Alexis Delabriere
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/proFIA |
| Branch: RELEASE_3_9 |
| Last Commit: ea10171 |
| Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:59:06 -0400 (Wed, 16 Oct 2019).
| Package 1255/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| proFIA 1.10.0 Alexis Delabriere
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: proFIA |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:proFIA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings proFIA_1.10.0.tar.gz |
| StartedAt: 2019-10-16 05:45:03 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:53:09 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 485.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: proFIA.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:proFIA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings proFIA_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/proFIA.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 ‘proFIA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proFIA’ version ‘1.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘proFIA’ 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
persoConv: no visible global function definition for ‘dexp’
Undefined global functions or variables:
dexp
Consider adding
importFrom("stats", "dexp")
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
Undocumented arguments in documentation object 'findFIASignal'
‘shiftFactor’
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
proFIAset 133.775 3.092 137.002
findFIASignal 21.146 0.783 21.941
impute.FIA-proFIAset-method 16.527 0.803 17.337
impute.randomForest-proFIAset-method 15.292 0.763 16.060
estimateNoiseMS 6.557 0.318 6.884
group.FIA-proFIAset-method 4.834 0.264 5.100
* 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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/proFIA.Rcheck/00check.log’
for details.
proFIA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL proFIA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘proFIA’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c UtilFunc.c -o UtilFunc.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c fastMatchPpm.c -o fastMatchPpm.o clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o proFIA.so FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-proFIA/00new/proFIA/libs ** R ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (proFIA)
proFIA.Rcheck/tests/runTests.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("proFIA")
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
Loading required package: plasFIA
A mass interval of 0.0153m/z will be used for the density estimation.
0 :0 10 :29 20 :54 30 :78 30 :105 40 :141 50 :174 60 :196 70 :208 80 :215 90 :219
219 groups have been done .
RUNIT TEST PROTOCOL -- Wed Oct 16 05:53:00 2019
***********************************************
Number of test functions: 5
Number of errors: 0
Number of failures: 0
1 Test Suite :
proFIA 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
15.402 1.185 16.556
proFIA.Rcheck/proFIA-Ex.timings
| name | user | system | elapsed | |
| acquisitionDirectory | 0.095 | 0.009 | 0.110 | |
| analyzeAcquisitionFIA | 0.014 | 0.001 | 0.015 | |
| determiningInjectionZone | 0.841 | 0.049 | 0.895 | |
| determiningSizePeak.Geom | 0.879 | 0.030 | 0.910 | |
| estimateNoiseMS | 6.557 | 0.318 | 6.884 | |
| exportDataMatrix-proFIAset-method | 0.044 | 0.008 | 0.051 | |
| exportExpressionSet-proFIAset-method | 0.137 | 0.007 | 0.144 | |
| exportPeakTable-proFIAset-method | 0.048 | 0.005 | 0.053 | |
| exportSampleMetadata-proFIAset-method | 0.035 | 0.005 | 0.040 | |
| exportVariableMetadata-proFIAset-method | 0.038 | 0.005 | 0.043 | |
| findBandsFIA | 1.811 | 0.070 | 1.881 | |
| findFIASignal | 21.146 | 0.783 | 21.941 | |
| findMzGroup-proFIAset-method | 0.074 | 0.008 | 0.083 | |
| getInjectionPeak | 4.208 | 0.237 | 4.448 | |
| group.FIA-proFIAset-method | 4.834 | 0.264 | 5.100 | |
| impute.FIA-proFIAset-method | 16.527 | 0.803 | 17.337 | |
| impute.KNN_TN-proFIAset-method | 0.687 | 0.046 | 0.733 | |
| impute.randomForest-proFIAset-method | 15.292 | 0.763 | 16.060 | |
| makeDataMatrix-proFIAset-method | 0.041 | 0.006 | 0.047 | |
| peaksGroup-proFIAset-method | 0.060 | 0.007 | 0.066 | |
| plot | 1.803 | 0.032 | 1.836 | |
| plotFlowgrams-proFIAset-method | 4.706 | 0.230 | 4.957 | |
| plotNoise | 0.446 | 0.005 | 0.451 | |
| plotRaw-proFIAset-method | 1.638 | 0.072 | 1.711 | |
| plotSamplePeaks-proFIAset-method | 0.030 | 0.004 | 0.035 | |
| proFIAset | 133.775 | 3.092 | 137.002 | |