.2.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.13.2.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-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 '1.13.2'
* 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' ... [105s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_richness 7.74   0.03    7.77
plot_net      7.56   0.02    7.58
plot_clusgap  6.37   0.04    6.68
plot_heatmap  5.46   0.03    5.50
mt-methods    5.35   0.00    5.36
make_network  5.04   0.03    5.07
** running examples for arch 'x64' ... [101s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_richness 7.53   0.00    7.65
plot_net      7.11   0.02    7.13
plot_heatmap  5.84   0.03    5.87
plot_clusgap  5.29   0.05    5.35
DPCoA         5.12   0.08    5.51
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat-phyloseq.R' [106s]
 [106s] OK
** running tests for arch 'x64' ...
  Running 'testthat-phyloseq.R' [114s]
 [114s] 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
  'D:/biocbld/bbs-3.2-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.
** 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.

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.
* MD5 sums
packaged installation of 'phyloseq' as phyloseq_1.13.2.zip
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	4.57	0.03	4.63
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	0.04	0.00	0.05
assign-sample_data	0.78	0.00	0.78
assign-sample_names	0.02	0.00	0.01
assign-tax_table	0	0	0
assign-taxa_are_rows	0.00	0.01	0.02
assign-taxa_names	0.01	0.00	0.01
build_tax_table	0.03	0.00	0.03
capscale-phyloseq-methods	1.27	0.02	1.28
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	2.81	0.05	2.86
data-enterotype	2.73	0.03	2.76
data-esophagus	0.76	0.01	1.14
data-soilrep	2.25	0.00	2.26
distance	0.37	0.00	3.16
envHash2otu_table	0	0	0
estimate_richness	0.03	0.00	0.13
export_env_file	0	0	0
export_mothur_dist	0.10	0.03	0.12
extract-methods	0.01	0.00	0.02
filter_taxa	0.2	0.0	0.2
filterfun_sample	0.04	0.00	0.03
gapstat_ord	2.59	0.00	2.61
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0	0	0
get_taxa-methods	0.00	0.02	0.01
get_taxa_unique	0.32	0.01	0.35
get_variable	0.22	0.00	0.21
getslots.phyloseq	0.25	0.00	0.25
import	0	0	0
import_RDP_otu	2.72	0.00	2.72
import_biom	0.20	0.00	0.28
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	0.78	0.00	0.78
import_qiime_otu_tax	0.75	0.02	0.76
import_qiime_sample_data	0.02	0.01	0.03
import_usearch_uc	0.03	0.00	0.41
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	5.04	0.03	5.07
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	1.53	0.00	1.53
merge_taxa-methods	0.07	0.00	0.07
microbio_me_qiime	0.81	0.00	0.93
mt-methods	5.35	0.00	5.36
nodeplotblank	0.38	0.00	0.37
nodeplotboot	0	0	0
nodeplotdefault	0	0	0
nsamples-methods	0.03	0.00	0.03
ntaxa-methods	0.02	0.00	0.01
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.33	0.00	0.33
phyloseq	0.03	0.00	0.03
phyloseq_to_deseq2	1.89	0.05	1.94
plot_bar	2.88	0.05	2.93
plot_clusgap	6.37	0.04	6.68
plot_heatmap	5.46	0.03	5.50
plot_net	7.56	0.02	7.58
plot_network	3.26	0.00	3.26
plot_ordination	0.97	0.00	0.97
plot_phyloseq-methods	0.45	0.02	0.47
plot_richness	7.74	0.03	7.77
plot_scree	2.11	0.01	2.12
plot_tree	0.57	0.00	1.09
prune_samples-methods	1.10	0.02	1.11
