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) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:25:25 -0400 (Thu, 12 Apr 2018).
| Package 817/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Metab 1.12.0 Raphael Aggio
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: Metab |
| Version: 1.12.0 |
| Command: rm -rf Metab.buildbin-libdir Metab.Rcheck && mkdir Metab.buildbin-libdir Metab.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Metab.buildbin-libdir Metab_1.12.0.tar.gz >Metab.Rcheck\00install.out 2>&1 && cp Metab.Rcheck\00install.out Metab-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Metab.buildbin-libdir --install="check:Metab-install.out" --force-multiarch --no-vignettes --timings Metab_1.12.0.tar.gz |
| StartedAt: 2018-04-12 01:15:08 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:19:20 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 252.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Metab.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### rm -rf Metab.buildbin-libdir Metab.Rcheck && mkdir Metab.buildbin-libdir Metab.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Metab.buildbin-libdir Metab_1.12.0.tar.gz >Metab.Rcheck\00install.out 2>&1 && cp Metab.Rcheck\00install.out Metab-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Metab.buildbin-libdir --install="check:Metab-install.out" --force-multiarch --no-vignettes --timings Metab_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Metab.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.12.0'
* 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 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
** checking loading without being on the library search path ... 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 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 ...
** 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-3.6-bioc/meat/Metab.Rcheck/00check.log'
for details.
Metab.Rcheck/00install.out
install for i386
* installing *source* package 'Metab' ...
** R
** data
** inst
** preparing 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_1.12.0.zip
* DONE (Metab)
In R CMD INSTALL
In R CMD INSTALL
|
Metab.Rcheck/tests_i386/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: 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, 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 01:19:05 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
7.71 0.28 8.14
|
Metab.Rcheck/tests_x64/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-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, 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 01:19:15 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
9.76 0.21 10.17
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Metab.Rcheck/examples_i386/Metab-Ex.timings
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Metab.Rcheck/examples_x64/Metab-Ex.timings
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