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CHECK report for proFIA on malbec1

This page was generated on 2020-04-15 12:12:04 -0400 (Wed, 15 Apr 2020).

Package 1308/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proFIA 1.12.0
Alexis Delabriere
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/proFIA
Branch: RELEASE_3_10
Last Commit: a45a537
Last Changed Date: 2019-10-29 13:10:13 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: proFIA
Version: 1.12.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:proFIA.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings proFIA_1.12.0.tar.gz
StartedAt: 2020-04-15 04:20:31 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:27:01 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 390.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: proFIA.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:proFIA.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings proFIA_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/proFIA.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.0’
* 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                            113.908  0.568 115.592
impute.FIA-proFIAset-method           18.116  0.004  18.410
impute.randomForest-proFIAset-method  16.696  0.000  16.937
findFIASignal                         16.388  0.116  16.710
estimateNoiseMS                        5.976  0.044   6.201
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/proFIA.Rcheck/00check.log’
for details.



Installation output

proFIA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL proFIA
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘proFIA’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c UtilFunc.c -o UtilFunc.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c fastMatchPpm.c -o fastMatchPpm.o
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o proFIA.so FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/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)

Tests output

proFIA.Rcheck/tests/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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


Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth


This is MSnbase version 2.12.0 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:base':

    trimws


This is xcms version 3.8.2 


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 Apr 15 04:26:54 2020 
*********************************************** 
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 
 13.780   0.332  14.883 

Example timings

proFIA.Rcheck/proFIA-Ex.timings

nameusersystemelapsed
acquisitionDirectory0.0880.0080.147
analyzeAcquisitionFIA0.0200.0000.019
determiningInjectionZone0.6640.0241.082
determiningSizePeak.Geom0.8120.0160.839
estimateNoiseMS5.9760.0446.201
exportDataMatrix-proFIAset-method0.0200.0040.024
exportExpressionSet-proFIAset-method0.0880.0000.087
exportPeakTable-proFIAset-method0.0240.0000.024
exportSampleMetadata-proFIAset-method0.0200.0000.018
exportVariableMetadata-proFIAset-method0.0280.0000.030
findBandsFIA1.5840.0001.589
findFIASignal16.388 0.11616.710
findMzGroup-proFIAset-method0.0360.0000.041
getInjectionPeak3.6240.0243.675
group.FIA-proFIAset-method3.7960.0083.885
impute.FIA-proFIAset-method18.116 0.00418.410
impute.KNN_TN-proFIAset-method0.6000.0000.602
impute.randomForest-proFIAset-method16.696 0.00016.937
makeDataMatrix-proFIAset-method0.0320.0000.033
peaksGroup-proFIAset-method0.0600.0000.062
plot1.3400.0041.359
plotFlowgrams-proFIAset-method4.1280.0484.391
plotNoise0.3720.0000.375
plotRaw-proFIAset-method1.3880.0041.403
plotSamplePeaks-proFIAset-method0.0280.0000.028
proFIAset113.908 0.568115.592