prune_taxa-methods	0.03	0.00	0.03
psmelt	1.31	0.01	1.33
rank_names	0.07	0.00	0.06
rarefy_even_depth	0.15	0.00	0.16
read_tree	0.2	0.0	0.2
read_tree_greengenes	0.08	0.00	0.08
reconcile_categories	0.00	0.02	0.01
refseq-methods	0.22	0.00	0.46
rm_outlierf	0.02	0.00	0.02
sample_data-methods	0.08	0.00	0.07
sample_names-methods	0.00	0.02	0.02
sample_sums	0.04	0.00	0.05
sample_variables	0.02	0.01	0.03
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	0.04	0.00	0.04
threshrank	3.91	0.38	4.29
threshrankfun	0.09	0.00	0.09
tip_glom	0.93	0.00	0.92
topf	0.03	0.00	0.03
topk	0.03	0.00	0.03
topp	0.01	0.00	0.02
transformcounts	0.13	0.00	0.12
transpose-methods	1.57	0.18	1.77
tree_layout	0.58	0.02	1.12

name	user	system	elapsed
DPCoA	5.12	0.08	5.51
JSD	0	0	0
UniFrac-methods	0.18	0.00	0.18
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.05	0.00	0.05
assign-sample_data	0.63	0.01	0.64
assign-sample_names	0.01	0.00	0.02
assign-tax_table	0.02	0.00	0.01
assign-taxa_are_rows	0	0	0
assign-taxa_names	0.01	0.00	0.02
build_tax_table	0.02	0.00	0.01
capscale-phyloseq-methods	1.36	0.00	1.36
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	1.80	0.02	1.83
data-enterotype	2.89	0.03	2.91
data-esophagus	0.86	0.00	0.86
data-soilrep	2.92	0.08	3.00
distance	0.26	0.03	0.29
envHash2otu_table	0	0	0
estimate_richness	0.03	0.00	0.03
export_env_file	0	0	0
export_mothur_dist	0.11	0.00	0.11
extract-methods	0	0	0
filter_taxa	0.26	0.00	0.27
filterfun_sample	0.03	0.00	0.03
gapstat_ord	2.73	0.02	2.75
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	0.3	0.0	0.3
get_variable	0.2	0.0	0.2
getslots.phyloseq	0.32	0.00	0.31
import	0	0	0
import_RDP_otu	1.64	0.00	1.64
import_biom	0.20	0.00	1.27
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	0.98	0.02	1.00
import_qiime_otu_tax	1.03	0.01	1.04
import_qiime_sample_data	0.03	0.00	0.04
import_usearch_uc	0.03	0.00	0.03
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	4.18	0.02	4.21
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	2.03	0.04	2.07
merge_taxa-methods	0.1	0.0	0.1
microbio_me_qiime	0.82	0.03	1.32
mt-methods	2.28	0.02	2.30
nodeplotblank	0.41	0.00	0.42
nodeplotboot	0	0	0
nodeplotdefault	0	0	0
nsamples-methods	0.04	0.00	0.04
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	0.02	0.22
phyloseq	0.04	0.00	0.03
phyloseq_to_deseq2	0.90	0.03	0.94
plot_bar	3.31	0.01	3.59
plot_clusgap	5.29	0.05	5.35
plot_heatmap	5.84	0.03	5.87
plot_net	7.11	0.02	7.13
plot_network	3.65	0.00	3.65
plot_ordination	0.91	0.00	0.90
plot_phyloseq-methods	0.34	0.01	0.36
plot_richness	7.53	0.00	7.65
plot_scree	2.69	0.02	2.71
plot_tree	1.06	0.00	1.06
prune_samples-methods	0.93	0.01	0.95
prune_taxa-methods	0.05	0.00	0.05
psmelt	1.56	0.03	1.61
rank_names	0.03	0.00	0.03
rarefy_even_depth	0.14	0.00	0.14
read_tree	0.2	0.0	0.2
read_tree_greengenes	0.08	0.00	0.08
reconcile_categories	0	0	0
refseq-methods	0.37	0.02	0.39
rm_outlierf	0.03	0.00	0.03
sample_data-methods	0.07	0.00	0.06
sample_names-methods	0.01	0.00	0.02
sample_sums	0.03	0.00	0.03
sample_variables	0.05	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	3.32	0.33	3.71
threshrankfun	0.08	0.00	0.08
tip_glom	0.95	0.01	0.97
topf	0.03	0.00	0.03
topk	0.02	0.00	0.02
topp	0.01	0.00	0.01
transformcounts	0.13	0.00	0.13
transpose-methods	1.54	0.22	1.76
tree_layout	0.61	0.02	1.17