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Package 430/671HostnameOS / ArchBUILDCHECKBUILD BIN
Mulcom 1.10.0
Claudio Isella
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/Mulcom
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: Mulcom
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Mulcom_1.10.0.tar.gz
StartedAt: 2013-05-01 08:31:33 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 08:34:50 -0700 (Wed, 01 May 2013)
EllapsedTime: 197.0 seconds
RetCode: 0
Status:  OK 
CheckDir: Mulcom.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Mulcom.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 'Mulcom/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Mulcom' version '1.10.0'
* 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 'Mulcom' can be installed ... [8s/10s] 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
File 'Mulcom/R/mulib.R':
  .First.lib calls:
    cat("Mulcom loaded\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
* 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 ... [93s/111s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
mulInt     20.935  3.116  24.443
mulOpt     16.221  2.801  27.052
mulOptPlot  6.617  0.492   7.495
mulParOpt   6.435  0.512   7.606
mulCAND     6.391  0.135   9.936
mulFSG      5.534  0.131   5.866
mulDiff     5.260  0.116   5.486
mulPerm     4.909  0.078   5.050
mulOptPars  4.853  0.096   5.098
* 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/Mulcom.Rcheck/00check.log'
for details.

Mulcom.Rcheck/00install.out:

* installing *source* package 'Mulcom' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mulLibs.cc -o mulLibs.o
mulLibs.cc:39:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                sum = sum + array [i];
                            ˜˜˜˜˜  ^
mulLibs.cc:49:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                sum = sum + ( 1 / array [i] ) ;
                                  ˜˜˜˜˜  ^
mulLibs.cc:62:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                sum = sum + array [i];
                            ˜˜˜˜˜  ^
mulLibs.cc:63:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                STD_DEV = STD_DEV + pow( array [i], 2 );
                                         ˜˜˜˜˜  ^
mulLibs.cc:79:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                sum = sum + array [i];
                            ˜˜˜˜˜  ^
mulLibs.cc:80:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                STD_DEV = STD_DEV + pow( array [i], 2 );
                                         ˜˜˜˜˜  ^
mulLibs.cc:97:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                sum = sum + array [i];
                            ˜˜˜˜˜  ^
mulLibs.cc:98:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                sum_squares = sum_squares + pow( array [i], 2 );                        
                                                 ˜˜˜˜˜  ^
mulLibs.cc:153:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                current_cluster = clusters[j] ;
                                                  ˜˜˜˜˜˜˜˜ ^
mulLibs.cc:245:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                current_cluster = clusters[j] ;
                                                  ˜˜˜˜˜˜˜˜ ^
mulLibs.cc:331:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                current_cluster = clusters[j] ;
                                                  ˜˜˜˜˜˜˜˜ ^
mulLibs.cc:467:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                current_cluster = clusters[j] ;
                                                  ˜˜˜˜˜˜˜˜ ^
mulLibs.cc:538:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ( buffer[i] > local_m ) { b.push_back( 1 ) ; }
                             ˜˜˜˜˜˜ ^
mulLibs.cc:551:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                if ( b[ i + jump * j ] > 0 ) { v[i] += 1 ; }
                                     ˜  ˜˜^˜˜˜˜˜˜˜˜˜
mulLibs.cc:601:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                current_cluster = clusters[j] ;
                                                  ˜˜˜˜˜˜˜˜ ^
mulLibs.cc:717:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                current_cluster = clusters[j] ;
                                                  ˜˜˜˜˜˜˜˜ ^
mulLibs.cc:708:17: warning: expression result unused [-Wunused-value]
                current_cluster ;
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mulLibs.cc:851:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        current_cluster = clusters[j] ;
                                                          ˜˜˜˜˜˜˜˜ ^
mulLibs.cc:962:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        current_cluster = clusters[j] ;
                                                          ˜˜˜˜˜˜˜˜ ^
mulLibs.cc:1015:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        sum += ss[ j + jump * i ] ;
                                               ˜˜  ˜˜^˜˜˜˜˜˜˜˜˜
mulLibs.cc:1025:88: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        mse[mse_local_index + ( ( (*N) * (*ngroups - 1) ) * simulation )] = sqrt ( ( sss2[i] * 2 / df ) / harmonic_means[j] );
                                                                                                                     ˜˜˜˜ ^
mulLibs.cc:1025:119: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        mse[mse_local_index + ( ( (*N) * (*ngroups - 1) ) * simulation )] = sqrt ( ( sss2[i] * 2 / df ) / harmonic_means[j] );
                                                                                                                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
22 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 Mulcom.so mulLibs.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Mulcom.Rcheck/Mulcom/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 'Mulcom'
* DONE (Mulcom)

Mulcom.Rcheck/Mulcom-Ex.timings:

nameusersystemelapsed
MULCOM-class1.3820.0482.723
MULCOM_P0.8900.0331.724
mulCAND6.3910.1359.936
mulCalc0.7310.0490.825
mulDELTA0.3070.0200.357
mulDiff5.2600.1165.486
mulFSG5.5340.1315.866
mulIndex0.4300.0340.470
mulInt20.935 3.11624.443
mulOpt16.221 2.80127.052
mulOptPars4.8530.0965.098
mulOptPlot6.6170.4927.495
mulParOpt6.4350.5127.606
mulPerm4.9090.0785.050
mulPermC0.2910.0200.312
mulScores0.7320.0320.811