Nathan D. Olson
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/metagenomeFeatures |
| Branch: RELEASE_3_7 |
| Last Commit: c295899 |
| Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:41:12 -0400 (Wed, 17 Oct 2018).
| Package 872/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| metagenomeFeatures 2.0.0 Nathan D. Olson
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: metagenomeFeatures |
| Version: 2.0.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagenomeFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings metagenomeFeatures_2.0.0.tar.gz |
| StartedAt: 2018-10-17 03:11:47 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 03:14:10 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 143.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: metagenomeFeatures.Rcheck |
| Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagenomeFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings metagenomeFeatures_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/metagenomeFeatures.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * 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 '2.0.0' * 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: Warning: subclass "QualityScaledDNAStringSet" of class "DNAStringSet" is not local and cannot be updated for new inheritance information; consider setClassUnion() Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0mLViE/R.INSTALL1538dcf2909/metagenomeFeatures/man/mgFeatures-class.Rd:12: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0mLViE/R.INSTALL1538dcf2909/metagenomeFeatures/man/reexports.Rd:14: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic Warning: replacing previous import 'lazyeval::is_formula' by 'purrr::is_formula' when loading 'metagenomeFeatures' Warning: replacing previous import 'lazyeval::is_atomic' by 'purrr::is_atomic' when loading 'metagenomeFeatures' See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/metagenomeFeatures.Rcheck/00install.out' for details. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .select: no visible binding for global variable 'identifier' .select.taxa: no visible binding for global variable 'Keys' .select.taxa: no visible binding for global variable '.' get_gg13.8_85MgDb: no visible binding for global variable 'metadata' Undefined global functions or variables: . Keys identifier metadata * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '[' and siglist 'mgFeatures' All user-level objects in a package (including S4 classes and methods) 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 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, 1 NOTE See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/metagenomeFeatures.Rcheck/00check.log' for details.
metagenomeFeatures.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/metagenomeFeatures_2.0.0.tar.gz && rm -rf metagenomeFeatures.buildbin-libdir && mkdir metagenomeFeatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metagenomeFeatures.buildbin-libdir metagenomeFeatures_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL metagenomeFeatures_2.0.0.zip && rm metagenomeFeatures_2.0.0.tar.gz metagenomeFeatures_2.0.0.zip
###
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install for i386
* installing *source* package 'metagenomeFeatures' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'lazyeval::is_formula' by 'purrr::is_formula' when loading 'metagenomeFeatures'
Warning: replacing previous import 'lazyeval::is_atomic' by 'purrr::is_atomic' when loading 'metagenomeFeatures'
Warning: subclass "QualityScaledDNAStringSet" of class "DNAStringSet" is not local and cannot be updated for new inheritance information; consider setClassUnion()
** help
*** installing help indices
converting help for package 'metagenomeFeatures'
finding HTML links ... done
MgDb-class html
annotateFeatures-MgDb-method html
get_gg13.8_85MgDb html
make_mgdb_sqlite html
mgDb_ html
mgF_ html
mgFeatures-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0mLViE/R.INSTALL1538dcf2909/metagenomeFeatures/man/mgFeatures-class.Rd:12: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
mgFeatures html
mock_mgF html
mock_query_df html
newMgDb html
reexports html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0mLViE/R.INSTALL1538dcf2909/metagenomeFeatures/man/reexports.Rd:14: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
select-MgDb-method html
show-MgDb-method html
taxa_ html
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'lazyeval::is_formula' by 'purrr::is_formula' when loading 'metagenomeFeatures'
Warning: replacing previous import 'lazyeval::is_atomic' by 'purrr::is_atomic' when loading 'metagenomeFeatures'
In R CMD INSTALL
install for x64
* installing *source* package 'metagenomeFeatures' ...
** testing if installed package can be loaded
Warning: replacing previous import 'lazyeval::is_formula' by 'purrr::is_formula' when loading 'metagenomeFeatures'
Warning: replacing previous import 'lazyeval::is_atomic' by 'purrr::is_atomic' when loading 'metagenomeFeatures'
* MD5 sums
packaged installation of 'metagenomeFeatures' as metagenomeFeatures_2.0.0.zip
* DONE (metagenomeFeatures)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'metagenomeFeatures' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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metagenomeFeatures.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
dirname, 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")'.
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: 79 SKIPPED: 0 FAILED: 0
Warning messages:
1: replacing previous import 'lazyeval::is_formula' by 'purrr::is_formula' when loading 'metagenomeFeatures'
2: replacing previous import 'lazyeval::is_atomic' by 'purrr::is_atomic' when loading 'metagenomeFeatures'
3: call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
6.32 0.50 6.87
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metagenomeFeatures.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
dirname, 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")'.
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: 79 SKIPPED: 0 FAILED: 0
Warning messages:
1: replacing previous import 'lazyeval::is_formula' by 'purrr::is_formula' when loading 'metagenomeFeatures'
2: replacing previous import 'lazyeval::is_atomic' by 'purrr::is_atomic' when loading 'metagenomeFeatures'
3: call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
4.57 0.21 4.78
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metagenomeFeatures.Rcheck/examples_i386/metagenomeFeatures-Ex.timings
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metagenomeFeatures.Rcheck/examples_x64/metagenomeFeatures-Ex.timings
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