Nathan D. Olson
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/metagenomeFeatures |
| Branch: RELEASE_3_11 |
| Last Commit: b3e4e05 |
| Last Changed Date: 2020-04-27 14:51:49 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:03 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE metagenomeFeatures PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1037/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| metagenomeFeatures 2.8.0 Nathan D. Olson
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: metagenomeFeatures |
| Version: 2.8.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagenomeFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings metagenomeFeatures_2.8.0.tar.gz |
| StartedAt: 2020-10-17 05:49:39 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:52:43 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 183.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: metagenomeFeatures.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagenomeFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings metagenomeFeatures_2.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/metagenomeFeatures.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '2.8.0'
* package encoding: UTF-8
* 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-3.11-bioc/tmpdir/RtmpSuHbZJ/R.INSTALL1a50240e4a97/metagenomeFeatures/man/mgFeatures-class.Rd:27: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpSuHbZJ/R.INSTALL1a50240e4a97/metagenomeFeatures/man/reexports.Rd:14: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/metagenomeFeatures.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
extdata 3.5Mb
* 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
Package in Depends field not imported from: 'Biobase'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.select.taxa: no visible binding for global variable 'Keys'
Undefined global functions or variables:
Keys
* 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 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: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-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/3.11/bioc/src/contrib/metagenomeFeatures_2.8.0.tar.gz && rm -rf metagenomeFeatures.buildbin-libdir && mkdir metagenomeFeatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metagenomeFeatures.buildbin-libdir metagenomeFeatures_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL metagenomeFeatures_2.8.0.zip && rm metagenomeFeatures_2.8.0.tar.gz metagenomeFeatures_2.8.0.zip
###
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install for i386
* installing *source* package 'metagenomeFeatures' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'metagenomeFeatures'
finding HTML links ... done
MgDb-accessor html
MgDb-class html
MgDb-methods html
annotateFeatures-MgDb-method html
get_gg13.8_85MgDb html
make_mgdb_sqlite html
mgFeatures-accessors html
mgFeatures-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpSuHbZJ/R.INSTALL1a50240e4a97/metagenomeFeatures/man/mgFeatures-class.Rd:27: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
mgFeatures-methods html
mock_mgF html
mock_query_df html
newMgDb html
qiita_study_94_gg_ids html
reexports html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpSuHbZJ/R.INSTALL1a50240e4a97/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
taxa_ html
** building package indices
** installing vignettes
** 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
install for x64
* installing *source* package 'metagenomeFeatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metagenomeFeatures' as metagenomeFeatures_2.8.0.zip
* DONE (metagenomeFeatures)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'metagenomeFeatures' successfully unpacked and MD5 sums checked
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metagenomeFeatures.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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 | WARNINGS: 2 | FAILED: 0 ]
Warning messages:
1: `as_data_frame()` is deprecated as of tibble 2.0.0.
Please use `as_tibble()` instead.
The signature and semantics have changed, see `?as_tibble`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
2: call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
8.01 0.45 8.45
|
metagenomeFeatures.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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 | WARNINGS: 2 | FAILED: 0 ]
Warning messages:
1: `as_data_frame()` is deprecated as of tibble 2.0.0.
Please use `as_tibble()` instead.
The signature and semantics have changed, see `?as_tibble`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
2: call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
8.81 0.32 9.12
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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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