Multiple platform build/check report for BioC 3.6 - CHECK report for flagme on tokay1

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### Running command:
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###   rm -rf flagme.buildbin-libdir flagme.Rcheck && mkdir flagme.buildbin-libdir flagme.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flagme.buildbin-libdir flagme_1.34.0.tar.gz >flagme.Rcheck\00install.out 2>&1 && cp flagme.Rcheck\00install.out flagme-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=flagme.buildbin-libdir --install="check:flagme-install.out" --force-multiarch --no-vignettes --timings flagme_1.34.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/flagme.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.34.0'
* 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 ... OK
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
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 'C:/Users/biocbuild/bbs-3.6-bioc/meat/flagme.buildbin-libdir/flagme/libs/i386/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 or elapsed time > 5s
                      user system elapsed
plotMultipleSpectra  38.39   0.74   40.14
corPrt               29.72   0.39   30.49
dynRT                27.03   0.45   27.49
plotSpectra          26.81   0.53   27.34
peaksAlignment       26.16   0.36   26.52
ndpRT                25.43   0.50   25.92
retFatMatrix         13.84   0.26   14.11
imputePeaks           9.93   0.07   10.28
plot                  8.29   0.05    8.34
addXCMSPeaks          8.09   0.10    8.22
rmaFitUnit            7.52   0.06    7.58
calcTimeDiffs         6.88   0.12   10.04
gatherInfo            6.30   0.13    6.42
dp                    5.69   0.08    5.77
compress              5.59   0.02    5.61
multipleAlignment     5.42   0.07    5.49
clusterAlignment      5.28   0.09    5.38
progressiveAlignment  5.22   0.05    5.27
normDotProduct        5.11   0.06    5.17
addAMDISPeaks         4.66   0.17    6.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
plotMultipleSpectra  45.67   1.00   46.67
plotSpectra          36.92   0.56   37.48
peaksAlignment       33.92   0.88   34.80
dynRT                32.32   0.70   33.03
corPrt               31.74   0.63   32.36
ndpRT                31.40   0.80   32.20
retFatMatrix         18.08   0.27   18.35
imputePeaks          12.36   0.14   12.50
addXCMSPeaks          9.07   0.14    9.23
plot                  8.97   0.06    9.03
rmaFitUnit            8.24   0.06    8.29
calcTimeDiffs         7.85   0.06    7.91
gatherInfo            7.60   0.17    7.77
multipleAlignment     7.38   0.14    7.52
clusterAlignment      6.62   0.07    6.69
progressiveAlignment  6.59   0.05    6.64
compress              6.25   0.04    6.29
peaksDataset          6.19   0.08    6.27
dp                    6.09   0.11    6.21
normDotProduct        5.69   0.09    5.78
addAMDISPeaks         5.06   0.01    5.08
* 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: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/flagme.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'flagme' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c dp.c -o dp.o
dp.c: In function 'dp':
dp.c:218:21: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized]
   double gap=*gap_, cur_min, a, b, c;
                     ^
dp.c:217:30: warning: 'tb' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int i,j, nr=*nr_, nc=*nc_, tb, count=0, done=0;
                              ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c pearson.c -o pearson.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flagme.dll tmp.def dp.o init.o pearson.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/flagme.buildbin-libdir/flagme/libs/i386
** R
** inst
** preparing package for lazy loading
** 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
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flagme' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pearson.c -o pearson.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flagme.dll tmp.def dp.o init.o pearson.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/flagme.buildbin-libdir/flagme/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flagme' as flagme_1.34.0.zip
* DONE (flagme)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for flagme on tokay1

Summary

Command output

Installation output

Tests output

Example timings