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CHECK report for proFIA on malbec2

This page was generated on 2018-10-17 08:29:38 -0400 (Wed, 17 Oct 2018).

Package 1130/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proFIA 1.6.0
Alexis Delabriere
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/proFIA
Branch: RELEASE_3_7
Last Commit: ef65247
Last Changed Date: 2018-04-30 10:35:44 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: proFIA
Version: 1.6.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:proFIA.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings proFIA_1.6.0.tar.gz
StartedAt: 2018-10-16 02:50:08 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:54:46 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 278.2 seconds
RetCode: 0
Status:  OK 
CheckDir: proFIA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:proFIA.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings proFIA_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/proFIA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.0’
* 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 ... 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                            74.164  1.532  75.787
impute.FIA-proFIAset-method          13.132  0.008  13.148
impute.randomForest-proFIAset-method 12.552  0.000  12.560
findFIASignal                        10.904  0.240  11.159
plotFlowgrams-proFIAset-method        5.524  0.024   5.615
estimateNoiseMS                       4.940  0.264   5.448
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/proFIA.Rcheck/00check.log’
for details.



Installation output

proFIA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL proFIA
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘proFIA’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c UtilFunc.c -o UtilFunc.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fastMatchPpm.c -o fastMatchPpm.o
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o proFIA.so FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/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)

Tests output

proFIA.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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("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")'.


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

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 Oct 16 02:54:43 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 
  8.008   0.192   8.796 

Example timings

proFIA.Rcheck/proFIA-Ex.timings

nameusersystemelapsed
acquisitionDirectory0.0600.0000.115
analyzeAcquisitionFIA0.0120.0000.010
determiningInjectionZone0.9360.0120.979
determiningSizePeak.Geom0.9720.0000.975
estimateNoiseMS4.9400.2645.448
exportDataMatrix-proFIAset-method0.0160.0000.014
exportExpressionSet-proFIAset-method0.0640.0000.062
exportPeakTable-proFIAset-method0.0160.0000.018
exportSampleMetadata-proFIAset-method0.0160.0000.016
exportVariableMetadata-proFIAset-method0.0160.0000.017
findBandsFIA1.2720.1361.412
findFIASignal10.904 0.24011.159
findMzGroup-proFIAset-method0.0320.0000.044
getInjectionPeak2.4720.0962.571
group.FIA-proFIAset-method2.2280.0002.231
impute.FIA-proFIAset-method13.132 0.00813.148
impute.KNN_TN-proFIAset-method0.80.00.8
impute.randomForest-proFIAset-method12.552 0.00012.560
makeDataMatrix-proFIAset-method0.0200.0000.021
peaksGroup-proFIAset-method0.0440.0000.041
plot1.0560.0001.057
plotFlowgrams-proFIAset-method5.5240.0245.615
plotNoise0.2000.0000.201
plotRaw-proFIAset-method1.8760.0081.883
plotSamplePeaks-proFIAset-method0.020.000.02
proFIAset74.164 1.53275.787