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CHECK report for Metab on tokay2

This page was generated on 2018-10-17 08:39:41 -0400 (Wed, 17 Oct 2018).

Package 866/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Metab 1.14.0
Raphael Aggio
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Metab
Branch: RELEASE_3_7
Last Commit: 152eb53
Last Changed Date: 2018-04-30 10:35:35 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Metab
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Metab.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Metab_1.14.0.tar.gz
StartedAt: 2018-10-17 03:11:02 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:14:52 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 230.2 seconds
RetCode: 0
Status:  OK  
CheckDir: Metab.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Metab.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Metab_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Metab.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 'Metab/DESCRIPTION' ... OK
* this is package 'Metab' version '1.14.0'
* 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 'Metab' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
MetReport: no visible global function definition for 'read.csv'
MetReport: no visible global function definition for 'write.csv'
MetReportNames: no visible global function definition for 'read.csv'
MetReportNames: no visible global function definition for 'write.csv'
buildLib: no visible global function definition for 'read.csv'
buildLib: no visible global function definition for 'txtProgressBar'
buildLib: no visible global function definition for 'setTxtProgressBar'
buildLib: no visible global function definition for 'write.csv'
htest : test.t : <anonymous>: no visible global function definition for
  't.test'
htest : anova.t : <anonymous>: no visible global function definition
  for 'lm'
htest : anova.t: no visible binding for global variable 'anova'
htest: no visible global function definition for 'read.csv'
htest: no visible global function definition for 'p.adjust'
htest: no visible global function definition for 'write.csv'
normalizeByBiomass: no visible global function definition for
  'read.csv'
normalizeByBiomass: no visible global function definition for
  'write.csv'
normalizeByInternalStandard: no visible global function definition for
  'read.csv'
normalizeByInternalStandard: no visible global function definition for
  'select.list'
normalizeByInternalStandard: no visible global function definition for
  'write.csv'
removeFalsePositives: no visible global function definition for
  'read.csv'
removeFalsePositives: no visible global function definition for
  'write.csv'
Undefined global functions or variables:
  anova lm p.adjust read.csv select.list setTxtProgressBar t.test
  txtProgressBar write.csv
Consider adding
  importFrom("stats", "anova", "lm", "p.adjust", "t.test")
  importFrom("utils", "read.csv", "select.list", "setTxtProgressBar",
             "txtProgressBar", "write.csv")
to your NAMESPACE file.
* 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 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/Metab.Rcheck/00check.log'
for details.



Installation output

Metab.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/Metab_1.14.0.tar.gz && rm -rf Metab.buildbin-libdir && mkdir Metab.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Metab.buildbin-libdir Metab_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Metab_1.14.0.zip && rm Metab_1.14.0.tar.gz Metab_1.14.0.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     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3095k  100 3095k    0     0  26.8M      0 --:--:-- --:--:-- --:--:-- 28.5M

install for i386

* installing *source* package 'Metab' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Metab'
    finding HTML links ... done
    MetReport                               html  
    MetReportNames                          html  
    Metab-package                           html  
    buildLib                                html  
    exampleAMDISReport                      html  
    exampleBiomass                          html  
    exampleHtest                            html  
    exampleIonLib                           html  
    exampleMSLfile                          html  
    exampleMetReport                        html  
    htest                                   html  
    normalizeByBiomass                      html  
    normalizeByInternalStandard             html  
    removeFalsePositives                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Metab' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Metab' as Metab_1.14.0.zip
* DONE (Metab)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Metab' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Metab.Rcheck/tests_i386/test-all.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.

> BiocGenerics:::testPackage("Metab")

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")'.


This is MSnbase version 2.6.4 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws


This is xcms version 3.2.0 


Attaching package: 'xcms'

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

    sigma

AMDIS Report - Data frame loaded...
File 1 (130513_REF_SOL2_2_50_50_1.CDF) done!
AmdisReport - Data frame loaded...
File 130513_REF_SOL2_2_100_1 done!
Data frame loaded...
Biomass loaded...
Data frame loaded...
Data frame loaded...


RUNIT TEST PROTOCOL -- Wed Oct 17 03:14:38 2018 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Metab RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.90    0.56    6.75 

Metab.Rcheck/tests_x64/test-all.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.

> BiocGenerics:::testPackage("Metab")

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")'.


This is MSnbase version 2.6.4 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws


This is xcms version 3.2.0 


Attaching package: 'xcms'

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

    sigma

AMDIS Report - Data frame loaded...
File 1 (130513_REF_SOL2_2_50_50_1.CDF) done!
AmdisReport - Data frame loaded...
File 130513_REF_SOL2_2_100_1 done!
Data frame loaded...
Biomass loaded...
Data frame loaded...
Data frame loaded...


RUNIT TEST PROTOCOL -- Wed Oct 17 03:14:46 2018 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Metab RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   6.82    0.51    7.46 

Example timings

Metab.Rcheck/examples_i386/Metab-Ex.timings

nameusersystemelapsed
MetReport0.280.000.72
MetReportNames0.130.040.17
Metab-package0.010.000.01
buildLib0.610.210.82
exampleAMDISReport0.020.010.03
exampleBiomass000
exampleHtest000
exampleIonLib0.020.000.02
exampleMSLfile0.000.020.02
exampleMetReport000
htest0.060.010.07
normalizeByBiomass0.030.000.03
normalizeByInternalStandard0.020.000.02
removeFalsePositives0.010.000.02

Metab.Rcheck/examples_x64/Metab-Ex.timings

nameusersystemelapsed
MetReport0.170.010.19
MetReportNames0.110.020.12
Metab-package0.020.000.01
buildLib0.800.070.86
exampleAMDISReport0.010.030.05
exampleBiomass000
exampleHtest0.000.010.02
exampleIonLib000
exampleMSLfile0.000.020.01
exampleMetReport000
htest0.090.000.10
normalizeByBiomass0.020.000.01
normalizeByInternalStandard0.020.000.02
removeFalsePositives0.010.000.01