BioC 3.3: CHECK report for phyloseq on windows2.bioconductor.org

Package: phyloseq

Version: 1.15.0

Command: rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.15.0.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.15.0.tar.gz

StartedAt: 2015-10-27 04:57:26 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:04:22 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 415.7 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.15.0.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.15.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/phyloseq.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '1.15.0'
* 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'
Undefined global functions or variables:
  #OTU ID .SD := Abundance Consensus Lineage J OTU SE.sim Sample V1 V2
  X0 eigenvalue esophagus gap h.adj.index i k label read se value
  vertex vmax vmin x xdodge xend xfartiplab xleft xright y yend
* 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' ... [60s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat-phyloseq.R' [60s]
 [60s] OK
** running tests for arch 'x64' ...
  Running 'testthat-phyloseq.R' [60s]
 [60s] 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-3.3-bioc/meat/phyloseq.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'phyloseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'phyloseq' as phyloseq_1.15.0.zip
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	2.59	0.03	2.63
JSD	0	0	0
UniFrac-methods	0.08	0.00	0.07
access	0.02	0.00	0.02
assign-otu_table	0	0	0
assign-phy_tree	0.03	0.00	0.03
assign-sample_data	0.45	0.03	0.49
assign-sample_names	0.02	0.00	0.01
assign-tax_table	0	0	0
assign-taxa_are_rows	0	0	0
assign-taxa_names	0.01	0.00	0.02
build_tax_table	0	0	0
capscale-phyloseq-methods	0.53	0.05	0.57
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0	0	0
data-GlobalPatterns	1.44	0.01	1.46
data-enterotype	1.30	0.02	1.31
data-esophagus	0.43	0.01	0.45
data-soilrep	1.69	0.04	1.72
distance	0.13	0.03	0.22
distanceMethodList	0	0	0
envHash2otu_table	0	0	0
estimate_richness	0.01	0.00	0.02
export_env_file	0	0	0
export_mothur_dist	0.08	0.00	0.07
extract-methods	0	0	0
filter_taxa	0.70	0.00	0.71
filterfun_sample	0	0	0
gapstat_ord	1.44	0.08	1.52
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0.00	0.01	0.01
get_taxa-methods	0	0	0
get_taxa_unique	0.20	0.02	0.22
get_variable	0.17	0.01	0.19
getslots.phyloseq	0.19	0.00	0.19
import	0	0	0
import_RDP_otu	1.58	0.02	1.59
import_biom	0.11	0.04	0.17
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	0.45	0.00	0.46
import_qiime_otu_tax	0.48	0.04	0.51
import_qiime_sample_data	0.00	0.01	0.01
import_usearch_uc	0.02	0.00	0.02
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	2.62	0.02	2.64
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	1.13	0.01	1.14
merge_taxa-methods	0.03	0.00	0.03
microbio_me_qiime	0.42	0.02	0.46
mt-methods	2.19	0.01	2.20
nodeplotblank	0.21	0.02	0.23
nodeplotboot	0	0	0
nodeplotdefault	0	0	0
nsamples-methods	0.02	0.00	0.02
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	0.17	0.02	0.19
phyloseq	0.01	0.00	0.02
phyloseq_to_deseq2	2.57	0.06	2.62
phyloseq_to_metagenomeSeq	1.23	0.06	1.30
plot_bar	1.63	0.03	1.66
plot_clusgap	3.46	0.17	3.64
plot_heatmap	2.77	0.08	2.84
plot_net	4.25	0.02	4.27
plot_network	2.00	0.03	2.03
plot_ordination	0.53	0.00	0.53
plot_phyloseq-methods	0.17	0.00	0.17
plot_richness	3.46	0.08	3.53
plot_scree	1.53	0.01	1.55
plot_tree	0.42	0.02	0.44
prune_samples-methods	0.36	0.01	0.37
prune_taxa-methods	0.03	0.00	0.03
psmelt	0.58	0.02	0.60
rank_names	0.01	0.00	0.01
rarefy_even_depth	0.06	0.00	0.06
read_tree	0.08	0.00	0.08
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	0.02	0.06
sample_names-methods	0	0	0
sample_sums	0.03	0.00	0.03
sample_variables	0.03	0.00	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	0.02	0.00	0.02
taxa_names-methods	0.01	0.00	0.01
taxa_sums	0.03	0.00	0.03
threshrank	2.25	0.55	2.80
threshrankfun	0.05	0.00	0.05
tip_glom	0.55	0.00	0.54
topf	0	0	0
topk	0.01	0.00	0.02
topp	0.02	0.00	0.02
transformcounts	0.08	0.00	0.07
transpose-methods	0.70	0.23	0.94
tree_layout	0.44	0.03	0.47

