Package: ADaCGH2

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ADaCGH2_1.10.0.tar.gz

StartedAt: 2013-05-01 01:48:21 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 01:53:32 -0700 (Wed, 01 May 2013)

EllapsedTime: 311.6 seconds

RetCode: 0

Status:  OK

CheckDir: ADaCGH2.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ADaCGH2.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 'ADaCGH2/DESCRIPTION' ... OK
* this is package 'ADaCGH2' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'Rmpi' 'multicore'
* 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 'ADaCGH2' can be installed ... [21s/23s] 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 ... NOTE
Foreign function calls with 'PACKAGE' argument in a different package:
  .Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
  .Fortran("wfindcpt", ..., PACKAGE = "DNAcopy")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
mpi.clean.quit.Web: no visible global function definition for
  'mpi.comm.size'
mpi.clean.quit.Web: no visible global function definition for
  'mpi.close.Rslaves'
mpi.clean.quit.Web: no visible global function definition for
  'mpi.exit'
snowfallInit: no visible global function definition for
  'mpi.universe.size'
* 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' ... OK
* checking examples ... [20s/111s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
pSegment              2.846  0.150  30.579
outputToCGHregions    2.205  0.101  22.426
pChromPlot            1.853  0.052  20.817
inputDataToADaCGHData 1.542  0.033   8.654
snowfallInit          0.104  0.021  17.702
* 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 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/ADaCGH2.Rcheck/00check.log'
for details.

* installing *source* package 'ADaCGH2' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c r_haarseg.c -o r_haarseg.o
r_haarseg.c:65:12: warning: unused variable 'totalNorm' [-Wunused-variable]
    double totalNorm;
           ^
r_haarseg.c:152:8: warning: '/*' within block comment [-Wcomment]
                                         }/* for j */
                                          ^
r_haarseg.c:176:8: warning: '/*' within block comment [-Wcomment]
                                         }/* for j */
                                          ^
r_haarseg.c:128:9: warning: unused variable 'j' [-Wunused-variable]
         int k,j;
               ^
4 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 ADaCGH2.so r_haarseg.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/ADaCGH2.Rcheck/ADaCGH2/libs
** R
** data
** inst
** preparing package for lazy loading
Setting adacgh_changepoints to DNAcopy:::changepoints
Setting adacgh_trimmed.variance to DNAcopy:::trimmed.variance
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ADaCGH2)

name	user	system	elapsed
inputDataToADaCGHData	1.542	0.033	8.654
outputToCGHregions	2.205	0.101	22.426
pChromPlot	1.853	0.052	20.817
pSegment	2.846	0.150	30.579
snowfallInit	0.104	0.021	17.702