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Package 649/671HostnameOS / ArchBUILDCHECKBUILD BIN
twilight 1.36.0
Stefanie Scheid
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/twilight
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: twilight
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch twilight_1.36.0.tar.gz
StartedAt: 2013-05-01 11:37:11 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 11:38:13 -0700 (Wed, 01 May 2013)
EllapsedTime: 61.8 seconds
RetCode: 0
Status:  OK 
CheckDir: twilight.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/twilight.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'twilight/DESCRIPTION' ... OK
* this is package 'twilight' version '1.36.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'twilight' can be installed ... [6s/6s] OK
* checking installed package size ... OK
* checking package 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
* 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 for unstated 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 ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

twilight: no visible binding for '<<-' assignment to
  '.twilight.lambda.xxx'
twilight: no visible binding for '<<-' assignment to
  '.twilight.pval.xxx'
twilight: no visible binding for '<<-' assignment to
  '.twilight.score.xxx'
twilight: no visible binding for global variable '.twilight.lambda.xxx'
twilight: no visible binding for global variable '.twilight.pval.xxx'
twilight: no visible binding for global variable '.twilight.score.xxx'
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'Makefile', 'compdiag.sty', 'tr_2004_01.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [3s/3s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/twilight.Rcheck/00check.log'
for details.

twilight.Rcheck/00install.out:

* installing *source* package 'twilight' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c confidence.line.c -o confidence.line.o
confidence.line.c:86:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort((void*)stat,*ngene,sizeof(double),compare1);
    ˜˜˜˜˜             ^˜˜˜˜˜
confidence.line.c:87:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort((void*)sobs,*ngene,sizeof(double),compare1);
    ˜˜˜˜˜             ^˜˜˜˜˜
confidence.line.c:94:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort((void*)stat,*ngene,sizeof(double),compare1);
    ˜˜˜˜˜             ^˜˜˜˜˜
confidence.line.c:207:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort((void*)stat,*ngene,sizeof(double),compare1);
    ˜˜˜˜˜             ^˜˜˜˜˜
confidence.line.c:208:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort((void*)sobs,*ngene,sizeof(double),compare1);
    ˜˜˜˜˜             ^˜˜˜˜˜
confidence.line.c:215:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort((void*)stat,*ngene,sizeof(double),compare1);
    ˜˜˜˜˜             ^˜˜˜˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c correlation.c -o correlation.o
correlation.c:102:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort((void*)stat,*ngene,sizeof(double),compare7);
    ˜˜˜˜˜             ^˜˜˜˜˜
correlation.c:183:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort((void*)stat,*ngene,sizeof(double),compare7);
    ˜˜˜˜˜             ^˜˜˜˜˜
correlation.c:184:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort((void*)sobs,*ngene,sizeof(double),compare7);
    ˜˜˜˜˜             ^˜˜˜˜˜
correlation.c:191:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort((void*)stat,*ngene,sizeof(double),compare7);
    ˜˜˜˜˜             ^˜˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c kstest.c -o kstest.o
kstest.c:72:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort((void*)asort,nrowa,sizeof(double),compare11);    
    ˜˜˜˜˜              ^˜˜˜˜
kstest.c:182:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        qsort((void*)ssort,*ngene,sizeof(double),compare11);
        ˜˜˜˜˜              ^˜˜˜˜˜
kstest.c:296:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        qsort((void*)ssort,*ngene,sizeof(double),compare11);
        ˜˜˜˜˜              ^˜˜˜˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sep.c -o sep.o
sep.c:70:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
          ix[randnum]=fabs(1-ix[randnum]);
                     ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sep.c:97:20: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
              ix[randnum]=fabs(1-ix[randnum]);
                         ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sep.c:116:19: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
      ix[randnum]=fabs(1-ix[randnum]);
                 ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sep.c:143:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
          ix[randnum]=fabs(1-ix[randnum]);
                     ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c twosample.perm.c -o twosample.perm.o
twosample.perm.c:100:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort((void*)stat,*ngene,sizeof(double),compare2);
    ˜˜˜˜˜             ^˜˜˜˜˜
twosample.perm.c:214:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort((void*)stat,*ngene,sizeof(double),compare2);
    ˜˜˜˜˜             ^˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c twosample.single.c -o twosample.single.o
twosample.single.c:75:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      qsort((void*)ssort,*ngene,sizeof(double),compare3);
      ˜˜˜˜˜              ^˜˜˜˜˜
twosample.single.c:152:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      qsort((void*)ssort,*ngene,sizeof(double),compare3);
      ˜˜˜˜˜              ^˜˜˜˜˜
2 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o twilight.so confidence.line.o correlation.o kstest.o sep.o twosample.perm.o twosample.single.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/twilight.Rcheck/twilight/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: ignoring .First.lib() for package 'twilight'
* DONE (twilight)

twilight.Rcheck/twilight-Ex.timings:

nameusersystemelapsed
plot.twilight0.1920.0200.214
print.twilight0.0870.0100.109
twilight0.2030.0200.230
twilight.combi0.0170.0010.019
twilight.filtering0.1050.0020.107
twilight.pval0.1560.0200.183
twilight.teststat0.0250.0030.028