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CHECK report for curatedMetagenomicData on riesling1

This page was generated on 2021-01-14 15:59:07 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE curatedMetagenomicData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 85/385HostnameOS / ArchINSTALLBUILDCHECK
curatedMetagenomicData 1.21.0
Lucas Schiffer
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/curatedMetagenomicData
Branch: master
Last Commit: 8f99117
Last Changed Date: 2020-10-27 10:20:00 -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 [ OK ]

Summary

Package: curatedMetagenomicData
Version: 1.21.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:curatedMetagenomicData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings curatedMetagenomicData_1.21.0.tar.gz
StartedAt: 2021-01-14 11:12:55 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:22:21 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 565.8 seconds
RetCode: 0
Status:  OK  
CheckDir: curatedMetagenomicData.Rcheck
Warnings: 0

Command output

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##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:curatedMetagenomicData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings curatedMetagenomicData_1.21.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/curatedMetagenomicData.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 'curatedMetagenomicData/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'curatedMetagenomicData' version '1.21.0'
* 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 'curatedMetagenomicData' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    help      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 ... 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
mergeData              4.92   0.36    6.61
curatedMetagenomicData 4.84   0.29    6.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
curatedMetagenomicData 5.50   0.25    6.33
mergeData              5.22   0.33    6.14
ExpressionSet2phyloseq 4.53   0.30    5.14
* 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 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/curatedMetagenomicData.Rcheck/00check.log'
for details.



Installation output

curatedMetagenomicData.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/curatedMetagenomicData_1.21.0.tar.gz && rm -rf curatedMetagenomicData.buildbin-libdir && mkdir curatedMetagenomicData.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=curatedMetagenomicData.buildbin-libdir curatedMetagenomicData_1.21.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL curatedMetagenomicData_1.21.0.zip && rm curatedMetagenomicData_1.21.0.tar.gz curatedMetagenomicData_1.21.0.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
100 4522k  100 4522k    0     0  61.3M      0 --:--:-- --:--:-- --:--:-- 61.3M

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'curatedMetagenomicData' ...
** 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 'curatedMetagenomicData'
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    JieZ_2017                               html  
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    KieserS_2018                            html  
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    LiJ_2014                                html  
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    LiJ_2017                                html  
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    LiSS_2016                               html  
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    LiuW_2016                               html  
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    LomanNJ_2013                            html  
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    LoombaR_2017                            html  
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    LouisS_2016                             html  
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    MatsonV_2018                            html  
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    OhJ_2014                                html  
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    OlmMR_2017                              html  
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    PasolliE_2018                           html  
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    PehrssonE_2016                          html  
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    QinJ_2012                               html  
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    QinN_2014                               html  
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    RampelliS_2015                          html  
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    SchirmerM_2016                          html  
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    ShiB_2015                               html  
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    SmitsSA_2017                            html  
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    TettAJ_2016                             html  
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    TettAJ_2019_a                           html  
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    TettAJ_2019_b                           html  
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    TettAJ_2019_c                           html  
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*** copying figures
** 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

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'curatedMetagenomicData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'curatedMetagenomicData' as curatedMetagenomicData_1.21.0.zip
* DONE (curatedMetagenomicData)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'curatedMetagenomicData' successfully unpacked and MD5 sums checked

Tests output

curatedMetagenomicData.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(curatedMetagenomicData)
Loading required package: AnnotationHub
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: BiocFileCache
Loading required package: dbplyr
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:AnnotationHub':

    cache

Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:Biobase':

    combine

The following objects are masked from 'package:dbplyr':

    ident, sql

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

Loading required package: ExperimentHub
                      _           _
  ___ _   _ _ __ __ _| |_ ___  __| |
 / __| | | | '__/ _` | __/ _ \/ _` |
| (__| |_| | | | (_| | ||  __/ (_| |
 \___|\__,_|_|  \__,_|\__\___|\__,_|
 __  __      _                                         _
|  \/  | ___| |_ __ _  __ _  ___ _ __   ___  _ __ ___ (_) ___
| |\/| |/ _ \ __/ _` |/ _` |/ _ \ '_ \ / _ \| '_ ` _ \| |/ __|
| |  | |  __/ || (_| | (_| |  __/ | | | (_) | | | | | | | (__
|_|  |_|\___|\__\__,_|\__, |\___|_| |_|\___/|_| |_| |_|_|\___|
 ____        _        |___/
|  _ \  __ _| |_ __ _
| | | |/ _` | __/ _` |
| |_| | (_| | || (_| |
|____/ \__,_|\__\__,_|

