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CHECK report for dpeak on tokay1

This page was generated on 2021-05-06 12:30:59 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the dpeak package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 507/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dpeak 1.2.0  (landing page)
Dongjun Chung
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/dpeak
Branch: RELEASE_3_12
Last Commit: bd5fad4
Last Changed Date: 2020-10-27 11:56:41 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: dpeak
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dpeak.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings dpeak_1.2.0.tar.gz
StartedAt: 2021-05-06 02:21:50 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:27:36 -0400 (Thu, 06 May 2021)
EllapsedTime: 346.7 seconds
RetCode: 0
Status:   OK   
CheckDir: dpeak.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dpeak.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings dpeak_1.2.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/dpeak.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dpeak/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dpeak' version '1.2.0'
* 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 'dpeak' 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... 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
DpeakFit-class 6.46   1.11    7.56
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
DpeakFit-class 7.79   1.01    8.94
exportPlot     5.08   0.00    5.23
exportPeakList 5.03   0.00    5.42
* 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-3.12-bioc/meat/dpeak.Rcheck/00check.log'
for details.



Installation output

dpeak.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/dpeak_1.2.0.tar.gz && rm -rf dpeak.buildbin-libdir && mkdir dpeak.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dpeak.buildbin-libdir dpeak_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL dpeak_1.2.0.zip && rm dpeak_1.2.0.tar.gz dpeak_1.2.0.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  156k  100  156k    0     0  10.4M      0 --:--:-- --:--:-- --:--:-- 10.9M

install for i386

* installing *source* package 'dpeak' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c dlength.cpp -o dlength.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fraglen.cpp -o fraglen.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ismaxZ0.cpp -o ismaxZ0.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c normalize.cpp -o normalize.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c samp.cpp -o samp.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c score.cpp -o score.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c stack.cpp -o stack.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o dpeak.dll tmp.def dlength.o fraglen.o ismaxZ0.o normalize.o samp.o score.o stack.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/dpeak.buildbin-libdir/00LOCK-dpeak/00new/dpeak/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'dpeak'
    finding HTML links ... done
    DpeakData-class                         html  
    DpeakFit-class                          html  
    DpeakMotif-class                        html  
    dpeak-internal                          html  
    dpeak-package                           html  
    dpeakFit                                html  
    dpeakMotif                              html  
    dpeakRead                               html  
    exampleData                             html  
    exportPeakList                          html  
    exportPlot                              html  
    printEmpty                              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 'dpeak' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c dlength.cpp -o dlength.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fraglen.cpp -o fraglen.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ismaxZ0.cpp -o ismaxZ0.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c normalize.cpp -o normalize.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c samp.cpp -o samp.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c score.cpp -o score.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c stack.cpp -o stack.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o dpeak.dll tmp.def dlength.o fraglen.o ismaxZ0.o normalize.o samp.o score.o stack.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/dpeak.buildbin-libdir/dpeak/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dpeak' as dpeak_1.2.0.zip
* DONE (dpeak)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'dpeak' successfully unpacked and MD5 sums checked

Tests output


Example timings

dpeak.Rcheck/examples_i386/dpeak-Ex.timings

nameusersystemelapsed
DpeakData-class000
DpeakFit-class6.461.117.56
DpeakMotif-class000
dpeak-package000
dpeakFit3.750.003.75
dpeakMotif000
dpeakRead000
exampleData0.020.000.01
exportPeakList3.580.003.58
exportPlot3.590.003.62
printEmpty0.020.000.02

dpeak.Rcheck/examples_x64/dpeak-Ex.timings

nameusersystemelapsed
DpeakData-class0.000.020.01
DpeakFit-class7.791.018.94
DpeakMotif-class000
dpeak-package000
dpeakFit4.990.004.99
dpeakMotif000
dpeakRead0.010.000.01
exampleData0.020.000.02
exportPeakList5.030.005.42
exportPlot5.080.005.23
printEmpty0.010.000.02