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CHECK report for Metab on malbec1

This page was generated on 2018-04-12 13:13:01 -0400 (Thu, 12 Apr 2018).

Package 817/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Metab 1.12.0
Raphael Aggio
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/Metab
Branch: RELEASE_3_6
Last Commit: 068aef7
Last Changed Date: 2017-10-30 12:40:46 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Metab
Version: 1.12.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Metab_1.12.0.tar.gz
StartedAt: 2018-04-12 00:53:13 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:55:50 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 157.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Metab.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Metab_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/Metab.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Metab/DESCRIPTION’ ... OK
* this is package ‘Metab’ version ‘1.12.0’
* 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 for sufficient/correct file permissions ... 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
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/Metab.Rcheck/00check.log’
for details.



Installation output

Metab.Rcheck/00install.out

* installing *source* package ‘Metab’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Metab)

Tests output

Metab.Rcheck/tests/test-all.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, cbind, colMeans, colSums, colnames, 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 2.4.2 
  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 3.0.2 


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 -- Thu Apr 12 00:55:48 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 
  7.932   0.216   8.547 

Example timings

Metab.Rcheck/Metab-Ex.timings

nameusersystemelapsed
MetReport0.0880.0080.098
MetReportNames0.2920.0080.301
Metab-package0.0040.0000.005
buildLib0.5240.0000.526
exampleAMDISReport0.0320.0080.043
exampleBiomass0.0000.0000.001
exampleHtest0.0040.0000.001
exampleIonLib0.0040.0000.003
exampleMSLfile0.0000.0040.006
exampleMetReport0.0000.0000.002
htest0.2440.0000.242
normalizeByBiomass0.0120.0000.010
normalizeByInternalStandard0.0080.0000.007
removeFalsePositives0.0160.0040.019