Ron Wehrens
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/metaMS |
| Branch: RELEASE_3_7 |
| Last Commit: c5d519a |
| Last Changed Date: 2018-04-30 10:35:32 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:38:28 -0400 (Wed, 17 Oct 2018).
| Package 875/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| metaMS 1.16.0 Ron Wehrens
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: metaMS |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaMS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings metaMS_1.16.0.tar.gz |
| StartedAt: 2018-10-17 03:12:01 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 03:16:53 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 292.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: metaMS.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaMS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings metaMS_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/metaMS.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metaMS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metaMS' version '1.16.0'
* 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 '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
* 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
* 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 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 ...
** 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 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.7-bioc/meat/metaMS.Rcheck/00check.log'
for details.
metaMS.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/metaMS_1.16.0.tar.gz && rm -rf metaMS.buildbin-libdir && mkdir metaMS.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metaMS.buildbin-libdir metaMS_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL metaMS_1.16.0.zip && rm metaMS_1.16.0.tar.gz metaMS_1.16.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 3420k 100 3420k 0 0 37.5M 0 --:--:-- --:--:-- --:--:-- 40.7M
install for i386
* installing *source* package 'metaMS' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'metaMS'
finding HTML links ... done
AnnotateTable html
FEMsettings html
finding level-2 HTML links ... done
GCresults html
LCDBtest html
LCresults html
addRI html
alignmentLC html
annotations2tab html
constructExpPseudoSpectra html
createSTDdbGC html
createSTDdbLC html
errf html
exptable html
getAnnotationLC html
getAnnotationMat html
getFeatureInfo html
getPeakTable html
match2ExtDB html
matchExpSpec html
matchSamples2DB html
matchSamples2Samples html
metaMS-package html
metaMSsettings-class html
metaSetting-methods html
msp html
peakDetection html
plotPseudoSpectrum html
printString html
processStandards html
readStdInfo html
removeDoubleMasses html
runCAMERA html
runGC html
runLC html
threeStdsDB html
treat.DB html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'metaMS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metaMS' as metaMS_1.16.0.zip
* DONE (metaMS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'metaMS' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
metaMS.Rcheck/tests_i386/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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("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")'.
This is MSnbase version 2.6.4
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 3.2.0
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 -- Wed Oct 17 03:16:30 2018
***********************************************
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
16.14 1.14 17.60
|
metaMS.Rcheck/tests_x64/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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("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")'.
This is MSnbase version 2.6.4
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 3.2.0
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 -- Wed Oct 17 03:16:47 2018
***********************************************
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
14.79 0.64 15.59
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metaMS.Rcheck/examples_i386/metaMS-Ex.timings
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metaMS.Rcheck/examples_x64/metaMS-Ex.timings
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