Lucas Schiffer
| Snapshot Date: 2021-01-11 09:00:09 -0500 (Mon, 11 Jan 2021) |
| URL: https://git.bioconductor.org/packages/HMP16SData |
| Branch: master |
| Last Commit: 092364b |
| Last Changed Date: 2020-10-27 10:24:33 -0500 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.13 experimental data |
|
This page was generated on 2021-01-11 15:59:31 -0500 (Mon, 11 Jan 2021).
| TO THE DEVELOPERS/MAINTAINERS OF THE HMP16SData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 177/385 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| HMP16SData 1.11.0 Lucas Schiffer
| malbec2 | Linux (Ubuntu 20.04.1 LTS) / x86_64 | OK | OK | OK | | |||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | [ WARNINGS ] |
| Package: HMP16SData |
| Version: 1.11.0 |
| Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HMP16SData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings HMP16SData_1.11.0.tar.gz |
| StartedAt: 2021-01-11 11:28:47 -0500 (Mon, 11 Jan 2021) |
| EndedAt: 2021-01-11 11:34:17 -0500 (Mon, 11 Jan 2021) |
| EllapsedTime: 329.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HMP16SData.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HMP16SData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings HMP16SData_1.11.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/HMP16SData.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HMP16SData/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HMP16SData' version '1.11.0'
* 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 'HMP16SData' can be installed ... WARNING
Found the following significant warnings:
Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-data-experiment/meat/HMP16SData.buildbin-libdir/00LOCK-HMP16SData/00new/HMP16SData/help/%>%.html': Invalid argument
See 'D:/biocbuild/bbs-3.13-data-experiment/meat/HMP16SData.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 17.6Mb
sub-directories of 1Mb or more:
extdata 17.4Mb
* 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 ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
as_phyloseq 8.67 0.73 9.77
V35 7.33 0.44 8.03
V13 6.39 0.90 7.61
table_one 5.56 0.70 6.54
kable_one 5.22 0.33 5.93
reexports 4.96 0.57 5.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
as_phyloseq 8.61 0.82 9.78
V35 7.17 0.33 7.82
V13 6.64 0.75 7.70
table_one 5.50 0.64 6.43
kable_one 5.00 0.32 5.69
reexports 4.80 0.49 5.59
* 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, 1 NOTE
See
'D:/biocbuild/bbs-3.13-data-experiment/meat/HMP16SData.Rcheck/00check.log'
for details.
HMP16SData.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/HMP16SData_1.11.0.tar.gz && rm -rf HMP16SData.buildbin-libdir && mkdir HMP16SData.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HMP16SData.buildbin-libdir HMP16SData_1.11.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL HMP16SData_1.11.0.zip && rm HMP16SData_1.11.0.tar.gz HMP16SData_1.11.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 15.5M 0 1214 0 0 1157 0 3:54:21 0:00:01 3:54:20 1157
36 15.5M 36 5731k 0 0 3728k 0 0:00:04 0:00:01 0:00:03 3728k
100 15.5M 100 15.5M 0 0 8052k 0 0:00:01 0:00:01 --:--:-- 8052k
install for i386
* installing *source* package 'HMP16SData' ...
** 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 'HMP16SData'
finding HTML links ... done
HMP16SData html
REDIRECT:topic HMP16SData -> HMP16SData.html [ SUCCESS ]
V13 html
REDIRECT:topic V13 -> V13.html [ SUCCESS ]
V35 html
REDIRECT:topic V35 -> V35.html [ SUCCESS ]
as_phyloseq html
REDIRECT:topic as_phyloseq -> as_phyloseq.html [ SUCCESS ]
attach_dbGaP html
REDIRECT:topic attach_dbGaP -> attach_dbGaP.html [ SUCCESS ]
dictionary html
REDIRECT:topic dictionary -> dictionary.html [ SUCCESS ]
kable_one html
REDIRECT:topic kable_one -> kable_one.html [ SUCCESS ]
reexports html
REDIRECT:topic reexports -> reexports.html [ SUCCESS ]
REDIRECT:topic %>% -> reexports.html [ FAIL ]
Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-data-experiment/meat/HMP16SData.buildbin-libdir/00LOCK-HMP16SData/00new/HMP16SData/help/%>%.html': Invalid argument
table_one html
REDIRECT:topic table_one -> table_one.html [ SUCCESS ]
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2021-01-07
** testing if installed package can be loaded from final location
snapshotDate(): 2021-01-07
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'HMP16SData' ...
** testing if installed package can be loaded
snapshotDate(): 2021-01-07
* MD5 sums
packaged installation of 'HMP16SData' as HMP16SData_1.11.0.zip
* DONE (HMP16SData)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'HMP16SData' successfully unpacked and MD5 sums checked
|
HMP16SData.Rcheck/tests_i386/testthat.Rout
R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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)
> library(HMP16SData)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
snapshotDate(): 2021-01-07
>
> test_check("HMP16SData")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
20.23 1.40 22.71
|
HMP16SData.Rcheck/tests_x64/testthat.Rout
R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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)
> library(HMP16SData)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
snapshotDate(): 2021-01-07
>
> test_check("HMP16SData")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
21.00 1.45 23.43
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HMP16SData.Rcheck/examples_i386/HMP16SData-Ex.timings
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HMP16SData.Rcheck/examples_x64/HMP16SData-Ex.timings
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