name	user	system	elapsed
DPCoA	2.59	0.01	2.61
JSD	0	0	0
UniFrac-methods	0.13	0.00	0.13
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.03	0.00	0.03
assign-sample_data	0.62	0.02	0.64
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	0.56	0.00	0.56
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0	0	0
data-GlobalPatterns	1.20	0.02	1.22
data-enterotype	1.56	0.03	1.59
data-esophagus	0.52	0.02	0.53
data-soilrep	1.44	0.03	1.47
distance	0.20	0.02	0.21
distanceMethodList	0	0	0
envHash2otu_table	0	0	0
estimate_richness	0.02	0.00	0.02
export_env_file	0	0	0
export_mothur_dist	0.07	0.00	0.07
extract-methods	0	0	0
filter_taxa	0.74	0.04	0.77
filterfun_sample	0.01	0.00	0.02
gapstat_ord	1.58	0.01	1.59
genefilter_sample-methods	0	0	0
get.component.classes	0.02	0.00	0.01
get_sample-methods	0	0	0
get_taxa-methods	0	0	0
get_taxa_unique	0.19	0.00	0.19
get_variable	0.12	0.02	0.14
getslots.phyloseq	0.14	0.01	0.16
import	0	0	0
import_RDP_otu	1.17	0.00	1.18
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	0.63	0.00	0.63
import_qiime_otu_tax	0.46	0.03	0.49
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	2.62	0.04	2.65
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	0.66	0.01	0.68
merge_taxa-methods	0.05	0.00	0.04
microbio_me_qiime	0.50	0.00	0.52
mt-methods	1.31	0.00	1.31
nodeplotblank	0.29	0.00	0.28
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	0.15	0.00	0.16
phyloseq	0.01	0.00	0.02
phyloseq_to_deseq2	2.54	0.11	2.64
phyloseq_to_metagenomeSeq	1.43	0.05	1.48
plot_bar	2.27	0.00	2.27
plot_clusgap	3.19	0.06	3.25
plot_heatmap	3.34	0.06	3.40
plot_net	4.28	0.02	4.30
plot_network	2.05	0.00	2.05
plot_ordination	0.55	0.00	0.54
plot_phyloseq-methods	0.18	0.01	0.21
plot_richness	4.55	0.10	4.64
plot_scree	1.75	0.00	1.76
plot_tree	0.52	0.00	0.51
prune_samples-methods	0.39	0.00	0.40
prune_taxa-methods	0.03	0.00	0.03
psmelt	1.22	0.02	1.23
rank_names	0.02	0.00	0.01
rarefy_even_depth	0.08	0.00	0.08
read_tree	0.09	0.00	0.09
read_tree_greengenes	0.03	0.00	0.04
reconcile_categories	0	0	0
refseq-methods	0.14	0.00	0.14
rm_outlierf	0.02	0.00	0.01
sample_data-methods	0.06	0.00	0.06
sample_names-methods	0	0	0
sample_sums	0.01	0.01	0.04
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	0.01	0.00	0.01
taxa_sums	0.03	0.00	0.03
threshrank	2.05	0.44	2.49
threshrankfun	0.05	0.00	0.04
tip_glom	0.67	0.02	0.69
topf	0.01	0.00	0.02
topk	0	0	0
topp	0.02	0.00	0.01
transformcounts	0.11	0.00	0.11
transpose-methods	0.81	0.34	1.16
tree_layout	0.47	0.00	0.47