Paul J. McMurdie
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/phyloseq |
| Branch: RELEASE_3_10 |
| Last Commit: 2d3021b |
| Last Changed Date: 2019-10-29 13:08:27 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:06:47 -0400 (Wed, 15 Apr 2020).
| Package 1262/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| phyloseq 1.30.0 Paul J. McMurdie
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: phyloseq |
| Version: 1.30.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings phyloseq_1.30.0.tar.gz |
| StartedAt: 2020-04-15 01:13:55 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:20:12 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 377.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: phyloseq.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings phyloseq_1.30.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/phyloseq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.30.0’
* 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 ... 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 15.196 0.060 7.505
plot_heatmap 7.356 0.024 7.404
tip_glom 6.600 0.028 2.152
plot_tree 5.232 0.028 1.753
* 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
‘/home/biocbuild/bbs-3.10-bioc/meat/phyloseq.Rcheck/00check.log’
for details.
phyloseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL phyloseq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘phyloseq’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (phyloseq)
phyloseq.Rcheck/tests/testthat-phyloseq.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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] '1.30.0'
> # 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...
/home/biocbuild/bbs-3.10-bioc/R/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...
/home/biocbuild/bbs-3.10-bioc/R/library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 604 | SKIPPED: 0 | WARNINGS: 49 | FAILED: 0 ]
>
> proc.time()
user system elapsed
95.064 0.760 88.443
phyloseq.Rcheck/phyloseq-Ex.timings
| name | user | system | elapsed | |
| DPCoA | 3.376 | 0.096 | 3.519 | |
| JSD | 0 | 0 | 0 | |
| UniFrac-methods | 0.084 | 0.000 | 0.085 | |
| access | 0 | 0 | 0 | |
| assign-otu_table | 0 | 0 | 0 | |
| assign-phy_tree | 0.028 | 0.000 | 0.031 | |
| assign-sample_data | 0.108 | 0.008 | 0.117 | |
| assign-sample_names | 0.004 | 0.004 | 0.006 | |
| assign-tax_table | 0 | 0 | 0 | |
| assign-taxa_are_rows | 0.000 | 0.000 | 0.002 | |
| assign-taxa_names | 0.004 | 0.000 | 0.006 | |
| build_tax_table | 0.012 | 0.000 | 0.009 | |
| capscale-phyloseq-methods | 0.968 | 0.004 | 0.973 | |
| cca-rda-phyloseq-methods | 0 | 0 | 0 | |
| chunkReOrder | 0 | 0 | 0 | |
| data-GlobalPatterns | 1.480 | 0.004 | 1.483 | |
| data-enterotype | 0.988 | 0.004 | 0.996 | |
| data-esophagus | 0.684 | 0.000 | 0.747 | |
| data-soilrep | 1.332 | 0.024 | 1.361 | |
| distance | 0.244 | 0.060 | 1.240 | |
| distanceMethodList | 0 | 0 | 0 | |
| envHash2otu_table | 0 | 0 | 0 | |
| estimate_richness | 0.024 | 0.012 | 0.038 | |
| export_env_file | 0 | 0 | 0 | |
| export_mothur_dist | 0.068 | 0.012 | 0.078 | |
| extract-methods | 0.012 | 0.000 | 0.012 | |
| filter_taxa | 1.332 | 0.080 | 1.416 | |
| filterfun_sample | 0.024 | 0.000 | 0.027 | |
| gapstat_ord | 2.164 | 0.092 | 2.254 | |
| genefilter_sample-methods | 0 | 0 | 0 | |
| get.component.classes | 0.000 | 0.000 | 0.001 | |
