BioC 2.14: CHECK report for phyloseq on moscato2

Package: phyloseq

Version: 1.8.2

Command: rm -rf phyloseq.buildbin-libdir && mkdir phyloseq.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.8.2.tar.gz >phyloseq-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.8.2.tar.gz

StartedAt: 2014-10-08 03:49:15 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 04:00:56 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 701.7 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf phyloseq.buildbin-libdir && mkdir phyloseq.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.8.2.tar.gz >phyloseq-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/phyloseq.Rcheck'
* using R version 3.1.1 (2014-07-10)
* 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 '1.8.2'
* 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 ... 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'JSD.pair' 'UFwi' 'internal2tips_self' 'ufnum'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
JSD: no visible binding for global variable 'i'
fastUniFrac: 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_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 'type'
plot_tree_only: no visible binding for global variable 'type'
plot_tree_only: no visible binding for global variable 'x'
plot_tree_only: no visible binding for global variable 'y'
plot_tree_only: no visible binding for global variable 'xend'
plot_tree_only: no visible binding for global variable 'yend'
plot_tree_sampledodge: no visible binding for global variable 'type'
plot_tree_sampledodge: no visible binding for global variable 'value'
plot_tree_sampledodge: no visible binding for global variable 'x'
plot_tree_sampledodge: no visible binding for global variable 'x.adj'
plot_tree_sampledodge: no visible binding for global variable 'y'
plot_tree_sampledodge: no visible binding for global variable
  'tipLabels'
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 ... NOTE
  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.
* 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' ... [88s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_heatmap  5.49   0.08    5.57
nodeplotblank 5.34   0.00    5.34
plot_clusgap  5.01   0.05    5.09
** running examples for arch 'x64' ... [96s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_heatmap  6.33   0.05    6.38
nodeplotblank 6.09   0.00    6.08
plot_clusgap  5.15   0.08    5.23
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat-phyloseq.R' [70s]
 [71s] OK
** running tests for arch 'x64' ...
  Running 'testthat-phyloseq.R' [83s]
 [83s] 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

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.14-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_1.8.2.zip
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	3.40	0.00	3.43
JSD	0	0	0
UniFrac-methods	1.87	0.01	1.89
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.05	0.00	0.05
assign-sample_data	0.61	0.00	0.60
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	0	0
capscale-phyloseq-methods	1.06	0.03	1.10
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	2.39	0.00	2.39
data-enterotype	2.23	0.00	2.23
data-esophagus	1.31	0.00	1.31
data-soilrep	2.39	0.06	2.45
distance	1.51	0.02	2.26
envHash2otu_table	0	0	0
estimate_richness	0.03	0.00	0.03
export_env_file	0	0	0
export_mothur_dist	0.05	0.03	0.08
extract-methods	0.01	0.00	0.02
filter_taxa	0.53	0.02	0.55
filterfun_sample	0.02	0.00	0.02
gapstat_ord	2.06	0.00	2.05
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	0.00	0.25
get_variable	0.22	0.00	0.22
getslots.phyloseq	0.2	0.0	0.2
import	0	0	0
import_RDP_otu	2.19	0.04	2.23
import_biom	0.13	0.02	0.22
import_env_file	0.01	0.00	0.01
import_mothur	0	0	0
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	0.49	0.00	0.48
import_qiime_otu_tax	0.40	0.01	0.43
import_qiime_sample_data	0.02	0.00	0.01
import_usearch_uc	0.01	0.00	0.02
index_reorder	0.02	0.00	0.01
intersect_taxa	0	0	0
make_network	4.85	0.02	4.87
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	1.2	0.0	1.2
merge_taxa-methods	0.05	0.00	0.05
microbio_me_qiime	0.62	0.00	0.78
mt-methods	0	0	0
nodeplotblank	5.34	0.00	5.34
nodeplotboot	0	0	0
nodeplotdefault	0	0	0
nsamples-methods	0.02	0.00	0.02
ntaxa-methods	0	0	0
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.21	0.00	0.20
phyloseq	0.03	0.00	0.03
phyloseq_to_deseq2	1.29	0.05	1.34
plot_bar	2.26	0.00	2.26
plot_clusgap	5.01	0.05	5.09
plot_heatmap	5.49	0.08	5.57
plot_network	3.31	0.01	3.32
plot_ordination	0.80	0.02	0.81
plot_phyloseq-methods	2.88	0.00	2.89
plot_richness	4.51	0.03	4.54
plot_scree	2.87	0.01	2.88
plot_tree	3.09	0.00	3.09
prune_samples-methods	0.61	0.00	0.61
prune_taxa-methods	0.03	0.00	0.03
psmelt	1.12	0.02	1.14
rank_names	0.01	0.00	0.01
rarefy_even_depth	0.08	0.00	0.08
read_tree	0.11	0.02	0.12
read_tree_greengenes	0.04	0.00	0.05
reconcile_categories	0	0	0
refseq-methods	0.24	0.00	0.23
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	0.01	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	2.79	0.27	3.05
threshrankfun	0.06	0.00	0.07
tip_glom	1.76	0.00	1.76
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	1.11	0.25	1.36
tree.get.tags	0	0	0
tree.has.tags	0	0	0

