BioC 2.13: CHECK report for phyloseq on moscato1

Package: phyloseq

Version: 1.6.1

Command: rm -rf phyloseq.buildbin-libdir && mkdir phyloseq.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.6.1.tar.gz >phyloseq-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.6.1.tar.gz && mv phyloseq.buildbin-libdir/* phyloseq.Rcheck/ && rmdir phyloseq.buildbin-libdir

StartedAt: 2014-04-05 05:49:42 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 06:06:09 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 987.6 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/phyloseq.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.6.1'
* 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 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
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'ade4' 'methods' 'picante'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 binding for global variable 'i'
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' ... [278s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
rarefy_even_depth   102.80   0.12  102.93
plot_scree           27.94   0.17   28.12
plot_tree            21.98   0.00   21.98
plot_ordination      12.92   0.12   13.11
nodeplotblank        10.19   0.03   10.22
plot_clusgap          8.99   0.17    9.22
data-GlobalPatterns   7.70   0.05    7.77
make_network          6.35   0.03    6.38
plot_richness         6.02   0.10    6.13
gapstat_ord           5.54   0.07    5.61
estimate_richness     5.37   0.11    5.48
data-enterotype       5.26   0.09    5.35
** running examples for arch 'x64' ... [275s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
rarefy_even_depth   115.36   0.05  115.42
plot_scree           25.70   0.08   25.79
plot_tree            19.81   0.00   19.81
plot_ordination      14.33   0.25   14.60
data-GlobalPatterns   8.25   0.05    8.30
plot_clusgap          7.82   0.11    7.92
nodeplotblank         7.02   0.00    7.02
gapstat_ord           5.35   0.08    5.43
data-enterotype       5.10   0.02    5.12
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'testthat-phyloseq.R' [43s]
 [44s] OK
** running tests for arch 'x64'
  Running 'testthat-phyloseq.R' [66s]
 [67s] OK
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-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_1.6.1.zip
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	0	0	0
JSD	0	0	0
UniFrac-methods	0.02	0.00	0.02
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0	0	0
assign-sample_data	0	0	0
assign-sample_names	0.02	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	0.03	0.00	0.03
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	7.70	0.05	7.77
data-enterotype	5.26	0.09	5.35
data-esophagus	2.28	0.02	2.30
data-soilrep	2.63	0.01	2.65
distance	1.70	0.00	1.78
edgelist2clique	0	0	0
envHash2otu_table	0	0	0
estimate_richness	5.37	0.11	5.48
export_env_file	0	0	0
export_mothur_dist	0	0	0
extract-methods	0.03	0.00	0.04
filter_taxa	1.70	0.06	1.76
filterfun_sample	0.03	0.00	0.03
gapstat_ord	5.54	0.07	5.61
genefilter_sample-methods	0.01	0.00	0.01
get.component.classes	0	0	0
get_sample-methods	0	0	0
get_taxa-methods	0	0	0
get_taxa_unique	0.39	0.02	0.40
get_variable	0.34	0.00	0.35
getslots.phyloseq	0.31	0.00	0.31
import	0	0	0
import_RDP_otu	1.84	0.00	1.84
import_biom	0.28	0.00	0.35
import_env_file	0.01	0.00	0.02
import_mothur	0	0	0
import_mothur_dist	0	0	0
import_pyrotagger_tab	0.01	0.00	0.01
import_qiime	1.06	0.00	1.06
import_qiime_otu_tax	0.88	0.03	0.91
import_qiime_sample_data	0.03	0.00	0.03
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	6.35	0.03	6.38
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0.02	0.00	0.02
merge_samples-methods	2.82	0.03	2.85
merge_taxa-methods	2.47	0.00	2.67
microbio_me_qiime	1.18	0.03	1.29
mt-methods	0.02	0.00	0.02
nodeplotblank	10.19	0.03	10.22
nodeplotboot	0.01	0.00	0.02
nodeplotdefault	0	0	0
nsamples-methods	0.02	0.00	0.01
ntaxa-methods	0.01	0.00	0.02
ordinate	0.01	0.00	0.02
otu_table-methods	0	0	0
parseTaxonomy-functions	0.02	0.00	0.02
phy_tree-methods	0.35	0.00	0.36
phyloseq	0.07	0.00	0.06
plot_bar	4.75	0.05	4.81
plot_clusgap	8.99	0.17	9.22
plot_heatmap	2.67	0.04	2.71
plot_network	3.88	0.02	3.90
plot_ordination	12.92	0.12	13.11
plot_phyloseq-methods	4.18	0.00	4.18
plot_richness	6.02	0.10	6.13
plot_scree	27.94	0.17	28.12
plot_tree	21.98	0.00	21.98
prune_samples-methods	0.70	0.00	0.71
prune_taxa-methods	0.08	0.00	0.08
psmelt	1.48	0.00	1.48
rank_names	0.04	0.00	0.03
rarefy_even_depth	102.80	0.12	102.93
read_tree	0.14	0.04	0.17
read_tree_greengenes	0.06	0.00	0.06
reconcile_categories	0	0	0
refseq-methods	0.25	0.00	0.25
rm_outlierf	0.03	0.00	0.03
sample_data-methods	0	0	0
sample_names-methods	0	0	0
sample_sums	0.06	0.00	0.06
sample_variables	0.05	0.00	0.05
show-methods	0	0	0
splat.phyloseq.objects	0.01	0.00	0.01
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	0.05	0.00	0.04
threshrank	2.97	0.20	3.19
threshrankfun	0.07	0.00	0.06
tip_glom-methods	0	0	0
topf	0.03	0.00	0.04
topk	0.02	0.00	0.01
topp	0.01	0.00	0.01
transformcounts	0.13	0.00	0.13
transpose-methods	1.03	0.22	1.25
tree.get.tags	0	0	0
tree.has.tags	0	0	0