| get_sample-methods | 0.004 | 0.000 | 0.003 | |
| get_taxa-methods | 0.004 | 0.000 | 0.003 | |
| get_taxa_unique | 0.196 | 0.004 | 0.201 | |
| get_variable | 0.168 | 0.000 | 0.166 | |
| getslots.phyloseq | 0.160 | 0.008 | 0.171 | |
| import | 0 | 0 | 0 | |
| import_RDP_otu | 0.324 | 0.004 | 0.341 | |
| import_biom | 0.192 | 0.000 | 0.189 | |
| import_env_file | 0.000 | 0.000 | 0.001 | |
| import_mothur | 0 | 0 | 0 | |
| import_mothur_dist | 0 | 0 | 0 | |
| import_pyrotagger_tab | 0 | 0 | 0 | |
| import_qiime | 0.752 | 0.004 | 0.778 | |
| import_qiime_otu_tax | 0.872 | 0.032 | 0.902 | |
| import_qiime_sample_data | 0.020 | 0.000 | 0.018 | |
| import_uparse | 0.000 | 0.000 | 0.001 | |
| import_usearch_uc | 0.016 | 0.004 | 0.020 | |
| index_reorder | 0 | 0 | 0 | |
| intersect_taxa | 0.000 | 0.000 | 0.001 | |
| make_network | 2.744 | 0.012 | 2.758 | |
| merge_phyloseq | 0 | 0 | 0 | |
| merge_phyloseq_pair-methods | 0 | 0 | 0 | |
| merge_samples-methods | 0.776 | 0.012 | 0.790 | |
| merge_taxa-methods | 0.060 | 0.000 | 0.059 | |
| microbio_me_qiime | 1.644 | 0.088 | 1.764 | |
| mt-methods | 1.608 | 0.016 | 1.626 | |
| nodeplotblank | 4.756 | 0.032 | 1.347 | |
| nodeplotboot | 0.004 | 0.000 | 0.001 | |
| nodeplotdefault | 0.000 | 0.000 | 0.001 | |
| nsamples-methods | 0.012 | 0.004 | 0.017 | |
| ntaxa-methods | 0.004 | 0.000 | 0.003 | |
| ordinate | 0 | 0 | 0 | |
| otu_table-methods | 0.000 | 0.000 | 0.001 | |
| parseTaxonomy-functions | 0.004 | 0.000 | 0.001 | |
| phy_tree-methods | 0.156 | 0.004 | 0.160 | |
| phyloseq | 0.016 | 0.000 | 0.019 | |
| phyloseq_to_deseq2 | 4.096 | 0.260 | 4.370 | |
| phyloseq_to_metagenomeSeq | 2.088 | 0.020 | 2.109 | |
| plot_bar | 2.932 | 0.104 | 3.043 | |
| plot_clusgap | 4.076 | 0.016 | 4.121 | |
| plot_heatmap | 7.356 | 0.024 | 7.404 | |
| plot_net | 15.196 | 0.060 | 7.505 | |
| plot_network | 2.084 | 0.008 | 2.103 | |
| plot_ordination | 0.552 | 0.004 | 0.554 | |
| plot_phyloseq-methods | 2.412 | 0.020 | 0.696 | |
| plot_richness | 4.112 | 0.020 | 4.147 | |
| plot_scree | 1.680 | 0.008 | 1.694 | |
| plot_tree | 5.232 | 0.028 | 1.753 | |
| prune_samples-methods | 0.548 | 0.016 | 0.568 | |
| prune_taxa-methods | 0.052 | 0.000 | 0.052 | |
| psmelt | 1.232 | 0.000 | 1.235 | |
| rank_names | 0.028 | 0.004 | 0.032 | |
| rarefy_even_depth | 0.104 | 0.000 | 0.105 | |
| read_tree | 0.028 | 0.000 | 0.029 | |
| read_tree_greengenes | 0.012 | 0.000 | 0.023 | |
| reconcile_categories | 0.000 | 0.004 | 0.001 | |
| refseq-methods | 0.248 | 0.012 | 0.263 | |
| rm_outlierf | 0.024 | 0.000 | 0.025 | |
| sample_data-methods | 0.08 | 0.00 | 0.08 | |
| sample_names-methods | 0.004 | 0.000 | 0.002 | |
| sample_sums | 0.036 | 0.000 | 0.037 | |
| sample_variables | 0.028 | 0.004 | 0.031 | |
| 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 | 0.000 | 0.000 | 0.001 | |
| tax_table-methods | 0.000 | 0.000 | 0.001 | |
| taxa_names-methods | 0.028 | 0.000 | 0.028 | |
| taxa_sums | 0.036 | 0.008 | 0.042 | |
| threshrank | 2.312 | 0.456 | 2.771 | |
| threshrankfun | 0.040 | 0.000 | 0.041 | |
| tip_glom | 6.600 | 0.028 | 2.152 | |
| topf | 0.016 | 0.000 | 0.015 | |
| topk | 0.012 | 0.000 | 0.013 | |
| topp | 0.012 | 0.000 | 0.012 | |
| transformcounts | 0.096 | 0.000 | 0.100 | |
| transpose-methods | 0.700 | 0.376 | 1.080 | |
| tree_layout | 2.292 | 0.016 | 0.790 | |