phyloseq 1.20.0 Paul J. McMurdie
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | URL: https://git.bioconductor.org/packages/phyloseq | Branch: RELEASE_3_5 | Last Commit: 107d1d5 | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.20.0.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/phyloseq.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* 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
':::' 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_heatmap 7.16 0.06 7.22
DPCoA 5.25 0.06 5.31
plot_net 5.08 0.08 5.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat-phyloseq.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.5-bioc/meat/phyloseq.Rcheck/00check.log'
for details.
install for i386
* 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
install for x64
* installing *source* package 'phyloseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'phyloseq' as phyloseq_1.20.0.zip
* DONE (phyloseq)