Alexis Delabriere
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/proFIA |
| Branch: RELEASE_3_8 |
| Last Commit: 1f1f209 |
| Last Changed Date: 2019-04-06 08:28:35 -0400 (Sat, 06 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:00:07 -0400 (Tue, 16 Apr 2019).
| Package 1195/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| proFIA 1.8.1 Alexis Delabriere
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: proFIA |
| Version: 1.8.1 |
| 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_1.8.1.tar.gz |
| StartedAt: 2019-04-16 02:01:30 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:07:32 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 362.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: proFIA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running 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_1.8.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/proFIA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.1’
* 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 ... 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 ... OK
* 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 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 98.116 3.234 101.647
findFIASignal 15.855 0.561 16.463
impute.FIA-proFIAset-method 15.693 0.408 16.165
impute.randomForest-proFIAset-method 13.882 0.367 14.282
estimateNoiseMS 6.497 0.770 7.302
plotFlowgrams-proFIAset-method 5.803 0.123 5.954
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.8-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/3.5/Resources/library’ * installing *source* package ‘proFIA’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c UtilFunc.c -o UtilFunc.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/3.5/Resources/library/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 * DONE (proFIA)
proFIA.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-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, 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
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 -- Tue Apr 16 02:07:25 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
12.126 0.580 12.766
proFIA.Rcheck/proFIA-Ex.timings
| name | user | system | elapsed | |
| acquisitionDirectory | 0.071 | 0.004 | 0.077 | |
| analyzeAcquisitionFIA | 0.014 | 0.001 | 0.014 | |
| determiningInjectionZone | 1.034 | 0.026 | 1.066 | |
| determiningSizePeak.Geom | 1.117 | 0.018 | 1.143 | |
| estimateNoiseMS | 6.497 | 0.770 | 7.302 | |
| exportDataMatrix-proFIAset-method | 0.023 | 0.003 | 0.025 | |
| exportExpressionSet-proFIAset-method | 0.094 | 0.003 | 0.097 | |
| exportPeakTable-proFIAset-method | 0.028 | 0.003 | 0.031 | |
| exportSampleMetadata-proFIAset-method | 0.021 | 0.003 | 0.024 | |
| exportVariableMetadata-proFIAset-method | 0.022 | 0.003 | 0.025 | |
| findBandsFIA | 1.827 | 0.176 | 2.007 | |
| findFIASignal | 15.855 | 0.561 | 16.463 | |
| findMzGroup-proFIAset-method | 0.024 | 0.003 | 0.028 | |
| getInjectionPeak | 3.408 | 0.304 | 3.726 | |
| group.FIA-proFIAset-method | 3.415 | 0.105 | 3.537 | |
| impute.FIA-proFIAset-method | 15.693 | 0.408 | 16.165 | |
| impute.KNN_TN-proFIAset-method | 0.577 | 0.016 | 0.593 | |
| impute.randomForest-proFIAset-method | 13.882 | 0.367 | 14.282 | |
| makeDataMatrix-proFIAset-method | 0.019 | 0.002 | 0.021 | |
| peaksGroup-proFIAset-method | 0.055 | 0.005 | 0.061 | |
| plot | 2.058 | 0.065 | 2.132 | |
| plotFlowgrams-proFIAset-method | 5.803 | 0.123 | 5.954 | |
| plotNoise | 0.320 | 0.004 | 0.325 | |
| plotRaw-proFIAset-method | 2.102 | 0.038 | 2.145 | |
| plotSamplePeaks-proFIAset-method | 0.024 | 0.004 | 0.028 | |
| proFIAset | 98.116 | 3.234 | 101.647 | |