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CHECK report for adSplit on tokay2

This page was generated on 2019-10-16 12:20:27 -0400 (Wed, 16 Oct 2019).

Package 20/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
adSplit 1.54.0
Claudio Lottaz
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/adSplit
Branch: RELEASE_3_9
Last Commit: ce8fb61
Last Changed Date: 2019-05-02 11:53:05 -0400 (Thu, 02 May 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 [ OK ] 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

Summary

Package: adSplit
Version: 1.54.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:adSplit.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings adSplit_1.54.0.tar.gz
StartedAt: 2019-10-16 01:49:17 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:54:59 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 342.1 seconds
RetCode: 0
Status:  OK  
CheckDir: adSplit.Rcheck
Warnings: 0

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:adSplit.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings adSplit_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/adSplit.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'adSplit/DESCRIPTION' ... OK
* this is package 'adSplit' version '1.54.0'
* 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 'adSplit' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
* 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 for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... 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/adSplit/libs/i386/adSplit.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/adSplit/libs/x64/adSplit.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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
Examples with CPU or elapsed time > 5s
                   user system elapsed
randomDiana2means 38.55   1.26   39.81
makeEID2PROBESenv 31.39   0.94   32.34
drawRandomPS      27.45   0.69   28.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
randomDiana2means 32.83   0.88   33.72
drawRandomPS      31.31   0.65   31.99
makeEID2PROBESenv 29.84   0.79   30.64
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/adSplit.Rcheck/00check.log'
for details.



Installation output

adSplit.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/adSplit_1.54.0.tar.gz && rm -rf adSplit.buildbin-libdir && mkdir adSplit.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=adSplit.buildbin-libdir adSplit_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL adSplit_1.54.0.zip && rm adSplit_1.54.0.tar.gz adSplit_1.54.0.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 51068  100 51068    0     0   466k      0 --:--:-- --:--:-- --:--:--  493k

install for i386

* installing *source* package 'adSplit' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c adSplit.cpp -o adSplit.o
adSplit.cpp: In function 'double tscore(double*, int, int, split&, isis_pars&)':
adSplit.cpp:256:77: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
     throw Tomato(__LINE__, "tscore: internal error, shame on the programmer");
                                                                             ^
adSplit.cpp: In function 'void isis(char**, double*, int*, int*, int*, int*, int*, double*, int*)':
adSplit.cpp:469:67: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
       throw Tomato(__LINE__, "isis() called with unknown function");
                                                                   ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o adSplit.dll tmp.def adSplit.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/adSplit.buildbin-libdir/00LOCK-adSplit/00new/adSplit/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'adSplit'
    finding HTML links ... done
    adSplit-internal                        html  
    adSplit                                 html  
    diana2means                             html  
    drawRandomPS                            html  
    golubKEGGSplits                         html  
    hist.splitSet                           html  
    image.splitSet                          html  
    makeEID2PROBESenv                       html  
    print.split                             html  
    print.splitSet                          html  
    randomDiana2means                       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 'adSplit' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c adSplit.cpp -o adSplit.o
adSplit.cpp: In function 'double tscore(double*, int, int, split&, isis_pars&)':
adSplit.cpp:256:77: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
     throw Tomato(__LINE__, "tscore: internal error, shame on the programmer");
                                                                             ^
adSplit.cpp: In function 'void isis(char**, double*, int*, int*, int*, int*, int*, double*, int*)':
adSplit.cpp:469:67: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
       throw Tomato(__LINE__, "isis() called with unknown function");
                                                                   ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o adSplit.dll tmp.def adSplit.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/adSplit.buildbin-libdir/adSplit/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'adSplit' as adSplit_1.54.0.zip
* DONE (adSplit)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'adSplit' successfully unpacked and MD5 sums checked

Tests output


Example timings

adSplit.Rcheck/examples_i386/adSplit-Ex.timings

nameusersystemelapsed
adSplit1.840.192.60
diana2means1.000.181.19
drawRandomPS27.45 0.6928.15
golubKEGGSplits000
hist.splitSet0.000.020.02
image.splitSet0.110.040.17
makeEID2PROBESenv31.39 0.9432.34
print.splitSet0.000.020.02
randomDiana2means38.55 1.2639.81

adSplit.Rcheck/examples_x64/adSplit-Ex.timings

nameusersystemelapsed
adSplit2.430.112.55
diana2means0.980.041.02
drawRandomPS31.31 0.6531.99
golubKEGGSplits000
hist.splitSet000
image.splitSet0.090.020.11
makeEID2PROBESenv29.84 0.7930.64
print.splitSet000
randomDiana2means32.83 0.8833.72