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BioC 3.5: CHECK report for phyloseq on malbec2

This page was generated on 2017-08-16 13:14:20 -0400 (Wed, 16 Aug 2017).

Package 979/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phyloseq 1.20.0
Paul J. McMurdie
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/phyloseq
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: phyloseq
Version: 1.20.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.20.0.tar.gz
StartedAt: 2017-08-16 01:16:15 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:20:19 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 244.4 seconds
RetCode: 0
Status:  OK 
CheckDir: phyloseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/phyloseq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.20.0’
* 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 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-3.5-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
DPCoA4.0360.0284.068
JSD000
UniFrac-methods0.3880.0040.390
access0.0000.0000.001
assign-otu_table000
assign-phy_tree0.1920.0000.191
assign-sample_data0.4880.0040.493
assign-sample_names0.0040.0000.006
assign-tax_table0.0000.0000.001
assign-taxa_are_rows0.0040.0000.003
assign-taxa_names0.0040.0000.006
build_tax_table0.0240.0000.022
capscale-phyloseq-methods0.6440.0160.660
cca-rda-phyloseq-methods000
chunkReOrder0.0000.0040.001
data-GlobalPatterns1.5320.0041.540
data-enterotype1.6720.0001.674
data-esophagus0.4600.0000.463
data-soilrep0.9960.0041.001
distance0.2040.0321.093
distanceMethodList0.0000.0000.001
envHash2otu_table0.0040.0000.001
estimate_richness0.0640.0080.072
export_env_file0.0000.0000.001
export_mothur_dist0.0840.0280.112
extract-methods0.0080.0000.010
filter_taxa1.3840.0521.439
filterfun_sample0.0320.0000.033
gapstat_ord1.3680.0121.381
genefilter_sample-methods0.0040.0000.001
get.component.classes0.0000.0000.001
get_sample-methods0.0040.0000.003
get_taxa-methods0.0040.0000.002
get_taxa_unique0.2040.0040.210
get_variable0.1640.0000.162
getslots.phyloseq0.1600.0000.161
import000
import_RDP_otu0.3480.0080.356
import_biom0.3320.0000.330
import_env_file000
import_mothur0.0000.0000.001
import_mothur_dist0.0040.0000.000
import_pyrotagger_tab000
import_qiime0.8320.0360.866
import_qiime_otu_tax0.5480.0200.568
import_qiime_sample_data0.0120.0000.012
import_uparse0.0000.0000.001
import_usearch_uc0.0120.0000.011
index_reorder0.0040.0000.001
intersect_taxa0.0000.0000.001
make_network1.9120.0041.917
merge_phyloseq000
merge_phyloseq_pair-methods0.0040.0000.001
merge_samples-methods0.6480.0000.648
merge_taxa-methods0.0640.0000.064
microbio_me_qiime0.6360.0680.716
mt-methods1.2640.0001.265
nodeplotblank0.6960.0000.544
nodeplotboot0.0200.0000.022
nodeplotdefault000
nsamples-methods0.0160.0000.018
ntaxa-methods0.0000.0000.003
ordinate0.0000.0000.001
otu_table-methods0.0000.0000.001
parseTaxonomy-functions0.0040.0000.002
phy_tree-methods0.1560.0000.157
phyloseq0.0160.0000.017
phyloseq_to_deseq22.2800.0482.330
phyloseq_to_metagenomeSeq1.3560.0121.370
plot_bar1.6560.0081.666
plot_clusgap3.3400.0163.366
plot_heatmap3.7640.0043.770
plot_net3.2200.0082.975
plot_network1.5280.0001.529
plot_ordination0.5480.0040.553
plot_phyloseq-methods0.2880.0040.205
plot_richness3.4400.0083.449
plot_scree2.2040.0042.210
plot_tree0.6480.0040.488
prune_samples-methods0.3720.0000.373
prune_taxa-methods0.0320.0040.036
psmelt0.6480.0040.652
rank_names0.0200.0000.022
rarefy_even_depth0.0960.0000.096
read_tree0.0680.0000.069
read_tree_greengenes0.0240.0000.023
reconcile_categories0.0040.0000.001
refseq-methods0.1400.0040.148
rm_outlierf0.0240.0000.024
sample_data-methods0.0640.0000.064
sample_names-methods0.0040.0000.003
sample_sums0.0240.0000.026
sample_variables0.0200.0000.022
show-methods000
splat.phyloseq.objects000
subset_ord_plot000
subset_samples-methods000
subset_taxa-methods000
tax_glom0.0000.0000.001
tax_table-methods0.0000.0000.001
taxa_names-methods0.020.000.02
taxa_sums0.0320.0000.029
threshrank1.9080.3562.265
threshrankfun0.0640.0000.063
tip_glom1.3720.0081.108
topf0.0120.0000.010
topk0.0120.0000.011
topp0.0120.0000.011
transformcounts0.0800.0000.078
transpose-methods0.4480.2280.675
tree_layout0.5400.0000.526