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This page was generated on 2021-08-03 12:06:10 -0400 (Tue, 03 Aug 2021).

CHECK results for flagme on riesling1

To the developers/maintainers of the flagme package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flagme.git to
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raw results

Package 627/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.49.0  (landing page)
Mark Robinson , Riccardo Romoli
Snapshot Date: 2021-08-02 14:50:09 -0400 (Mon, 02 Aug 2021)
URL: https://git.bioconductor.org/packages/flagme
Branch: master
Last Commit: 214f9ee
Last Changed Date: 2021-05-19 11:42:23 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  NO, package depends on 'xcms' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: flagme
Version: 1.49.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flagme.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flagme_1.49.0.tar.gz
StartedAt: 2021-08-03 00:25:44 -0400 (Tue, 03 Aug 2021)
EndedAt: 2021-08-03 00:37:03 -0400 (Tue, 03 Aug 2021)
EllapsedTime: 679.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flagme.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flagme.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flagme_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/flagme.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flagme/DESCRIPTION' ... OK
* this is package 'flagme' version '1.49.0'
* checking package namespace information ... NOTE
  Namespace with empty importFrom: 'gcspikelite'
* 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 'flagme' can be installed ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for 'bin'
See 'D:/biocbuild/bbs-3.14-bioc/meat/flagme.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... WARNING
man/plotMultipleSpectra.Rd: non-ASCII input and no declared encoding
problem found in 'plotMultipleSpectra.Rd'
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'show' and siglist 'betweenAlignment'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 'D:/biocbuild/bbs-3.14-bioc/R/library/flagme/libs/i386/flagme.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbuild/bbs-3.14-bioc/R/library/flagme/libs/x64/flagme.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 installed files from 'inst/doc' ... OK
* 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
plotMultipleSpectra 25.20   0.17   25.38
corPrt              19.01   0.14   19.16
ndpRT               19.03   0.11   19.14
peaksAlignment      18.70   0.17   18.88
plotSpectra         18.39   0.14   18.53
dynRT               18.23   0.13   18.36
retFatMatrix        10.22   0.05   10.27
addXCMSPeaks         5.93   0.09    6.03
imputePeaks          5.25   0.03    5.29
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
plotMultipleSpectra 25.61   0.42   26.09
corPrt              18.30   0.31   18.61
ndpRT               17.82   0.33   18.14
plotSpectra         17.52   0.27   17.81
dynRT               17.25   0.28   17.53
peaksAlignment      17.17   0.35   17.52
retFatMatrix        10.48   0.20   10.69
addXCMSPeaks         5.81   0.05    5.86
imputePeaks          5.24   0.06    5.30
* 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: 3 WARNINGs, 3 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/flagme.Rcheck/00check.log'
for details.



Installation output

flagme.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/flagme_1.49.0.tar.gz && rm -rf flagme.buildbin-libdir && mkdir flagme.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flagme.buildbin-libdir flagme_1.49.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL flagme_1.49.0.zip && rm flagme_1.49.0.tar.gz flagme_1.49.0.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  402k  100  402k    0     0  2246k      0 --:--:-- --:--:-- --:--:-- 2246k

install for i386

* installing *source* package 'flagme' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c dp.c -o dp.o
dp.c: In function 'dp':
dp.c:263:26: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized]
    D[(i+1)+(j+1)*(nr+1)] = cur_min;
    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
dp.c:264:28: warning: 'tb' may be used uninitialized in this function [-Wmaybe-uninitialized]
    phi[(i+1)+(j+1)*(nr+1)] = tb;
    ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c pearson.c -o pearson.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o flagme.dll tmp.def dp.o init.o pearson.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/flagme.buildbin-libdir/00LOCK-flagme/00new/flagme/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
multiple methods tables found for 'bin' 
** help
*** installing help indices
  converting help for package 'flagme'
    finding HTML links ... done
    addAMDISPeaks                           html  
    addChromaTOFPeaks                       html  
    addXCMSPeaks                            html  
    finding level-2 HTML links ... done

