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This page was generated on 2021-10-15 15:06:17 -0400 (Fri, 15 Oct 2021).

CHECK results for ptairMS on tokay2

To the developers/maintainers of the ptairMS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ptairMS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1457/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ptairMS 1.0.1  (landing page)
camille Roquencourt
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/ptairMS
git_branch: RELEASE_3_13
git_last_commit: 701b577
git_last_commit_date: 2021-09-27 16:14:12 -0400 (Mon, 27 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ptairMS
Version: 1.0.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ptairMS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ptairMS_1.0.1.tar.gz
StartedAt: 2021-10-15 03:51:12 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 04:07:21 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 969.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ptairMS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ptairMS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ptairMS_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ptairMS.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ptairMS/DESCRIPTION' ... OK
* this is package 'ptairMS' version '1.0.1'
* package encoding: UTF-8
* 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 'ptairMS' 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 ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/ptairMS/libs/i386/ptairMS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/ptairMS/libs/x64/ptairMS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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
detectPeak           88.59   1.58   90.18
alignSamples         17.48   1.06   19.70
imputeMat            15.11   1.05   16.16
writeEset            14.57   0.96   15.53
impute               12.87   1.07   13.95
getPeakList          12.94   0.87   13.82
annotation           11.83   0.83   12.69
plot                 10.52   0.52   11.03
plotTIC              10.34   0.36   10.71
plotRaw               9.85   0.50   10.34
plotFeatures          9.84   0.42   10.27
plotCalib             9.53   0.34    9.87
createPtrSet          9.42   0.42   11.22
updatePtrSet          9.31   0.32    9.65
rmPeakList            9.33   0.27    9.59
defineKnots           9.25   0.31    9.57
getDirectory          8.62   0.39    9.19
setSampleMetadata     8.58   0.42    9.00
changeTimeLimits      8.50   0.48    8.99
importSampleMetadata  8.61   0.35    8.95
exportSampleMetada    8.47   0.38    8.86
getSampleMetadata     8.39   0.39    8.79
getFileNames          8.27   0.47    8.78
resetSampleMetadata   8.06   0.34    8.41
convert_to_mzML       6.99   0.27    7.26
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
detectPeak           96.75   1.02   97.80
alignSamples         16.19   0.70   16.89
imputeMat            15.74   0.66   16.39
writeEset            14.53   0.46   14.99
getPeakList          14.08   0.70   14.78
impute               14.02   0.73   14.75
annotation           13.70   0.56   14.27
plotTIC              10.72   0.28   11.00
plotRaw              10.44   0.39   10.83
plot                 10.36   0.29   10.66
rmPeakList           10.18   0.36   10.55
defineKnots           9.92   0.47   10.39
importSampleMetadata  9.64   0.40   10.03
getDirectory          9.47   0.41    9.88
setSampleMetadata     9.54   0.34    9.88
plotFeatures          9.34   0.42    9.76
resetSampleMetadata   9.49   0.27    9.75
createPtrSet          9.39   0.23    9.62
updatePtrSet          9.16   0.29    9.45
exportSampleMetada    9.03   0.31    9.34
getSampleMetadata     8.83   0.34    9.18
getFileNames          8.70   0.28    8.98
changeTimeLimits      8.58   0.36    8.94
plotCalib             8.56   0.32    8.88
convert_to_mzML       6.48   0.27    6.76
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/ptairMS.Rcheck/00check.log'
for details.

Installation output

ptairMS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ptairMS_1.0.1.tar.gz && rm -rf ptairMS.buildbin-libdir && mkdir ptairMS.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ptairMS.buildbin-libdir ptairMS_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ptairMS_1.0.1.zip && rm ptairMS_1.0.1.tar.gz ptairMS_1.0.1.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  704k  100  704k    0     0  1327k      0 --:--:-- --:--:-- --:--:-- 1329k

install for i386

* installing *source* package 'ptairMS' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c align.cpp -o align.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c findEqualGreaterM.cpp -o findEqualGreaterM.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ptairMS.dll tmp.def RcppExports.o align.o findEqualGreaterM.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/ptairMS.buildbin-libdir/00LOCK-ptairMS/00new/ptairMS/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
in method for 'annotateVOC' with signature '"ExpressionSet"': no definition for class "ExpressionSet"
in method for 'writeEset' with signature '"ExpressionSet"': no definition for class "ExpressionSet"
** help
*** installing help indices
  converting help for package 'ptairMS'
    finding HTML links ... done
    LocalMaximaSG                           html  
    OptimalWindowsSG                        html  
    PeakList                                html  
    TransmissionCurve                       html  
    aggregate                               html  
    align                                   html  
    alignSamples                            html  
    annotation                              html  
    calibration                             html  
    calibrationFun                          html  
    changeTimeLimits                        html  
    convert_to_mzML                         html  
    createPtrSet                            html  
    cumulative_fit_function                 html  
    deadTimeCorr                            html  
    defineKnots                             html  
    detectPeak                              html  
    determinePeakShape                      html  
    exportSampleMetada                      html  
    extractEIC                              html  
    fit_averagePeak                         html  
    fit_averagePeak_function                html  
    formula2mass                            html  
    getDirectory                            html  
    getFileNames                            html  
    getPeakList                             html  
    getSampleMetadata                       html  
    importSampleMetadata                    html  
    impute                                  html  
    imputeMat                               html  
    initializeFit                           html  
    makeSubGroup                            html  
    plot                                    html  
    plotCalib                               html  
    plotFeatures                            html  
    plotPeakShape                           html  
    plotRaw                                 html  
    plotTIC                                 html  
    ptairMS-package                         html  
    ptrRaw                                  html  
    ptrSet                                  html  
    readRaw                                 html  
    resetSampleMetadata                     html  
    rmPeakList                              html  
    setSampleMetadata                       html  
    show-ptrRaw-method                      html  
    show-ptrSet-method                      html  
    snipBase                                html  
    timeLimits                              html  
    updatePtrSet                            html  
    width                                   html  
    writeEset                               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 'ptairMS' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c align.cpp -o align.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c findEqualGreaterM.cpp -o findEqualGreaterM.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ptairMS.dll tmp.def RcppExports.o align.o findEqualGreaterM.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/ptairMS.buildbin-libdir/ptairMS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ptairMS' as ptairMS_1.0.1.zip
* DONE (ptairMS)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ptairMS' successfully unpacked and MD5 sums checked

