Nathan D. Olson
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/metagenomeFeatures |
| Branch: RELEASE_3_6 |
| Last Commit: af71628 |
| Last Changed Date: 2017-10-30 12:41:05 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:26:58 -0400 (Thu, 12 Apr 2018).
| Package 823/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| metagenomeFeatures 1.10.0 Nathan D. Olson
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| Package: metagenomeFeatures |
| Version: 1.10.0 |
| Command: rm -rf metagenomeFeatures.buildbin-libdir metagenomeFeatures.Rcheck && mkdir metagenomeFeatures.buildbin-libdir metagenomeFeatures.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metagenomeFeatures.buildbin-libdir metagenomeFeatures_1.10.0.tar.gz >metagenomeFeatures.Rcheck\00install.out 2>&1 && cp metagenomeFeatures.Rcheck\00install.out metagenomeFeatures-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=metagenomeFeatures.buildbin-libdir --install="check:metagenomeFeatures-install.out" --force-multiarch --no-vignettes --timings metagenomeFeatures_1.10.0.tar.gz |
| StartedAt: 2018-04-12 01:15:33 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:20:57 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 324.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: metagenomeFeatures.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf metagenomeFeatures.buildbin-libdir metagenomeFeatures.Rcheck && mkdir metagenomeFeatures.buildbin-libdir metagenomeFeatures.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metagenomeFeatures.buildbin-libdir metagenomeFeatures_1.10.0.tar.gz >metagenomeFeatures.Rcheck\00install.out 2>&1 && cp metagenomeFeatures.Rcheck\00install.out metagenomeFeatures-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=metagenomeFeatures.buildbin-libdir --install="check:metagenomeFeatures-install.out" --force-multiarch --no-vignettes --timings metagenomeFeatures_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/metagenomeFeatures.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metagenomeFeatures/DESCRIPTION' ... OK
* this is package 'metagenomeFeatures' version '1.10.0'
* 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 'metagenomeFeatures' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuEyB3R/R.INSTALL137025d73fc5/metagenomeFeatures/man/mgFeatures-class.Rd:12: missing file link 'AnnotatedDataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuEyB3R/R.INSTALL137025d73fc5/metagenomeFeatures/man/reexports.Rd:14: missing file link '%>%'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/metagenomeFeatures.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 9.9Mb
sub-directories of 1Mb or more:
data 2.1Mb
extdata 6.7Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
.mgDb_annotateFeatures: no visible binding for global variable
'db_keys'
.select.taxa: no visible binding for global variable 'Keys'
.select.taxa: no visible binding for global variable '.'
aggregate_taxa: no visible binding for global variable '.'
aggregate_taxa: no visible binding for global variable 'index'
vignette_pheno_data: no visible global function definition for
'read.csv'
Undefined global functions or variables:
. Keys db_keys index read.csv
Consider adding
importFrom("utils", "read.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'msd16s_metagenomeAnnotation' 'msd16s_query_df'
Undocumented data sets:
'msd16s_metagenomeAnnotation' 'msd16s_query_df'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/metagenomeFeatures.Rcheck/00check.log'
for details.
metagenomeFeatures.Rcheck/00install.out
install for i386
* installing *source* package 'metagenomeFeatures' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'metagenomeFeatures'
finding HTML links ... done
MgDb-class html
aggregate_taxa html
annotateFeatures-MgDb-method html
annotateMRexp_fData-MgDb-method html
get_demoMgDb html
get_mockMgDb html
mgF_meta html
mgF_seq html
mgF_taxa html
mgF_tree html
mgFeatures-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuEyB3R/R.INSTALL137025d73fc5/metagenomeFeatures/man/mgFeatures-class.Rd:12: missing file link 'AnnotatedDataFrame'
mgQuery html
mgdb_meta html
mgdb_seq html
mgdb_taxa html
mgdb_tree html
mock_mgF html
mock_query_df html
reexports html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuEyB3R/R.INSTALL137025d73fc5/metagenomeFeatures/man/reexports.Rd:14: missing file link '%>%'
select-MgDb-method html
show-MgDb-method html
taxa_columns html
taxa_keys html
taxa_keytypes html
taxa_levels html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'metagenomeFeatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metagenomeFeatures' as metagenomeFeatures_1.10.0.zip
* DONE (metagenomeFeatures)
In R CMD INSTALL
In R CMD INSTALL
|
metagenomeFeatures.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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)
>
> test_check("metagenomeFeatures")
Loading required package: metagenomeFeatures
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16
Loading required package: RColorBrewer
Attaching package: 'dplyr'
The following object is masked from 'package:Biobase':
combine
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
== testthat results ===========================================================
OK: 90 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
9.68 0.29 9.96
|
metagenomeFeatures.Rcheck/tests_x64/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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)
>
> test_check("metagenomeFeatures")
Loading required package: metagenomeFeatures
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16
Loading required package: RColorBrewer
Attaching package: 'dplyr'
The following object is masked from 'package:Biobase':
combine
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
== testthat results ===========================================================
OK: 90 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
11.65 0.29 11.95
|
|
metagenomeFeatures.Rcheck/examples_i386/metagenomeFeatures-Ex.timings
|
metagenomeFeatures.Rcheck/examples_x64/metagenomeFeatures-Ex.timings
|