Raphael Aggio
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/Metab |
| Branch: RELEASE_3_11 |
| Last Commit: 9ad8156 |
| Last Changed Date: 2020-04-27 14:45:27 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:53 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE Metab PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1030/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Metab 1.22.0 Raphael Aggio
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: Metab |
| Version: 1.22.0 |
| 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_1.22.0.tar.gz |
| StartedAt: 2020-10-17 02:46:55 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:52:09 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 313.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Metab.Rcheck |
| Warnings: 0 |
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### 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_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Metab.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Metab/DESCRIPTION’ ... OK
* this is package ‘Metab’ version ‘1.22.0’
* 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 : <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
‘/Users/biocbuild/bbs-3.11-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/4.0/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.14.2
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 3.10.2
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 -- Sat Oct 17 02:52:00 2020
***********************************************
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
15.193 0.729 15.915
Metab.Rcheck/Metab-Ex.timings
| name | user | system | elapsed | |
| MetReport | 0.109 | 0.074 | 0.190 | |
| MetReportNames | 0.119 | 0.015 | 0.134 | |
| Metab-package | 0.008 | 0.006 | 0.015 | |
| buildLib | 0.821 | 0.048 | 0.871 | |
| exampleAMDISReport | 0.083 | 0.054 | 0.138 | |
| exampleBiomass | 0.002 | 0.001 | 0.003 | |
| exampleHtest | 0.002 | 0.001 | 0.002 | |
| exampleIonLib | 0.006 | 0.003 | 0.008 | |
| exampleMSLfile | 0.015 | 0.007 | 0.022 | |
| exampleMetReport | 0.002 | 0.003 | 0.004 | |
| htest | 0.138 | 0.006 | 0.144 | |
| normalizeByBiomass | 0.019 | 0.006 | 0.025 | |
| normalizeByInternalStandard | 0.015 | 0.005 | 0.021 | |
| removeFalsePositives | 0.027 | 0.006 | 0.033 | |