name	user	system	elapsed
DPCoA	3.94	0.03	3.99
JSD	0	0	0
UniFrac-methods	2.07	0.00	2.07
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.06	0.00	0.06
assign-sample_data	1.00	0.02	1.01
assign-sample_names	0	0	0
assign-tax_table	0.02	0.00	0.02
assign-taxa_are_rows	0	0	0
assign-taxa_names	0	0	0
build_tax_table	0.01	0.00	0.01
capscale-phyloseq-methods	1.33	0.03	1.36
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	2.10	0.00	2.11
data-enterotype	2.72	0.00	2.74
data-esophagus	1.56	0.00	1.56
data-soilrep	2.20	0.02	2.22
distance	1.65	0.04	1.70
envHash2otu_table	0	0	0
estimate_richness	0.02	0.00	0.01
export_env_file	0	0	0
export_mothur_dist	0.07	0.00	0.06
extract-methods	0	0	0
filter_taxa	0.54	0.02	0.56
filterfun_sample	0.03	0.00	0.04
gapstat_ord	2.30	0.03	2.32
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0	0	0
get_taxa-methods	0.00	0.01	0.02
get_taxa_unique	0.21	0.00	0.21
get_variable	0.17	0.00	0.17
getslots.phyloseq	0.19	0.00	0.19
import	0	0	0
import_RDP_otu	1.96	0.02	1.98
import_biom	0.18	0.02	0.25
import_env_file	0	0	0
import_mothur	0	0	0
import_mothur_dist	0.01	0.00	0.01
import_pyrotagger_tab	0	0	0
import_qiime	0.59	0.00	0.60
import_qiime_otu_tax	0.50	0.01	0.51
import_qiime_sample_data	0.03	0.00	0.03
import_usearch_uc	0.02	0.00	0.02
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	4.95	0.03	4.98
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	1.56	0.00	1.56
merge_taxa-methods	0.06	0.00	0.06
microbio_me_qiime	0.68	0.00	0.78
mt-methods	0	0	0
nodeplotblank	6.09	0.00	6.08
nodeplotboot	0	0	0
nodeplotdefault	0	0	0
nsamples-methods	0.01	0.02	0.03
ntaxa-methods	0	0	0
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0.02	0.00	0.02
phy_tree-methods	0.16	0.03	0.19
phyloseq	0.01	0.00	0.01
phyloseq_to_deseq2	1.09	0.09	1.19
plot_bar	2.59	0.08	2.66
plot_clusgap	5.15	0.08	5.23
plot_heatmap	6.33	0.05	6.38
plot_network	3.4	0.0	3.4
plot_ordination	0.98	0.00	0.98
plot_phyloseq-methods	3.39	0.00	3.39
plot_richness	4.83	0.04	4.87
plot_scree	2.15	0.03	2.21
plot_tree	3.74	0.00	3.75
prune_samples-methods	1.05	0.03	1.07
prune_taxa-methods	0.04	0.02	0.07
psmelt	1.13	0.02	1.17
rank_names	0.01	0.00	0.01
rarefy_even_depth	0.08	0.00	0.08
read_tree	0.14	0.00	0.14
read_tree_greengenes	0.05	0.00	0.05
reconcile_categories	0	0	0
refseq-methods	0.19	0.00	0.19
rm_outlierf	0.01	0.00	0.01
sample_data-methods	0.06	0.00	0.06
sample_names-methods	0	0	0
sample_sums	0.04	0.00	0.03
sample_variables	0.01	0.00	0.02
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	2.68	0.24	2.92
threshrankfun	0.06	0.00	0.06
tip_glom	2.13	0.00	2.14
topf	0.01	0.00	0.02
topk	0.02	0.00	0.01
topp	0.02	0.00	0.01
transformcounts	0.11	0.00	0.11
transpose-methods	1.07	0.17	1.25
tree.get.tags	0	0	0
tree.has.tags	0	0	0