Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

CHECK report for proFIA on tokay2

This page was generated on 2019-10-16 12:37:13 -0400 (Wed, 16 Oct 2019).

Package 1255/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proFIA 1.10.0
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: proFIA
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proFIA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings proFIA_1.10.0.tar.gz
StartedAt: 2019-10-16 06:08:23 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:18:14 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 590.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: proFIA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proFIA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings proFIA_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/proFIA.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/proFIA/libs/i386/proFIA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/proFIA/libs/x64/proFIA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
proFIAset                            82.02   0.79   82.81
impute.randomForest-proFIAset-method 11.80   0.19   11.99
findFIASignal                        11.49   0.29   11.78
impute.FIA-proFIAset-method          11.45   0.15   11.61
estimateNoiseMS                       5.14   0.11   17.56
plotFlowgrams-proFIAset-method        4.44   0.22   12.92
acquisitionDirectory                  0.14   0.00   11.31
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
proFIAset                            86.59   0.66   87.28
impute.randomForest-proFIAset-method 15.95   0.11   16.08
impute.FIA-proFIAset-method          15.25   0.11   15.37
findFIASignal                        12.08   0.21   12.28
estimateNoiseMS                       6.01   0.18    6.19
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/proFIA.Rcheck/00check.log'
for details.



Installation output

proFIA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/proFIA_1.10.0.tar.gz && rm -rf proFIA.buildbin-libdir && mkdir proFIA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proFIA.buildbin-libdir proFIA_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL proFIA_1.10.0.zip && rm proFIA_1.10.0.tar.gz proFIA_1.10.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  311k  100  311k    0     0  4671k      0 --:--:-- --:--:-- --:--:-- 5193k

install for i386

* installing *source* package 'proFIA' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c UtilFunc.c -o UtilFunc.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c fastMatchPpm.c -o fastMatchPpm.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o proFIA.dll tmp.def FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/proFIA.buildbin-libdir/00LOCK-proFIA/00new/proFIA/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'proFIA'
    finding HTML links ... done
    acquisitionDirectory                    html  
    analyzeAcquisitionFIA                   html  
    determiningInjectionZone                html  
    determiningSizePeak.Geom                html  
    estimateNoiseMS                         html  
    exportDataMatrix-proFIAset-method       html  
    exportExpressionSet-proFIAset-method    html  
    exportPeakTable-proFIAset-method        html  
    exportSampleMetadata-proFIAset-method   html  
    exportVariableMetadata-proFIAset-method
                                            html  
    findBandsFIA                            html  
    findFIASignal                           html  
    findMzGroup-proFIAset-method            html  
    getInjectionPeak                        html  
    group.FIA-proFIAset-method              html  
    impute.FIA-proFIAset-method             html  
    impute.KNN_TN-proFIAset-method          html  
    impute.randomForest-proFIAset-method    html  
    makeDataMatrix-proFIAset-method         html  
    noiseEstimation-class                   html  
    peaksGroup-proFIAset-method             html  
    plot                                    html  
    plotFlowgrams-proFIAset-method          html  
    plotNoise                               html  
    plotRaw-proFIAset-method                html  
    plotSamplePeaks-proFIAset-method        html  
    proFIA-package                          html  
    proFIAset-class                         html  
    proFIAset                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'proFIA' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c UtilFunc.c -o UtilFunc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c fastMatchPpm.c -o fastMatchPpm.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o proFIA.dll tmp.def FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/proFIA.buildbin-libdir/proFIA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'proFIA' as proFIA_1.10.0.zip
* DONE (proFIA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'proFIA' successfully unpacked and MD5 sums checked

Tests output

proFIA.Rcheck/tests_i386/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 06:17:54 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 
   8.93    0.51    9.43 

proFIA.Rcheck/tests_x64/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-w64-mingw32/x64 (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 06:18:07 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 
  11.90    0.34   12.23 

Example timings

proFIA.Rcheck/examples_i386/proFIA-Ex.timings

nameusersystemelapsed
acquisitionDirectory 0.14 0.0011.31
analyzeAcquisitionFIA0.010.010.03
determiningInjectionZone0.890.081.34
determiningSizePeak.Geom0.730.040.78
estimateNoiseMS 5.14 0.1117.56
exportDataMatrix-proFIAset-method0.000.020.02
exportExpressionSet-proFIAset-method0.040.010.07
exportPeakTable-proFIAset-method0.040.000.03
exportSampleMetadata-proFIAset-method0.010.000.02
exportVariableMetadata-proFIAset-method0.030.000.03
findBandsFIA0.890.050.94
findFIASignal11.49 0.2911.78
findMzGroup-proFIAset-method0.010.020.31
getInjectionPeak2.970.053.02
group.FIA-proFIAset-method3.110.003.11
impute.FIA-proFIAset-method11.45 0.1511.61
impute.KNN_TN-proFIAset-method1.020.001.01
impute.randomForest-proFIAset-method11.80 0.1911.99
makeDataMatrix-proFIAset-method0.030.000.03
peaksGroup-proFIAset-method0.040.030.07
plot1.330.001.33
plotFlowgrams-proFIAset-method 4.44 0.2212.92
plotNoise0.300.030.33
plotRaw-proFIAset-method1.650.021.67
plotSamplePeaks-proFIAset-method0.050.000.05
proFIAset82.02 0.7982.81

proFIA.Rcheck/examples_x64/proFIA-Ex.timings

nameusersystemelapsed
acquisitionDirectory0.060.000.06
analyzeAcquisitionFIA0.010.000.02
determiningInjectionZone0.700.030.74
determiningSizePeak.Geom0.880.000.87
estimateNoiseMS6.010.186.19
exportDataMatrix-proFIAset-method0.030.000.03
exportExpressionSet-proFIAset-method0.110.000.11
exportPeakTable-proFIAset-method0.050.000.05
exportSampleMetadata-proFIAset-method0.000.030.03
exportVariableMetadata-proFIAset-method0.030.010.04
findBandsFIA1.300.031.33
findFIASignal12.08 0.2112.28
findMzGroup-proFIAset-method0.010.010.03
getInjectionPeak2.530.032.57
group.FIA-proFIAset-method3.100.043.20
impute.FIA-proFIAset-method15.25 0.1115.37
impute.KNN_TN-proFIAset-method0.670.020.69
impute.randomForest-proFIAset-method15.95 0.1116.08
makeDataMatrix-proFIAset-method0.030.020.04
peaksGroup-proFIAset-method0.080.010.10
plot1.010.001.01
plotFlowgrams-proFIAset-method3.740.143.88
plotNoise0.250.000.25
plotRaw-proFIAset-method1.560.051.61
plotSamplePeaks-proFIAset-method0.030.000.03
proFIAset86.59 0.6687.28