name	user	system	elapsed
DPCoA	0.00	0.02	0.03
JSD	0	0	0
UniFrac-methods	0.01	0.00	0.01
access	0.02	0.00	0.02
assign-otu_table	0.28	0.00	0.28
assign-phy_tree	0.01	0.00	0.02
assign-sample_data	0	0	0
assign-sample_names	0.02	0.01	0.03
assign-tax_table	0	0	0
assign-taxa_are_rows	0.02	0.00	0.01
assign-taxa_names	0.01	0.00	0.02
build_tax_table	0.03	0.00	0.03
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	8.25	0.05	8.30
data-enterotype	5.10	0.02	5.12
data-esophagus	1.92	0.00	1.92
data-soilrep	2.71	0.04	2.77
distance	1.59	0.04	1.67
edgelist2clique	0	0	0
envHash2otu_table	0	0	0
estimate_richness	4.20	0.04	4.25
export_env_file	0	0	0
export_mothur_dist	0	0	0
extract-methods	0	0	0
filter_taxa	1.17	0.06	1.24
filterfun_sample	0.07	0.00	0.06
gapstat_ord	5.35	0.08	5.43
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0	0	0
get_taxa-methods	0.02	0.00	0.02
get_taxa_unique	0.26	0.00	0.26
get_variable	0.19	0.00	0.19
getslots.phyloseq	0.2	0.0	0.2
import	0.02	0.00	0.02
import_RDP_otu	1.62	0.00	1.62
import_biom	0.33	0.02	0.41
import_env_file	0	0	0
import_mothur	0.02	0.00	0.01
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	1.33	0.00	1.32
import_qiime_otu_tax	0.94	0.00	0.94
import_qiime_sample_data	0.03	0.00	0.03
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	4.35	0.01	4.36
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0.00	0.02	0.02
merge_samples-methods	2.01	0.00	2.01
merge_taxa-methods	1.78	0.01	1.80
microbio_me_qiime	0.86	0.00	0.92
mt-methods	0	0	0
nodeplotblank	7.02	0.00	7.02
nodeplotboot	0	0	0
nodeplotdefault	0.02	0.00	0.01
nsamples-methods	0	0	0
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	0.02	0.19
phyloseq	0.03	0.00	0.03
plot_bar	3.51	0.02	3.53
plot_clusgap	7.82	0.11	7.92
plot_heatmap	4.26	0.04	4.30
plot_network	4.2	0.0	4.2
plot_ordination	14.33	0.25	14.60
plot_phyloseq-methods	3.76	0.00	3.76
plot_richness	4.76	0.06	4.82
plot_scree	25.70	0.08	25.79
plot_tree	19.81	0.00	19.81
prune_samples-methods	0.79	0.00	0.80
prune_taxa-methods	0.07	0.00	0.06
psmelt	1.27	0.00	1.28
rank_names	0.02	0.00	0.02
rarefy_even_depth	115.36	0.05	115.42
read_tree	0.18	0.00	0.17
read_tree_greengenes	0.06	0.00	0.06
reconcile_categories	0	0	0
refseq-methods	0.19	0.01	0.21
rm_outlierf	0.03	0.00	0.03
sample_data-methods	0	0	0
sample_names-methods	0.01	0.00	0.01
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	0	0
taxa_sums	0.04	0.00	0.05
threshrank	2.64	0.22	2.85
threshrankfun	0.08	0.00	0.08
tip_glom-methods	0.01	0.00	0.01
topf	0.02	0.00	0.02
topk	0.02	0.00	0.01
topp	0.03	0.00	0.03
transformcounts	0.14	0.00	0.14
transpose-methods	0.84	0.19	1.03
tree.get.tags	0	0	0
tree.has.tags	0	0	0