> 
> test_check("curatedMetagenomicData")
== Warnings ====================================================================
-- Warning (test-ExpressionSet2MRexperiment.R:6:3): ExpressionSet2MRexperiment works --
`data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Backtrace:
 1. curatedMetagenomicData::ExpressionSet2MRexperiment(eset) test-ExpressionSet2MRexperiment.R:6:2
 5. tibble::data_frame(.)

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 40 ]
> 
> proc.time()
   user  system elapsed 
  31.54    2.40   37.25 

curatedMetagenomicData.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(curatedMetagenomicData)
Loading required package: AnnotationHub
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: BiocFileCache
Loading required package: dbplyr
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:AnnotationHub':

    cache

Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:Biobase':

    combine

The following objects are masked from 'package:dbplyr':

    ident, sql

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

Loading required package: ExperimentHub
                      _           _
  ___ _   _ _ __ __ _| |_ ___  __| |
 / __| | | | '__/ _` | __/ _ \/ _` |
| (__| |_| | | | (_| | ||  __/ (_| |
 \___|\__,_|_|  \__,_|\__\___|\__,_|
 __  __      _                                         _
|  \/  | ___| |_ __ _  __ _  ___ _ __   ___  _ __ ___ (_) ___
| |\/| |/ _ \ __/ _` |/ _` |/ _ \ '_ \ / _ \| '_ ` _ \| |/ __|
| |  | |  __/ || (_| | (_| |  __/ | | | (_) | | | | | | | (__
|_|  |_|\___|\__\__,_|\__, |\___|_| |_|\___/|_| |_| |_|_|\___|
 ____        _        |___/
|  _ \  __ _| |_ __ _
| | | |/ _` | __/ _` |
| |_| | (_| | || (_| |
|____/ \__,_|\__\__,_|

> 
> test_check("curatedMetagenomicData")
== Warnings ====================================================================
-- Warning (test-ExpressionSet2MRexperiment.R:6:3): ExpressionSet2MRexperiment works --
`data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Backtrace:
 1. curatedMetagenomicData::ExpressionSet2MRexperiment(eset) test-ExpressionSet2MRexperiment.R:6:2
 5. tibble::data_frame(.)

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 40 ]
> 
> proc.time()
   user  system elapsed 
  32.79    2.43   38.64 

