Alexis Delabriere
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/proFIA |
| Branch: RELEASE_3_6 |
| Last Commit: a8ba1be |
| Last Changed Date: 2017-10-30 12:41:23 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:43:59 -0400 (Thu, 12 Apr 2018).
| Package 1069/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| proFIA 1.4.0 Alexis Delabriere
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: proFIA |
| Version: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings proFIA_1.4.0.tar.gz |
| StartedAt: 2018-04-12 07:53:12 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 07:58:51 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 338.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: proFIA.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings proFIA_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/proFIA.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.0’
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
proFIAset 86.058 2.962 90.518
impute.FIA-proFIAset-method 14.807 0.248 15.280
impute.randomForest-proFIAset-method 13.793 0.239 14.266
findFIAsignal 13.048 0.583 13.876
estimateNoiseMS 6.047 0.700 6.888
* 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
‘/Users/biocbuild/bbs-3.6-bioc/meat/proFIA.Rcheck/00check.log’
for details.
proFIA.Rcheck/00install.out
* 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 /Users/biocbuild/bbs-3.6-bioc/meat/proFIA.Rcheck/proFIA/libs ** R ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, 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 2.4.2
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 3.0.2
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 -- Thu Apr 12 07:58:46 2018
***********************************************
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
10.095 0.268 10.844
proFIA.Rcheck/proFIA-Ex.timings
| name | user | system | elapsed | |
| acquisitionDirectory | 0.066 | 0.004 | 0.074 | |
| analyzeAcquisitionFIA | 0.017 | 0.000 | 0.017 | |
| determiningInjectionZone | 0.802 | 0.024 | 0.839 | |
| determiningSizePeak.Geom | 1.090 | 0.024 | 1.149 | |
| estimateNoiseMS | 6.047 | 0.700 | 6.888 | |
| exportDataMatrix-proFIAset-method | 0.021 | 0.002 | 0.023 | |
| exportExpressionSet-proFIAset-method | 0.161 | 0.005 | 0.166 | |
| exportPeakTable-proFIAset-method | 0.038 | 0.002 | 0.040 | |
| exportSampleMetadata-proFIAset-method | 0.020 | 0.002 | 0.023 | |
| exportVariableMetadata-proFIAset-method | 0.024 | 0.002 | 0.026 | |
| findBandsFIA | 1.495 | 0.292 | 1.799 | |
| findFIAsignal | 13.048 | 0.583 | 13.876 | |
| findMzGroup-proFIAset-method | 0.025 | 0.003 | 0.029 | |
| getInjectionPeak | 2.648 | 0.273 | 2.991 | |
| group.FIA-proFIAset-method | 2.723 | 0.027 | 2.779 | |
| impute.FIA-proFIAset-method | 14.807 | 0.248 | 15.280 | |
| impute.KNN_TN-proFIAset-method | 0.560 | 0.004 | 0.568 | |
| impute.randomForest-proFIAset-method | 13.793 | 0.239 | 14.266 | |
| makeDataMatrix-proFIAset-method | 0.045 | 0.002 | 0.047 | |
| peaksGroup-proFIAset-method | 0.048 | 0.004 | 0.053 | |
| plot | 2.809 | 0.011 | 2.860 | |
| plotFlowgrams-proFIAset-method | 4.311 | 0.097 | 4.475 | |
| plotNoise | 0.292 | 0.002 | 0.298 | |
| plotRaw-proFIAset-method | 1.585 | 0.041 | 1.645 | |
| plotSamplePeaks-proFIAset-method | 0.021 | 0.002 | 0.023 | |
| proFIAset | 86.058 | 2.962 | 90.518 | |