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BioC 3.4: CHECK report for phyloseq on zin1

This page was generated on 2016-09-21 03:37:40 -0700 (Wed, 21 Sep 2016).

Package 895/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phyloseq 1.17.2
Paul J. McMurdie
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/phyloseq
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: phyloseq
Version: 1.17.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.17.2.tar.gz
StartedAt: 2016-09-20 10:32:20 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:36:10 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 230.4 seconds
RetCode: 0
Status:  OK 
CheckDir: phyloseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.17.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/phyloseq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.17.2’
* 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 for sufficient/correct file permissions ... 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
* 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
':::' 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
DPCoA: no visible global function definition for ‘as.dist’
chunkReOrder: no visible global function definition for ‘tail’
chunkReOrder: no visible global function definition for ‘head’
export_env_file: no visible global function definition for
  ‘write.table’
export_mothur_dist: no visible global function definition for ‘as.dist’
export_mothur_dist: no visible global function definition for
  ‘write.table’
fastUniFrac: no visible global function definition for ‘combn’
fastUniFrac: no visible global function definition for ‘as.dist’
import_RDP_otu: no visible global function definition for ‘read.table’
import_env_file: no visible global function definition for ‘read.table’
import_mothur_constaxonomy: no visible global function definition for
  ‘read.table’
import_mothur_dist: no visible global function definition for ‘as.dist’
import_mothur_groups: no visible global function definition for
  ‘read.table’
import_mothur_shared: no visible global function definition for
  ‘read.table’
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_qiime_sample_data: no visible global function definition for
  ‘read.table’
import_uparse: no visible global function definition for ‘:=’
import_uparse: no visible binding for global variable ‘count’
import_uparse: no visible binding for global variable ‘queryString’
import_uparse: no visible binding for global variable ‘queryID’
import_uparse: no visible binding for global variable ‘Classification’
import_uparse: no visible global function definition for
  ‘dcast.data.table’
import_uparse: no visible binding for global variable ‘OTULabel’
import_usearch_uc: no visible global function definition for ‘:=’
import_usearch_uc: no visible binding for global variable ‘read’
microbio_me_qiime: no visible global function definition for
  ‘download.file’
microbio_me_qiime: no visible global function definition for ‘unzip’
microbio_me_qiime: no visible global function definition for ‘untar’
nodeplotboot : <anonymous>: no visible global function definition for
  ‘complete.cases’
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’
ordinate: no visible global function definition for ‘as.formula’
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 global function definition for
  ‘capture.output’
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 ‘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: no visible binding for global variable ‘x’
plot_net: no visible binding for global variable ‘y’
plot_net: no visible binding for global variable ‘xend’
plot_net: 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 ‘axis’
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’
rp.joint.fill: no visible global function definition for ‘relevel’
tip_glom: no visible global function definition for ‘as.dist’
tip_glom: no visible global function definition for ‘cutree’
tip_glom: no visible global function definition for ‘as.hclust’
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 global function definition for ‘combn’
JSD,matrix: no visible binding for global variable ‘i’
JSD,matrix: no visible global function definition for ‘as.dist’
capscale.phyloseq,phyloseq-formula-character: no visible global
  function definition for ‘as.formula’
capscale.phyloseq,phyloseq-formula-dist: no visible global function
  definition for ‘as.formula’
cca.phyloseq,phyloseq-formula: no visible global function definition
  for ‘as.formula’
distance,phyloseq-character: no visible global function definition for
  ‘as.dist’
merge_phyloseq_pair,sample_data-sample_data : <anonymous>: no visible
  binding for global variable ‘X0’
merge_samples,sample_data: no visible global function definition for
  ‘aggregate’
plot_phyloseq,phyloseq: no visible binding for global variable
  ‘esophagus’
Undefined global functions or variables:
  #OTU ID .SD := Abundance Classification Consensus Lineage J OTU
  OTULabel SE.sim Sample V1 V2 X0 aggregate as.dist as.formula
  as.hclust axis capture.output combn complete.cases count cutree
  dcast.data.table download.file eigenvalue esophagus gap h.adj.index
  head i k label queryID queryString read read.table relevel se tail
  untar unzip value vmax vmin write.table x xdodge xend xfartiplab
  xleft xright y yend
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "aggregate", "as.dist", "as.formula", "as.hclust",
             "complete.cases", "cutree", "relevel")
  importFrom("utils", "capture.output", "combn", "download.file", "head",
             "read.table", "tail", "untar", "unzip", "write.table")
to your NAMESPACE file.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’
 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/phyloseq.Rcheck/00check.log’
for details.


