Raphael Aggio
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Metab |
| Branch: RELEASE_3_9 |
| Last Commit: 4af0374 |
| Last Changed Date: 2019-05-02 11:53:50 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:54:37 -0400 (Wed, 16 Oct 2019).
| Package 956/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Metab 1.18.0 Raphael Aggio
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: Metab |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Metab.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Metab_1.18.0.tar.gz |
| StartedAt: 2019-10-16 04:24:29 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:28:38 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 249.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Metab.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Metab.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Metab_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Metab.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Metab/DESCRIPTION’ ... OK * this is package ‘Metab’ version ‘1.18.0’ * 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 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 :: no visible global function definition for ‘t.test’ htest : anova.t : : 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 ‘/Users/biocbuild/bbs-3.9-bioc/meat/Metab.Rcheck/00check.log’ for details.
Metab.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Metab ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)
Metab.Rcheck/tests/test-all.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 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, 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 object is masked from 'package:base':
expand.grid
This is MSnbase version 2.10.1
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 3.6.2
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 -- Wed Oct 16 04:28:31 2019
***********************************************
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
11.574 1.131 12.661
Metab.Rcheck/Metab-Ex.timings
| name | user | system | elapsed | |
| MetReport | 0.154 | 0.070 | 0.237 | |
| MetReportNames | 0.144 | 0.005 | 0.150 | |
| Metab-package | 0.010 | 0.005 | 0.014 | |
| buildLib | 1.299 | 0.134 | 1.432 | |
| exampleAMDISReport | 0.126 | 0.063 | 0.190 | |
| exampleBiomass | 0.003 | 0.004 | 0.007 | |
| exampleHtest | 0.003 | 0.004 | 0.007 | |
| exampleIonLib | 0.009 | 0.006 | 0.015 | |
| exampleMSLfile | 0.016 | 0.006 | 0.022 | |
| exampleMetReport | 0.003 | 0.003 | 0.007 | |
| htest | 0.158 | 0.018 | 0.176 | |
| normalizeByBiomass | 0.024 | 0.011 | 0.036 | |
| normalizeByInternalStandard | 0.021 | 0.008 | 0.029 | |
| removeFalsePositives | 0.029 | 0.010 | 0.039 | |