BioC 3.2: CHECK report for phyloseq on windows1.bioconductor.org

Package: phyloseq

Version: 1.14.0

Command: rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.14.0.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out && C:\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_1.14.0.tar.gz

StartedAt: 2015-10-27 04:25:20 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:32:29 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 429.1 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.14.0.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out  && C:\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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/phyloseq.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.14.0'
* 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.
* 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
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'
JSD,matrix: no visible binding for global variable 'i'
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' ... [57s] OK
** running examples for arch 'x64' ... [61s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat-phyloseq.R' [64s]
 [64s] OK
** running tests for arch 'x64' ...
  Running 'testthat-phyloseq.R' [64s]
 [64s] 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: 3 NOTEs
See
  'C:/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_1.14.0.zip
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	2.31	0.02	2.32
JSD	0	0	0
UniFrac-methods	0.09	0.00	0.10
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.03	0.02	0.04
assign-sample_data	0.28	0.00	0.29
assign-sample_names	0	0	0
assign-tax_table	0	0	0
assign-taxa_are_rows	0	0	0
assign-taxa_names	0	0	0
build_tax_table	0.02	0.00	0.02
capscale-phyloseq-methods	0.59	0.00	0.59
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0	0	0
data-GlobalPatterns	1.80	0.03	1.83
data-enterotype	1.26	0.01	1.28
data-esophagus	0.44	0.03	0.47
data-soilrep	1.53	0.02	1.55
distance	0.16	0.02	0.21
distanceMethodList	0	0	0
envHash2otu_table	0	0	0
estimate_richness	0.03	0.00	0.04
export_env_file	0	0	0
export_mothur_dist	0.06	0.00	0.06
extract-methods	0.02	0.00	0.01
filter_taxa	0.92	0.01	0.94
filterfun_sample	0.01	0.00	0.02
gapstat_ord	1.52	0.03	1.54
genefilter_sample-methods	0.02	0.00	0.02
get.component.classes	0	0	0
get_sample-methods	0	0	0
get_taxa-methods	0	0	0
get_taxa_unique	0.20	0.02	0.22
get_variable	0.17	0.00	0.17
getslots.phyloseq	0.14	0.04	0.19
import	0	0	0
import_RDP_otu	1.33	0.00	1.33
import_biom	0.12	0.00	0.12
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	0.49	0.00	0.49
import_qiime_otu_tax	0.39	0.02	0.41
import_qiime_sample_data	0.02	0.00	0.01
import_usearch_uc	0.02	0.00	0.02
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	2.65	0.03	2.69
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	1.14	0.03	1.17
merge_taxa-methods	0.05	0.00	0.04
microbio_me_qiime	0.44	0.00	0.47
mt-methods	2.15	0.00	2.16
nodeplotblank	0.25	0.00	0.25
nodeplotboot	0.02	0.00	0.02
nodeplotdefault	0	0	0
nsamples-methods	0.01	0.00	0.01
ntaxa-methods	0	0	0
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.17	0.00	0.17
phyloseq	0.01	0.00	0.02
phyloseq_to_deseq2	2.18	0.08	2.25
phyloseq_to_metagenomeSeq	1.59	0.06	1.66
plot_bar	1.48	0.00	1.48
plot_clusgap	3.18	0.13	3.33
plot_heatmap	3.12	0.06	3.19
plot_net	4.13	0.09	4.21
plot_network	1.91	0.00	1.91
plot_ordination	0.53	0.00	0.53
plot_phyloseq-methods	0.15	0.02	0.17
plot_richness	3.90	0.02	3.91
plot_scree	1.25	0.01	1.26
plot_tree	0.45	0.00	0.45
prune_samples-methods	0.73	0.02	0.75
prune_taxa-methods	0.03	0.00	0.05
psmelt	0.80	0.00	0.79
rank_names	0.02	0.00	0.02
rarefy_even_depth	0.06	0.00	0.06
read_tree	0.09	0.00	0.10
read_tree_greengenes	0.03	0.00	0.03
reconcile_categories	0	0	0
refseq-methods	0.16	0.01	0.17
rm_outlierf	0.01	0.00	0.02
sample_data-methods	0.05	0.00	0.04
sample_names-methods	0	0	0
sample_sums	0.03	0.00	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	0.01	0.00	0.02
taxa_sums	0.03	0.02	0.04
threshrank	2.40	0.37	2.77
threshrankfun	0.04	0.00	0.05
tip_glom	0.53	0.00	0.53
topf	0.02	0.00	0.01
topk	0.01	0.00	0.02
topp	0.02	0.00	0.01
transformcounts	0.08	0.00	0.08
transpose-methods	0.76	0.24	1.00
tree_layout	0.39	0.00	0.39