phyloseq.Rcheck/00install.out:

* 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
* DONE (phyloseq)

phyloseq.Rcheck/phyloseq-Ex.timings:

nameusersystemelapsed
DPCoA2.6720.0242.699
JSD0.0000.0000.001
UniFrac-methods0.1080.0080.113
access0.0000.0000.001
assign-otu_table000
assign-phy_tree0.0360.0000.037
assign-sample_data0.5480.0040.552
assign-sample_names0.0040.0040.006
assign-tax_table0.0000.0000.001
assign-taxa_are_rows0.0000.0000.002
assign-taxa_names0.0080.0000.007
build_tax_table0.0120.0000.011
capscale-phyloseq-methods0.5440.0040.546
cca-rda-phyloseq-methods000
chunkReOrder0.0000.0040.001
data-GlobalPatterns1.0840.0001.087
data-enterotype1.3760.0041.382
data-esophagus0.5720.0000.571
data-soilrep1.3160.0041.317
distance0.1520.0120.437
distanceMethodList0.0040.0000.000
envHash2otu_table0.0000.0000.001
estimate_richness0.0160.0080.024
export_env_file0.0040.0000.001
export_mothur_dist0.0760.0120.088
extract-methods0.0080.0000.007
filter_taxa0.8720.0280.902
filterfun_sample0.0160.0000.016
gapstat_ord1.6320.0121.650
genefilter_sample-methods0.0000.0000.001
get.component.classes000
get_sample-methods0.0040.0000.003
get_taxa-methods0.0040.0000.004
get_taxa_unique0.1840.0120.197
get_variable0.1640.0000.164
getslots.phyloseq0.1600.0000.157
import000
import_RDP_otu0.3760.0040.380
import_biom0.140.000.14
import_env_file000
import_mothur000
import_mothur_dist0.0000.0000.001
import_pyrotagger_tab000
import_qiime0.5680.0000.572
import_qiime_otu_tax0.4600.0240.484
import_qiime_sample_data0.0160.0000.015
import_uparse0.0040.0000.001
import_usearch_uc0.0120.0000.013
index_reorder000
intersect_taxa000
make_network2.4920.0082.500
merge_phyloseq0.0000.0000.001
merge_phyloseq_pair-methods0.0000.0000.001
merge_samples-methods1.2000.0161.219
merge_taxa-methods0.0480.0000.048
microbio_me_qiime0.5240.0240.563
mt-methods1.4240.0121.439
nodeplotblank0.2560.0000.257
nodeplotboot0.0000.0000.001
nodeplotdefault0.0000.0000.001
nsamples-methods0.0320.0000.031
ntaxa-methods0.0000.0040.003
ordinate0.0000.0000.001
otu_table-methods000
parseTaxonomy-functions0.0000.0000.002
phy_tree-methods0.1600.0000.157
phyloseq0.0200.0000.022
phyloseq_to_deseq22.0360.0802.123
phyloseq_to_metagenomeSeq1.2360.0201.255
plot_bar1.9560.0161.969
plot_clusgap3.5720.0083.594
plot_heatmap3.0520.0083.068
plot_net3.7240.0083.735
plot_network2.0040.0042.007
plot_ordination0.5320.0000.532
plot_phyloseq-methods0.180.000.18
plot_richness3.6520.0043.656
plot_scree1.5080.0001.505
plot_tree0.4640.0000.464
prune_samples-methods0.7560.0000.757
prune_taxa-methods0.0240.0000.027
psmelt0.6280.0080.638
rank_names0.0200.0000.022
rarefy_even_depth0.0800.0000.077
read_tree0.1200.0000.123
read_tree_greengenes0.0360.0000.035
reconcile_categories000
refseq-methods0.1520.0000.152
rm_outlierf0.0160.0000.016
sample_data-methods0.0600.0000.059
sample_names-methods0.0000.0000.003
sample_sums0.0280.0000.027
sample_variables0.0240.0000.023
show-methods0.0000.0000.001
splat.phyloseq.objects000
subset_ord_plot000
subset_samples-methods000
subset_taxa-methods000
tax_glom0.0040.0000.001
tax_table-methods000
taxa_names-methods0.0240.0000.022
taxa_sums0.0280.0040.032
threshrank2.5000.4282.929
threshrankfun0.0480.0000.050
tip_glom0.6120.0000.615
topf0.0200.0000.017
topk0.0160.0000.015
topp0.0200.0000.017
transformcounts0.0880.0000.088
transpose-methods0.9880.3321.325
tree_layout0.4880.0040.492