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This page was generated on 2023-04-12 11:05:39 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for Metab on palomino4


To the developers/maintainers of the Metab package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Metab.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1138/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Metab 1.32.0  (landing page)
Raphael Aggio
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/Metab
git_branch: RELEASE_3_16
git_last_commit: 7502174
git_last_commit_date: 2022-11-01 11:10:47 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Metab
Version: 1.32.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Metab.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings Metab_1.32.0.tar.gz
StartedAt: 2023-04-11 03:05:38 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 03:09:18 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 220.6 seconds
RetCode: 0
Status:   OK  
CheckDir: Metab.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Metab.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings Metab_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/Metab.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Metab/DESCRIPTION' ... OK
* this is package 'Metab' version '1.32.0'
* 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
* 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 sizes of PDF files under '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
  'F:/biocbuild/bbs-3.16-bioc/meat/Metab.Rcheck/00check.log'
for details.



Installation output

Metab.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL Metab
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'Metab' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (Metab)

Tests output

Metab.Rcheck/tests/test-all.Rout


R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 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:stats':

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, 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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.24.2 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    trimws


This is xcms version 3.20.0 


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 -- Tue Apr 11 03:09:07 2023 
*********************************************** 
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 
Warning message:
In rbind(deparse.level, ...) :
  number of columns of result, 11, is not a multiple of vector length 12 of arg 1
> 
> proc.time()
   user  system elapsed 
  10.06    0.51   10.56 

Example timings

Metab.Rcheck/Metab-Ex.timings

nameusersystemelapsed
MetReport0.070.060.12
MetReportNames0.060.020.08
Metab-package0.000.010.01
buildLib0.440.000.44
exampleAMDISReport0.030.040.06
exampleBiomass0.000.010.02
exampleHtest000
exampleIonLib0.000.020.02
exampleMSLfile0.000.010.01
exampleMetReport0.010.000.02
htest0.790.020.79
normalizeByBiomass0.010.000.01
normalizeByInternalStandard0.000.020.02
removeFalsePositives0.020.000.02