    betweenAlignment                        html  
    calcTimeDiffs                           html  
    clusterAlignment                        html  
    compress                                html  
    corPrt                                  html  
    dp                                      html  
    dynRT                                   html  
    eitherMatrix                            html  
    exportSpectra                           html  
    gatherInfo                              html  
    imputePeaks                             html  
    multipleAlignment                       html  
    ndpRT                                   html  
    normDotProduct                          html  
    parseChromaTOF                          html  
    parseELU                                html  
    peaksAlignment                          html  
    peaksDataset                            html  
    plot                                    html  
    plotImage                               html  
    plotMultipleSpectra                     html  
    plotSpectra                             html  
    progressiveAlignment                    html  
    retFatMatrix                            html  
    rmaFitUnit                              html  
** building package indices
** installing vignettes
   'flagme.Rnw' using 'UTF-8' 
** testing if installed package can be loaded from temporary location
Warning: multiple methods tables found for 'bin'
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for 'bin'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'flagme' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c dp.c -o dp.o
dp.c: In function 'dp':
dp.c:263:26: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized]
    D[(i+1)+(j+1)*(nr+1)] = cur_min;
    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
dp.c:264:28: warning: 'tb' may be used uninitialized in this function [-Wmaybe-uninitialized]
    phi[(i+1)+(j+1)*(nr+1)] = tb;
    ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c pearson.c -o pearson.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o flagme.dll tmp.def dp.o init.o pearson.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/flagme.buildbin-libdir/flagme/libs/x64
** testing if installed package can be loaded
Warning: multiple methods tables found for 'bin'
* MD5 sums
packaged installation of 'flagme' as flagme_1.49.0.zip
* DONE (flagme)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'flagme' successfully unpacked and MD5 sums checked

Tests output


Example timings

flagme.Rcheck/examples_i386/flagme-Ex.timings

nameusersystemelapsed
addAMDISPeaks3.750.033.78
addChromaTOFPeaks2.450.072.51
addXCMSPeaks5.930.096.03
betweenAlignment000
calcTimeDiffs4.130.054.17
clusterAlignment3.330.033.36
compress3.280.013.30
corPrt19.01 0.1419.16
dp3.250.033.28
dynRT18.23 0.1318.36
gatherInfo3.670.033.70
imputePeaks5.250.035.29
multipleAlignment3.680.003.67
ndpRT19.03 0.1119.14
normDotProduct3.280.023.30
parseChromaTOF1.560.011.62
parseELU1.240.001.23
peaksAlignment18.70 0.1718.88
peaksDataset3.000.043.03
plot4.470.014.49
plotImage1.970.001.96
plotMultipleSpectra25.20 0.1725.38
plotSpectra18.39 0.1418.53
progressiveAlignment3.730.053.78
retFatMatrix10.22 0.0510.27
rmaFitUnit3.890.003.89

flagme.Rcheck/examples_x64/flagme-Ex.timings

nameusersystemelapsed
addAMDISPeaks3.700.083.78
addChromaTOFPeaks1.880.061.93
addXCMSPeaks5.810.055.86
betweenAlignment000
calcTimeDiffs3.740.043.78
clusterAlignment3.110.073.17
compress3.170.043.22
corPrt18.30 0.3118.61
dp3.140.083.22
dynRT17.25 0.2817.53
gatherInfo3.680.043.72
imputePeaks5.240.065.30
multipleAlignment3.730.063.79
ndpRT17.82 0.3318.14
normDotProduct3.110.093.21
parseChromaTOF1.450.001.45
parseELU1.230.001.23
peaksAlignment17.17 0.3517.52
peaksDataset2.930.073.00
plot4.260.084.34
plotImage1.970.021.99
plotMultipleSpectra25.61 0.4226.09
plotSpectra17.52 0.2717.81
progressiveAlignment3.810.063.88
retFatMatrix10.48 0.2010.69
rmaFitUnit3.750.033.78