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 |
* 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NB: .First.lib is obsolete and will not be used in R 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.
* 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)