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CHECK report for SIMD on tokay2

This page was generated on 2019-04-09 12:41:55 -0400 (Tue, 09 Apr 2019).

Package 1495/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMD 1.1.1
Jiadi Zhu
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/SIMD
Branch: master
Last Commit: 4c741ad
Last Changed Date: 2019-01-04 13:50:37 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: SIMD
Version: 1.1.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMD.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SIMD_1.1.1.tar.gz
StartedAt: 2019-04-09 05:59:44 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:00:25 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 41.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: SIMD.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMD.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SIMD_1.1.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SIMD.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SIMD/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SIMD' version '1.1.1'
* package encoding: UTF-8
* 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 'SIMD' 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 ... WARNING
Problems with news in 'inst/NEWS.Rd':
  Malformed NEWS.Rd file:
  Chunk starting
    \itemize{
  The latest one.
  }
  contains no \item.
  Malformed NEWS.Rd file:
  Chunk starting
    \itemize{
  Modify the NOTE in build procedure.
  }
  contains no \item.
* 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-3.9-bioc/R/library/SIMD/libs/i386/SIMD.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SIMD/libs/x64/SIMD.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
** running examples for arch 'x64' ... OK
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/SIMD.Rcheck/00check.log'
for details.



Installation output

SIMD.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SIMD_1.1.1.tar.gz && rm -rf SIMD.buildbin-libdir && mkdir SIMD.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SIMD.buildbin-libdir SIMD_1.1.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SIMD_1.1.1.zip && rm SIMD_1.1.1.tar.gz SIMD_1.1.1.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 92575  100 92575    0     0  1442k      0 --:--:-- --:--:-- --:--:-- 1614k

install for i386

* installing *source* package 'SIMD' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c pvalueclassify.c -o pvalueclassify.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o SIMD.dll tmp.def init.o pvalueclassify.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/SIMD.buildbin-libdir/00LOCK-SIMD/00new/SIMD/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SIMD'
    finding HTML links ... done
    EM2_H1ESB1_MeDIP_sigleCpG               html  
    EM2_H1ESB2_MeDIP_sigleCpG               html  
    EM_H1ESB1_MeDIP_sigleCpG                html  
    EMalgorithm                             html  
    EMtest                                  html  
    H1ESB1_MRE_sigleCpG                     html  
    H1ESB2_MRE_sigleCpG                     html  
    SIMD-package                            html  
    all_CpGsite_bin_chr18                   html  
    classifypvalue                          html  
    emalgth                                 html  
    emalgth1                                html  
    probBinom                               html  
    three_mre_cpg                           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 'SIMD' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pvalueclassify.c -o pvalueclassify.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o SIMD.dll tmp.def init.o pvalueclassify.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/SIMD.buildbin-libdir/SIMD/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIMD' as SIMD_1.1.1.zip
* DONE (SIMD)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SIMD' successfully unpacked and MD5 sums checked

Tests output


Example timings

SIMD.Rcheck/examples_i386/SIMD-Ex.timings

nameusersystemelapsed
EMalgorithm3.340.174.05
EMtest0.510.020.53
emalgth000
emalgth10.010.000.01
probBinom0.030.000.03

SIMD.Rcheck/examples_x64/SIMD-Ex.timings

nameusersystemelapsed
EMalgorithm3.520.173.69
EMtest0.500.010.51
emalgth0.020.000.02
emalgth10.010.000.01
probBinom0.000.050.05