Multiple platform build/check report for BioC 3.14 - CHECK results for proFIA on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: proFIA

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proFIA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings proFIA_1.20.0.tar.gz

StartedAt: 2022-04-13 00:51:04 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 01:01:06 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 602.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: proFIA.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proFIA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings proFIA_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/proFIA.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.20.0'
* 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 ... OK
* 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 ... 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 ... WARNING
Undocumented arguments in documentation object 'proFIAset'
  'f'

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-3.14-bioc/R/library/proFIA/libs/i386/proFIA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-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 (user + system) or elapsed time > 5s
                                      user system elapsed
proFIAset                            76.69   0.53   77.23
impute.randomForest-proFIAset-method 13.68   0.20   13.88
impute.FIA-proFIAset-method          13.61   0.19   13.80
findFIASignal                        11.37   0.20   11.59
plotFlowgrams-proFIAset-method        5.02   0.18    9.03
estimateNoiseMS                       3.75   0.33    5.09
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
proFIAset                            83.47   0.54   84.01
impute.randomForest-proFIAset-method 14.73   0.16   14.89
impute.FIA-proFIAset-method          14.72   0.06   14.78
findFIASignal                        11.55   0.16   11.70
plotFlowgrams-proFIAset-method        5.20   0.14    5.34
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/proFIA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/proFIA_1.20.0.tar.gz && rm -rf proFIA.buildbin-libdir && mkdir proFIA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proFIA.buildbin-libdir proFIA_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL proFIA_1.20.0.zip && rm proFIA_1.20.0.tar.gz proFIA_1.20.0.zip
###
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 36  744k   36  270k    0     0   515k      0  0:00:01 --:--:--  0:00:01  515k
100  744k  100  744k    0     0   741k      0  0:00:01  0:00:01 --:--:--  742k

install for i386

* installing *source* package 'proFIA' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c UtilFunc.c -o UtilFunc.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fastMatchPpm.c -o fastMatchPpm.o
C:/rtools40/mingw32/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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c UtilFunc.c -o UtilFunc.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fastMatchPpm.c -o fastMatchPpm.o
C:/rtools40/mingw64/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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/proFIA.buildbin-libdir/proFIA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'proFIA' as proFIA_1.20.0.zip
* DONE (proFIA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'proFIA' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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: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.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 objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.20.4 
  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 3.16.1 


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 13 01:00:43 2022 
*********************************************** 
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 
  12.12    0.73   12.82


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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: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.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 objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.20.4 
  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 3.16.1 


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 13 01:00:58 2022 
*********************************************** 
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 
  14.23    0.39   14.60

name	user	system	elapsed
acquisitionDirectory	0.12	0.03	0.35
analyzeAcquisitionFIA	0.02	0.00	0.01
determiningInjectionZone	1.00	0.04	1.85
determiningSizePeak.Geom	0.80	0.01	0.81
estimateNoiseMS	3.75	0.33	5.09
exportDataMatrix-proFIAset-method	0.03	0.00	0.04
exportExpressionSet-proFIAset-method	0.04	0.02	0.06
exportPeakTable-proFIAset-method	0.02	0.00	0.01
exportSampleMetadata-proFIAset-method	0.03	0.00	0.03
exportVariableMetadata-proFIAset-method	0.02	0.00	0.02
findBandsFIA	0.84	0.03	0.88
findFIASignal	11.37	0.20	11.59
findMzGroup-proFIAset-method	0.04	0.00	0.05
getInjectionPeak	2.86	0.06	2.92
group.FIA-proFIAset-method	2.26	0.08	2.34
impute.FIA-proFIAset-method	13.61	0.19	13.80
impute.KNN_TN-proFIAset-method	0.45	0.00	0.45
impute.randomForest-proFIAset-method	13.68	0.20	13.88
makeDataMatrix-proFIAset-method	0.03	0.00	0.03
peaksGroup-proFIAset-method	0.04	0.00	0.04
plot	0.78	0.02	0.80
plotFlowgrams-proFIAset-method	5.02	0.18	9.03
plotNoise	0.27	0.00	0.27
plotRaw-proFIAset-method	1.62	0.02	1.64
plotSamplePeaks-proFIAset-method	0.03	0.00	0.03
proFIAset	76.69	0.53	77.23

name	user	system	elapsed
acquisitionDirectory	0.07	0.00	0.06
analyzeAcquisitionFIA	0.01	0.00	0.02
determiningInjectionZone	0.90	0.02	0.93
determiningSizePeak.Geom	0.93	0.03	0.95
estimateNoiseMS	3.98	0.20	4.19
exportDataMatrix-proFIAset-method	0.00	0.02	0.02
exportExpressionSet-proFIAset-method	0.07	0.00	0.08
exportPeakTable-proFIAset-method	0.03	0.00	0.03
exportSampleMetadata-proFIAset-method	0.04	0.00	0.03
exportVariableMetadata-proFIAset-method	0.03	0.00	0.03
findBandsFIA	1.03	0.00	1.03
findFIASignal	11.55	0.16	11.70
findMzGroup-proFIAset-method	0.03	0.00	0.03
getInjectionPeak	2.55	0.03	2.58
group.FIA-proFIAset-method	2.45	0.00	2.45
impute.FIA-proFIAset-method	14.72	0.06	14.78
impute.KNN_TN-proFIAset-method	0.39	0.00	0.39
impute.randomForest-proFIAset-method	14.73	0.16	14.89
makeDataMatrix-proFIAset-method	0.03	0.00	0.03
peaksGroup-proFIAset-method	0.03	0.01	0.05
plot	0.91	0.00	0.91
plotFlowgrams-proFIAset-method	5.20	0.14	5.34
plotNoise	0.27	0.01	0.29
plotRaw-proFIAset-method	1.80	0.07	1.86
plotSamplePeaks-proFIAset-method	0.01	0.00	0.01
proFIAset	83.47	0.54	84.01

CHECK results for proFIA on tokay2

Summary

Command output

Installation output

Tests output

Example timings