Example timings

curatedMetagenomicData.Rcheck/examples_i386/curatedMetagenomicData-Ex.timings

nameusersystemelapsed
AsnicarF_20173.360.794.84
BackhedF_20152.440.142.90
Bengtsson-PalmeJ_20152.500.082.86
BritoIL_20162.370.142.84
Castro-NallarE_20152.360.162.81
ChengpingW_20172.270.192.73
ChngKR_20162.370.122.81
CosteaPI_20172.250.092.64
DavidLA_20152.180.102.59
DhakanDB_20192.220.092.66
ExpressionSet2MRexperiment3.140.193.62
ExpressionSet2phyloseq4.340.254.89
FengQ_20152.470.142.96
FerrettiP_20182.470.092.86
GopalakrishnanV_20182.400.183.16
HMP_20122.500.112.91
HanniganGD_20172.530.092.94
HansenLBS_20182.380.172.87
Heitz-BuschartA_20162.340.162.82
JieZ_20172.520.122.96
KarlssonFH_20132.480.132.89
KieserS_20182.470.142.88
KosticAD_20152.490.112.89
LeChatelierE_20132.420.222.95
LiJ_20142.700.173.23
LiJ_20172.30.22.8
LiSS_20162.340.132.84
LiuW_20162.330.142.79
LomanNJ_20132.310.182.76
LoombaR_20172.390.082.79
LouisS_20162.380.162.79
MatsonV_20182.530.122.95
NielsenHB_20142.470.072.88
Obregon-TitoAJ_20152.360.212.96
OhJ_20142.530.152.99
OlmMR_20172.450.152.87
PasolliE_20182.460.163.00
PehrssonE_20162.450.142.94
QinJ_20122.470.122.91
QinN_20142.470.143.01
RampelliS_20152.400.182.90
RaymondF_20162.500.122.92
SchirmerM_20162.470.192.92
ShiB_20152.470.122.90
SmitsSA_20172.450.192.92
TettAJ_20162.480.162.92
TettAJ_2019_a2.470.112.84
TettAJ_2019_b2.440.152.88
TettAJ_2019_c2.450.143.23
ThomasAM_2018a2.380.212.86
ThomasAM_2018b2.730.143.53
VatanenT_20162.420.152.86
VincentC_20162.270.212.81
VogtmannE_20162.370.092.77
XieH_20162.300.223.09
YeZ_20182.420.143.09
YuJ_20152.460.082.83
ZeeviD_20152.570.092.97
ZellerG_20142.460.113.49
cmdValidVersions0.000.020.01
curatedMetagenomicData4.840.296.14
getMetaphlanTree0.300.020.31
mergeData4.920.366.61

curatedMetagenomicData.Rcheck/examples_x64/curatedMetagenomicData-Ex.timings

nameusersystemelapsed
AsnicarF_20173.540.734.82
BackhedF_20152.620.113.00
Bengtsson-PalmeJ_20152.530.202.98
BritoIL_20162.440.162.86
Castro-NallarE_20152.420.202.91
ChengpingW_20172.530.132.93
ChngKR_20162.670.123.05
CosteaPI_20172.460.162.87
DavidLA_20152.510.062.91
DhakanDB_20192.500.112.98
ExpressionSet2MRexperiment3.390.173.84
ExpressionSet2phyloseq4.530.305.14
FengQ_20152.640.163.07
FerrettiP_20182.610.153.09
GopalakrishnanV_20182.940.113.38
HMP_20122.440.142.93
HanniganGD_20172.470.192.92
HansenLBS_20182.450.162.86
Heitz-BuschartA_20162.420.222.95
JieZ_20172.580.122.97
KarlssonFH_20132.550.172.97
KieserS_20182.510.102.92
KosticAD_20152.520.152.94
LeChatelierE_20132.510.142.97
LiJ_20142.660.083.03
LiJ_20172.610.133.01
LiSS_20162.640.143.08
LiuW_20162.560.153.04
LomanNJ_20132.600.163.10
LoombaR_20172.530.163.00
LouisS_20162.630.092.98
MatsonV_20182.610.143.03
NielsenHB_20142.610.143.08
Obregon-TitoAJ_20152.690.113.17
OhJ_20142.540.203.02
OlmMR_20172.580.163.01
PasolliE_20182.640.143.06
PehrssonE_20162.920.173.41
QinJ_20122.570.112.93
QinN_20142.570.113.09
RampelliS_20152.550.173.03
RaymondF_20162.660.113.05
SchirmerM_20162.590.173.04
ShiB_20152.580.102.97
SmitsSA_20172.590.092.98
TettAJ_20162.490.192.99
TettAJ_2019_a2.650.083.03
TettAJ_2019_b2.600.173.06
TettAJ_2019_c2.620.113.05
ThomasAM_2018a2.580.153.04
ThomasAM_2018b2.590.183.08
VatanenT_20162.550.143.00
VincentC_20162.670.063.33
VogtmannE_20162.580.193.03
XieH_20162.530.203.03
YeZ_20182.530.163.02
YuJ_20152.530.153.03
ZeeviD_20152.640.103.03
ZellerG_20142.650.123.05
cmdValidVersions0.010.000.01
curatedMetagenomicData5.500.256.33
getMetaphlanTree0.250.030.28
mergeData5.220.336.14