Ron Wehrens
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/metaMS |
| Branch: RELEASE_3_8 |
| Last Commit: 8284c97 |
| Last Changed Date: 2019-01-04 13:38:24 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:50:29 -0400 (Tue, 16 Apr 2019).
| Package 924/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| metaMS 1.18.1 Ron Wehrens
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: metaMS |
| Version: 1.18.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:metaMS.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings metaMS_1.18.1.tar.gz |
| StartedAt: 2019-04-16 01:16:51 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:20:01 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 189.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: metaMS.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:metaMS.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings metaMS_1.18.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/metaMS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaMS’ version ‘1.18.1’
* 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 ‘metaMS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
AnnotateFeature: no visible global function definition for ‘predict’
AnnotateTable: no visible global function definition for ‘predict’
AnnotateTable : <anonymous>: no visible global function definition for
‘hclust’
AnnotateTable : <anonymous>: no visible global function definition for
‘dist’
AnnotateTable : <anonymous>: no visible global function definition for
‘cutree’
addRI : <anonymous>: no visible global function definition for ‘approx’
getAnnotationLC: no visible binding for global variable ‘median’
matchExpSpec: no visible global function definition for ‘plot’
matchExpSpec: no visible global function definition for ‘lines’
matchExpSpec: no visible global function definition for ‘legend’
plotPseudoSpectrum: no visible global function definition for ‘plot’
read.msp : read.compound: no visible global function definition for
‘aggregate’
readStdInfo: no visible global function definition for ‘read.table’
relInt: no visible global function definition for ‘coef’
relInt: no visible global function definition for ‘lm’
removeDoubleMasses : <anonymous>: no visible global function definition
for ‘aggregate’
runCAMERA: no visible global function definition for ‘capture.output’
runGC: no visible global function definition for ‘sessionInfo’
runLC: no visible global function definition for ‘sessionInfo’
Undefined global functions or variables:
aggregate approx capture.output coef cutree dist hclust legend lines
lm median plot predict read.table sessionInfo
Consider adding
importFrom("graphics", "legend", "lines", "plot")
importFrom("stats", "aggregate", "approx", "coef", "cutree", "dist",
"hclust", "lm", "median", "predict")
importFrom("utils", "capture.output", "read.table", "sessionInfo")
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 ... WARNING
Documented arguments not in \usage in documentation object 'matchExpSpec':
‘spec1’ ‘spec2’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.8-bioc/meat/metaMS.Rcheck/00check.log’
for details.
metaMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL metaMS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘metaMS’ ... ** 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 * DONE (metaMS)
metaMS.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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("metaMS")
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, colMeans, colSums, colnames,
dirname, 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")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
This is MSnbase version 2.8.3
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 3.4.4
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
< -------- Experiment of 4 samples ------------------------------------- >
< -------- Instrument: TSQXLS.QQQ.GC ----------------------------------- >
< -------- Annotation using database of 3 spectra ---------------------- >
< -------- Using xcmsSet object - only doing annotation ---------------- >
< -------- Removing artefacts (Bleeding, Plasticizers) ----------------- >
< -------- Matching with database of standards ------------------------- >
< -------- Matching unknowns across samples ---------------------------- >
< -------- Formatting results ------------------------------------------ >
< -------- Done! ------------------------------------------------------- >
< -------- Experiment of 4 samples ------------------------------------- >
< -------- Instrument: Synapt.QTOF.RP - polarity: positive ------------ >
< -------- Database of 4 compounds ------------------------------------- >
< -------- Using xcmsSet object - only doing annotation ---------------- >
< -------- Performing annotation --------------------------------------- >
Fixed mass tolerance 0.005
Feature-wise Annotation ...
< -------- Formatting the output --------------------------------------- >
< -------- Done ! ------------------------------------------------------ >
RUNIT TEST PROTOCOL -- Tue Apr 16 01:19:57 2019
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
metaMS RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
12.552 0.524 13.109
metaMS.Rcheck/metaMS-Ex.timings
| name | user | system | elapsed | |
| FEMsettings | 0.004 | 0.000 | 0.001 | |
| addRI | 0.040 | 0.000 | 0.099 | |
| createSTDdbGC | 0.000 | 0.000 | 0.001 | |
| createSTDdbLC | 0.02 | 0.00 | 0.03 | |
| errf | 0.016 | 0.000 | 0.019 | |
| matchExpSpec | 0.012 | 0.012 | 0.027 | |
| metaMSsettings-class | 0.000 | 0.000 | 0.003 | |
| metaSetting-methods | 0 | 0 | 0 | |
| msp | 0.000 | 0.000 | 0.002 | |
| plotPseudoSpectrum | 0.028 | 0.000 | 0.028 | |
| readStdInfo | 0.028 | 0.000 | 0.030 | |
| runGC | 0.060 | 0.004 | 0.074 | |
| runLC | 0.032 | 0.004 | 0.043 | |
| threeStdsDB | 0.012 | 0.004 | 0.020 | |
| treat.DB | 0.004 | 0.000 | 0.005 | |