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CHECK report for HMP16SData on riesling1

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 177/385HostnameOS / ArchINSTALLBUILDCHECK
HMP16SData 1.11.0
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)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ]

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.



Installation output

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
###
##############################################################################
##############################################################################


  % 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

Tests output

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 

Example timings

HMP16SData.Rcheck/examples_i386/HMP16SData-Ex.timings

nameusersystemelapsed
V136.390.907.61
V357.330.448.03
as_phyloseq8.670.739.77
attach_dbGaP000
dictionary000
kable_one5.220.335.93
reexports4.960.575.86
table_one5.560.706.54

HMP16SData.Rcheck/examples_x64/HMP16SData-Ex.timings

nameusersystemelapsed
V136.640.757.70
V357.170.337.82
as_phyloseq8.610.829.78
attach_dbGaP000
dictionary000
kable_one5.000.325.69
reexports4.800.495.59
table_one5.500.646.43