name	user	system	elapsed
DPCoA	3.01	0.01	3.03
JSD	0	0	0
UniFrac-methods	0.11	0.00	0.11
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.05	0.00	0.04
assign-sample_data	0.44	0.04	0.47
assign-sample_names	0.01	0.00	0.02
assign-tax_table	0	0	0
assign-taxa_are_rows	0.00	0.01	0.01
assign-taxa_names	0	0	0
build_tax_table	0.02	0.00	0.02
capscale-phyloseq-methods	0.73	0.05	0.78
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0	0	0
data-GlobalPatterns	1.53	0.03	1.57
data-enterotype	1.48	0.00	1.48
data-esophagus	0.53	0.00	0.53
data-soilrep	1.56	0.03	1.59
distance	0.16	0.01	0.17
distanceMethodList	0	0	0
envHash2otu_table	0	0	0
estimate_richness	0.01	0.00	0.01
export_env_file	0	0	0
export_mothur_dist	0.06	0.02	0.08
extract-methods	0.02	0.00	0.02
filter_taxa	0.88	0.01	0.89
filterfun_sample	0.02	0.00	0.02
gapstat_ord	1.72	0.02	1.73
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	0.19	0.00	0.19
get_variable	0.14	0.00	0.14
getslots.phyloseq	0.14	0.00	0.14
import	0	0	0
import_RDP_otu	0.89	0.00	0.89
import_biom	0.14	0.01	0.15
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	0.58	0.00	0.58
import_qiime_otu_tax	0.50	0.02	0.52
import_qiime_sample_data	0.01	0.00	0.01
import_usearch_uc	0.02	0.00	0.02
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	2.91	0.00	2.91
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	0.82	0.00	0.84
merge_taxa-methods	0.05	0.00	0.05
microbio_me_qiime	0.47	0.00	0.50
mt-methods	1.31	0.00	1.31
nodeplotblank	0.3	0.0	0.3
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	0.14	0.02	0.15
phyloseq	0.02	0.00	0.02
phyloseq_to_deseq2	2.09	0.14	2.23
phyloseq_to_metagenomeSeq	1.97	0.03	2.00
plot_bar	2.03	0.03	2.07
plot_clusgap	3.25	0.09	3.34
plot_heatmap	3.72	0.02	3.73
plot_net	3.98	0.06	4.05
plot_network	2.25	0.03	2.28
plot_ordination	0.6	0.0	0.6
plot_phyloseq-methods	0.22	0.00	0.21
plot_richness	4.37	0.13	4.50
plot_scree	1.47	0.01	1.49
plot_tree	0.53	0.00	0.53
prune_samples-methods	0.5	0.0	0.5
prune_taxa-methods	0.03	0.00	0.03
psmelt	0.77	0.00	0.77
rank_names	0.01	0.00	0.02
rarefy_even_depth	0.08	0.00	0.08
read_tree	0.11	0.00	0.11
read_tree_greengenes	0.03	0.00	0.03
reconcile_categories	0	0	0
refseq-methods	0.13	0.01	0.14
rm_outlierf	0.02	0.00	0.02
sample_data-methods	0.03	0.00	0.03
sample_names-methods	0.02	0.00	0.02
sample_sums	0.01	0.00	0.01
sample_variables	0.01	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	0.01	0.00	0.01
taxa_sums	0.04	0.00	0.04
threshrank	2.17	0.41	2.58
threshrankfun	0.05	0.00	0.05
tip_glom	0.64	0.00	0.64
topf	0.02	0.00	0.01
topk	0.01	0.00	0.02
topp	0.02	0.00	0.01
transformcounts	0.09	0.00	0.10
transpose-methods	0.69	0.31	1.00
tree_layout	0.83	0.00	0.83