Tests output

ptairMS.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> library(testthat)
> library(ptairMS)
> 
> test_check("ptairMS")
Control1.h5 : 3 peaks detected 
Control2.h5 : 3 peaks detected 
Specie-a1.h5 : 2 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 4 peaks detected 
specie-b2.h5 : 3 peaks detected 
Control1.h5 : 2 peaks detected 
Control2.h5 : 2 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 2 peaks detected 
specie-b2.h5 : 3 peaks detected 
Control1.h5 : 4 peaks detected 
Control2.h5 : 5 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 4 peaks detected 
specie-b1.h5 : 5 peaks detected 
specie-b2.h5 : 4 peaks detected 
Control1.h5 : 3 peaks detected 
Control2.h5 : 2 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 5 peaks detected 
specie-b2.h5 : 4 peaks detected 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 59 ]
> 
> proc.time()
   user  system elapsed 
  73.62    2.57   76.34

ptairMS.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> library(testthat)
> library(ptairMS)
> 
> test_check("ptairMS")
Control1.h5 : 3 peaks detected 
Control2.h5 : 3 peaks detected 
Specie-a1.h5 : 2 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 4 peaks detected 
specie-b2.h5 : 3 peaks detected 
Control1.h5 : 2 peaks detected 
Control2.h5 : 2 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 2 peaks detected 
specie-b2.h5 : 3 peaks detected 
Control1.h5 : 4 peaks detected 
Control2.h5 : 5 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 4 peaks detected 
specie-b1.h5 : 5 peaks detected 
specie-b2.h5 : 4 peaks detected 
Control1.h5 : 3 peaks detected 
Control2.h5 : 2 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 5 peaks detected 
specie-b2.h5 : 4 peaks detected 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 59 ]
> 
> proc.time()
   user  system elapsed 
  75.51    2.15   77.67

Example timings

ptairMS.Rcheck/examples_i386/ptairMS-Ex.timings

nameusersystemelapsed
LocalMaximaSG0.040.000.03
PeakList0.980.161.36
alignSamples17.48 1.0619.70
annotation11.83 0.8312.69
calibration1.010.111.12
changeTimeLimits8.500.488.99
convert_to_mzML6.990.277.26
createPtrSet 9.42 0.4211.22
defineKnots9.250.319.57
detectPeak88.59 1.5890.18
exportSampleMetada8.470.388.86
formula2mass0.020.000.02
getDirectory8.620.399.19
getFileNames8.270.478.78
getPeakList12.94 0.8713.82
getSampleMetadata8.390.398.79
importSampleMetadata8.610.358.95
impute12.87 1.0713.95
imputeMat15.11 1.0516.16
plot10.52 0.5211.03
plotCalib9.530.349.87
plotFeatures 9.84 0.4210.27
plotRaw 9.85 0.5010.34
plotTIC10.34 0.3610.71
readRaw0.080.050.12
resetSampleMetadata8.060.348.41
rmPeakList9.330.279.59
setSampleMetadata8.580.429.00
timeLimits1.010.051.06
updatePtrSet9.310.329.65
writeEset14.57 0.9615.53

ptairMS.Rcheck/examples_x64/ptairMS-Ex.timings

nameusersystemelapsed
LocalMaximaSG0.030.000.03
PeakList0.690.080.77
alignSamples16.19 0.7016.89
annotation13.70 0.5614.27
calibration0.670.030.70
changeTimeLimits8.580.368.94
convert_to_mzML6.480.276.76
createPtrSet9.390.239.62
defineKnots 9.92 0.4710.39
detectPeak96.75 1.0297.80
exportSampleMetada9.030.319.34
formula2mass000
getDirectory9.470.419.88
getFileNames8.700.288.98
getPeakList14.08 0.7014.78
getSampleMetadata8.830.349.18
importSampleMetadata 9.64 0.4010.03
impute14.02 0.7314.75
imputeMat15.74 0.6616.39
plot10.36 0.2910.66
plotCalib8.560.328.88
plotFeatures9.340.429.76
plotRaw10.44 0.3910.83
plotTIC10.72 0.2811.00
readRaw0.090.030.12
resetSampleMetadata9.490.279.75
rmPeakList10.18 0.3610.55
setSampleMetadata9.540.349.88
timeLimits1.090.081.17
updatePtrSet9.160.299.45
writeEset14.53 0.4614.99