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CHECK report for CNORdt on tokay1

This page was generated on 2018-04-12 13:22:09 -0400 (Thu, 12 Apr 2018).

Package 259/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORdt 1.20.0
A. MacNamara
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/CNORdt
Branch: RELEASE_3_6
Last Commit: 5f57340
Last Changed Date: 2017-10-30 12:39:52 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNORdt
Version: 1.20.0
Command: rm -rf CNORdt.buildbin-libdir CNORdt.Rcheck && mkdir CNORdt.buildbin-libdir CNORdt.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNORdt.buildbin-libdir CNORdt_1.20.0.tar.gz >CNORdt.Rcheck\00install.out 2>&1 && cp CNORdt.Rcheck\00install.out CNORdt-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CNORdt.buildbin-libdir --install="check:CNORdt-install.out" --force-multiarch --no-vignettes --timings CNORdt_1.20.0.tar.gz
StartedAt: 2018-04-11 23:02:35 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:05:51 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 196.1 seconds
RetCode: 0
Status:  OK  
CheckDir: CNORdt.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CNORdt.buildbin-libdir CNORdt.Rcheck && mkdir CNORdt.buildbin-libdir CNORdt.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNORdt.buildbin-libdir CNORdt_1.20.0.tar.gz >CNORdt.Rcheck\00install.out 2>&1 && cp CNORdt.Rcheck\00install.out CNORdt-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CNORdt.buildbin-libdir --install="check:CNORdt-install.out" --force-multiarch --no-vignettes --timings CNORdt_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CNORdt.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 'CNORdt/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNORdt' version '1.20.0'
* 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 'CNORdt' 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
** 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 ... NOTE
Package in Depends field not imported from: 'abind'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gaBinaryDT: no visible global function definition for 'runif'
getFitDT: no visible global function definition for 'splinefun'
getFitDT: no visible global function definition for 'optim'
shift: no visible global function definition for 'tail'
shift: no visible global function definition for 'head'
Undefined global functions or variables:
  head optim runif splinefun tail
Consider adding
  importFrom("stats", "optim", "runif", "splinefun")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
* 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-3.6-bioc/meat/CNORdt.buildbin-libdir/CNORdt/libs/i386/CNORdt.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
cutAndPlotResultsDT 31.19   0.07   31.25
gaBinaryDT          30.26   0.03   30.30
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
cutAndPlotResultsDT 31.25   0.02   31.27
gaBinaryDT          30.55   0.02   30.56
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/CNORdt.Rcheck/00check.log'
for details.



Installation output

CNORdt.Rcheck/00install.out


install for i386

* installing *source* package 'CNORdt' ...
** 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 simulatorDT.c -o simulatorDT.o
simulatorDT.c: In function 'simulatorDT':
simulatorDT.c:55:6: warning: unused variable 'nTimes' [-Wunused-variable]
  int nTimes = INTEGER(nTimes_in)[0];
      ^
simulatorDT.c:53:6: warning: unused variable 'nSignals' [-Wunused-variable]
  int nSignals = INTEGER(nSignals_in)[0];
      ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CNORdt.dll tmp.def simulatorDT.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/CNORdt.buildbin-libdir/CNORdt/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CNORdt'
    finding HTML links ... done
    CNOlistPB                               html  
    computeScoreDT                          html  
    convert2array                           html  
    cutAndPlotResultsDT                     html  
    finding level-2 HTML links ... done

    gaBinaryDT                              html  
    getFitDT                                html  
    modelPB                                 html  
    simulatorDT                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CNORdt' ...
** 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 simulatorDT.c -o simulatorDT.o
simulatorDT.c: In function 'simulatorDT':
simulatorDT.c:55:6: warning: unused variable 'nTimes' [-Wunused-variable]
  int nTimes = INTEGER(nTimes_in)[0];
      ^
simulatorDT.c:53:6: warning: unused variable 'nSignals' [-Wunused-variable]
  int nSignals = INTEGER(nSignals_in)[0];
      ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CNORdt.dll tmp.def simulatorDT.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/CNORdt.buildbin-libdir/CNORdt/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNORdt' as CNORdt_1.20.0.zip
* DONE (CNORdt)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

CNORdt.Rcheck/examples_i386/CNORdt-Ex.timings

nameusersystemelapsed
computeScoreDT0.350.000.35
convert2array0.090.000.09
cutAndPlotResultsDT31.19 0.0731.25
gaBinaryDT30.26 0.0330.30
getFitDT0.030.000.03
simulatorDT000

CNORdt.Rcheck/examples_x64/CNORdt-Ex.timings

nameusersystemelapsed
computeScoreDT0.270.000.27
convert2array0.200.010.22
cutAndPlotResultsDT31.25 0.0231.27
gaBinaryDT30.55 0.0230.56
getFitDT0.030.000.03
simulatorDT0.000.010.02