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CHECK report for TargetSearch on tokay2

This page was generated on 2018-10-17 08:34:16 -0400 (Wed, 17 Oct 2018).

Package 1464/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetSearch 1.36.1
Alvaro Cuadros-Inostroza
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/TargetSearch
Branch: RELEASE_3_7
Last Commit: 17add3a
Last Changed Date: 2018-05-03 04:54:46 -0400 (Thu, 03 May 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: TargetSearch
Version: 1.36.1
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TargetSearch.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings TargetSearch_1.36.1.tar.gz
StartedAt: 2018-10-17 05:09:17 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 05:11:21 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 123.5 seconds
RetCode: 0
Status:  OK  
CheckDir: TargetSearch.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TargetSearch.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings TargetSearch_1.36.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/TargetSearch.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TargetSearch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TargetSearch' version '1.36.1'
* 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 'TargetSearch' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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-3.7-bioc/R/library/TargetSearch/libs/i386/TargetSearch.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
RIcorrect 13.09   1.28   22.83
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
RIcorrect 8.23   1.36     9.7
* 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-3.7-bioc/meat/TargetSearch.Rcheck/00check.log'
for details.



Installation output

TargetSearch.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/TargetSearch_1.36.1.tar.gz && rm -rf TargetSearch.buildbin-libdir && mkdir TargetSearch.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TargetSearch.buildbin-libdir TargetSearch_1.36.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL TargetSearch_1.36.1.zip && rm TargetSearch_1.36.1.tar.gz TargetSearch_1.36.1.zip
###
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  % 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  179k  100  179k    0     0  2902k      0 --:--:-- --:--:-- --:--:-- 3316k

install for i386

* installing *source* package 'TargetSearch' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Rinit.c -o Rinit.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c file.c -o file.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c find_peaks.c -o find_peaks.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c getLine.c -o getLine.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c hpf.c -o hpf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ncdf.c -o ncdf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c netcdf_peak_finding.c -o netcdf_peak_finding.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ppc.c -o ppc.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o TargetSearch.dll tmp.def Rinit.o file.o find_peaks.o getLine.o hpf.o ncdf.o netcdf_peak_finding.o ppc.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/TargetSearch.buildbin-libdir/TargetSearch/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TargetSearch'
    finding HTML links ... done
    FAMEoutliers                            html  
    FindAllPeaks                            html  
    FindPeaks                               html  
    ImportFameSettings                      html  
    ImportLibrary                           html  
    ImportSamples                           html  
    NetCDFPeakFinding                       html  
    Profile                                 html  
    ProfileCleanUp                          html  
    RIcorrect                               html  
    TSExample                               html  
    TargetSearch-package                    html  
    TargetSearchGUI                         html  
    Write.Results                           html  
    baseline                                html  
    defunct                                 html  
    file                                    html  
    fixRI                                   html  
    medianRILib                             html  
    peakCDFextraction                       html  
    peakFind                                html  
    plotFAME                                html  
    plotPeak                                html  
    plotPeakRI                              html  
    plotPeakSimple                          html  
    plotRIdev                               html  
    plotSpectra                             html  
    quantMatrix                             html  
    ri2rt                                   html  
    riMatrix                                html  
    rt2ri                                   html  
    sampleRI                                html  
    tsLib-class                             html  
    tsMSdata-class                          html  
    tsProfile-class                         html  
    tsRim-class                             html  
    tsSample-class                          html  
    writeLibText                            html  
    writeMSP                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'TargetSearch' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Rinit.c -o Rinit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c file.c -o file.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c find_peaks.c -o find_peaks.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c getLine.c -o getLine.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c hpf.c -o hpf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ncdf.c -o ncdf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c netcdf_peak_finding.c -o netcdf_peak_finding.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ppc.c -o ppc.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o TargetSearch.dll tmp.def Rinit.o file.o find_peaks.o getLine.o hpf.o ncdf.o netcdf_peak_finding.o ppc.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/TargetSearch.buildbin-libdir/TargetSearch/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TargetSearch' as TargetSearch_1.36.1.zip
* DONE (TargetSearch)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'TargetSearch' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

TargetSearch.Rcheck/examples_i386/TargetSearch-Ex.timings

nameusersystemelapsed
FAMEoutliers0.160.010.17
FindAllPeaks1.970.003.88
FindPeaks0.450.000.45
ImportFameSettings0.010.000.01
ImportLibrary0.020.000.04
ImportSamples000
NetCDFPeakFinding0.290.071.20
Profile2.020.032.05
ProfileCleanUp1.750.031.78
RIcorrect13.09 1.2822.83
TSExample3.100.443.53
fixRI1.250.191.44
medianRILib1.190.031.22
peakFind0.720.030.75
plotFAME0.030.000.03
plotPeak0.310.090.41
plotPeakRI1.380.051.42
plotPeakSimple0.610.060.71
plotRIdev0.890.020.90
plotSpectra0.680.010.71
quantMatrix1.600.081.67
ri2rt0.010.000.01
riMatrix0.940.141.08
rt2ri000
sampleRI1.160.031.19
tsLib-class0.030.000.04
tsMSdata-class000
tsProfile-class000
tsRim-class000
tsSample-class0.030.000.03
writeLibText0.050.000.04

TargetSearch.Rcheck/examples_x64/TargetSearch-Ex.timings

nameusersystemelapsed
FAMEoutliers0.150.000.16
FindAllPeaks1.470.051.51
FindPeaks0.370.000.37
ImportFameSettings0.020.000.02
ImportLibrary0.010.000.01
ImportSamples000
NetCDFPeakFinding0.190.020.21
Profile1.360.011.37
ProfileCleanUp1.190.051.24
RIcorrect8.231.369.70
TSExample2.830.363.20
fixRI0.850.060.91
medianRILib0.640.030.67
peakFind0.320.020.35
plotFAME0.000.010.01
plotPeak0.250.050.30
plotPeakRI1.170.081.25
plotPeakSimple0.350.040.39
plotRIdev0.460.040.50
plotSpectra0.330.010.34
quantMatrix1.060.021.08
ri2rt000
riMatrix0.590.060.66
rt2ri0.020.000.01
sampleRI0.660.030.69
tsLib-class0.010.000.02
tsMSdata-class000
tsProfile-class000
tsRim-class000
tsSample-class0.010.000.02
writeLibText0.020.000.01