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CHECK report for phyloseq on merida2

This page was generated on 2019-04-09 13:26:50 -0400 (Tue, 09 Apr 2019).

Package 1185/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phyloseq 1.27.2
Paul J. McMurdie
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/phyloseq
Branch: master
Last Commit: 6cf7446
Last Changed Date: 2019-02-17 17:28:11 -0400 (Sun, 17 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: phyloseq
Version: 1.27.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings phyloseq_1.27.2.tar.gz
StartedAt: 2019-04-09 02:51:41 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:57:38 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 356.9 seconds
RetCode: 0
Status:  OK 
CheckDir: phyloseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings phyloseq_1.27.2.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/phyloseq.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.27.2’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* 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
Examples with CPU or elapsed time > 5s
               user system elapsed
plot_net      9.014  4.385   5.227
plot_heatmap  8.432  0.227   8.728
plot_richness 4.689  0.459   5.184
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/phyloseq.Rcheck/00check.log’
for details.



Installation output

phyloseq.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL phyloseq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘phyloseq’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘phyloseq-FAQ.Rmd’ using ‘UTF-8’ 
   ‘phyloseq-analysis.Rmd’ 
   ‘phyloseq-basics.Rmd’ 
   ‘phyloseq-mixture-models.Rmd’ 
** testing if installed package can be loaded
* DONE (phyloseq)

Tests output

phyloseq.Rcheck/tests/testthat-phyloseq.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> packageVersion("phyloseq")
[1] '1.27.2'
> # As suggested for opt-out option on testing by users, recommended by CRAN
> # http://adv-r.had.co.nz/Testing.html
> # Previously, best practice was to put all test files in inst/tests and ensure that R CMD check ran them by putting the following code in tests/test-all.R:  
> # library(testthat)
> # library(yourpackage)
> # test_package("yourpackage")
> # Now, recommended practice is to put your tests in tests/testthat, and ensure R CMD check runs them by putting the following code in tests/test-all.R:
> # library(testthat)
> # test_check("yourpackage")
> # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, but now you have the flexibility as requested by CRAN maintainers.
> test_check("phyloseq")
Loading required package: phyloseq
Found biom-format file, now parsing it... 
Done parsing biom... 
Importing Sample Metdadata from mapping file...
Merging the imported objects... 
Successfully merged, phyloseq-class created. 
 Returning... 
Found biom-format file, now parsing it... 
Done parsing biom... 
Importing Sample Metdadata from mapping file...
Merging the imported objects... 
Successfully merged, phyloseq-class created. 
 Returning... 
Reading `ucfile` into memory and parsing into table 
Initially read 100 entries. 
... Now removing unassigned OTUs (* or NA)... 
Removed 7 entries that had no OTU assignment. 
A total of 93 will be assigned to the OTU table.
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 2  
Converting input file to a table...
Defining OTU table... 
Parsing taxonomy table...
Processing phylogenetic tree...
 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing map file...
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 2  
Converting input file to a table...
Defining OTU table... 
Parsing taxonomy table...
Processing phylogenetic tree...
 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 613 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 95.687   6.955  98.572 

Example timings

phyloseq.Rcheck/phyloseq-Ex.timings

nameusersystemelapsed
DPCoA3.8010.2784.099
JSD000
UniFrac-methods0.1470.0070.154
access000
assign-otu_table0.0000.0010.001
assign-phy_tree0.0460.0040.050
assign-sample_data0.1860.0190.205
assign-sample_names0.0060.0010.007
assign-tax_table0.0000.0000.001
assign-taxa_are_rows0.0020.0010.004
assign-taxa_names0.0090.0030.012
build_tax_table0.0140.0010.015
capscale-phyloseq-methods0.8320.0530.890
cca-rda-phyloseq-methods0.0000.0000.001
chunkReOrder000
data-GlobalPatterns1.4580.0951.557
data-enterotype1.9010.0571.963
data-esophagus0.6520.0040.666
data-soilrep1.0980.1601.262
distance0.2290.0360.279
distanceMethodList0.0010.0000.001
envHash2otu_table0.0000.0000.001
estimate_richness0.0290.0020.031
export_env_file000
export_mothur_dist0.0970.0280.126
extract-methods0.0080.0020.009
filter_taxa1.3140.0731.392
filterfun_sample0.0230.0000.023
gapstat_ord1.8030.0331.843
genefilter_sample-methods000
get.component.classes0.0010.0000.000
get_sample-methods0.0030.0010.005
get_taxa-methods0.0040.0020.006
get_taxa_unique0.2700.0200.291
get_variable0.2050.0100.216
getslots.phyloseq0.2710.0200.292
import0.0010.0000.000
import_RDP_otu1.2100.0101.223
import_biom0.2290.0040.235
import_env_file0.0000.0000.001
import_mothur0.0000.0000.001
import_mothur_dist000
import_pyrotagger_tab0.0010.0000.000
import_qiime0.7720.0160.797
import_qiime_otu_tax0.7720.0750.848
import_qiime_sample_data0.0200.0020.021
import_uparse000
import_usearch_uc0.0980.0850.031
index_reorder0.0010.0010.000
intersect_taxa0.0010.0010.000
make_network3.4840.7083.084
merge_phyloseq0.0000.0010.000
merge_phyloseq_pair-methods0.0000.0000.001
merge_samples-methods1.2500.1201.376
merge_taxa-methods0.0640.0010.065
microbio_me_qiime1.5740.0191.604
mt-methods1.6120.0161.636
nodeplotblank1.6471.2510.459
nodeplotboot0.0060.0050.002
nodeplotdefault0.0020.0010.001
nsamples-methods0.0810.0560.034
ntaxa-methods0.0040.0040.008
ordinate0.0010.0000.000
otu_table-methods000
parseTaxonomy-functions0.0020.0000.003
phy_tree-methods0.2620.0170.282
phyloseq0.0280.0060.035
phyloseq_to_deseq24.0220.1174.176
phyloseq_to_metagenomeSeq1.1800.1271.314
plot_bar3.8490.2104.080
plot_clusgap3.7370.0933.867
plot_heatmap8.4320.2278.728
plot_net9.0144.3855.227
plot_network2.3590.0432.413
plot_ordination0.7950.0460.844
plot_phyloseq-methods1.0201.0420.334
plot_richness4.6890.4595.184
plot_scree1.8590.0741.944
plot_tree1.9301.3380.982
prune_samples-methods0.5300.0810.620
prune_taxa-methods0.0580.0010.060
psmelt1.1070.0931.222
rank_names0.0300.0050.035
rarefy_even_depth0.1060.0030.111
read_tree0.0290.0020.031
read_tree_greengenes0.0150.0010.017
reconcile_categories0.0000.0000.001
refseq-methods0.2010.0140.217
rm_outlierf0.0220.0010.023
sample_data-methods0.0660.0060.073
sample_names-methods0.0030.0000.003
sample_sums0.0250.0030.028
sample_variables0.0260.0010.027
show-methods0.0010.0000.001
splat.phyloseq.objects0.0010.0000.000
subset_ord_plot0.0010.0000.000
subset_samples-methods0.0000.0010.000
subset_taxa-methods000
tax_glom0.0000.0000.001
tax_table-methods0.0000.0010.000
taxa_names-methods0.0280.0020.030
taxa_sums0.0450.0110.056
threshrank2.8901.2544.162
threshrankfun0.0660.0040.069
tip_glom2.4591.5641.078
topf0.0170.0010.019
topk0.0170.0010.019
topp0.0150.0010.016
transformcounts0.1210.0030.125
transpose-methods1.2680.8492.222
tree_layout2.2591.7520.787