BGmix 1.20.0
Alex Lewin
| 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/BGmix | | 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 | N O T S U P P O R T E D |
| 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/BGmix.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 'BGmix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BGmix' version '1.20.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'BGmix' can be installed ... [7s/11s] 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
ccSummary: warning in agrep("genes", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("conds", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("effects", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("mix comps", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("variance", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("mix prior", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("niter", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("nburn", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("nthin", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("seed", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("move", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("fullBayes", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("aa updated", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta updated", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambdas updated", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("tau's", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("t-dist", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("(params)", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("(predictive)", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta_up", summ, max = 0): partial argument
match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta_down", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambda+ for", summ, max = 0): partial
argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambda- for", summ, max = 0): partial
argument match of 'max' to 'max.distance'
plotFDR: warning in legend(xx, yy, leg = c("FDR=5%", "FDR=10%"), col =
c("red", "blue"), lty = c(1, 1), bg = "white"): partial argument
match of 'leg' to 'legend'
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/BGmix.Rcheck/BGmix/libs/BGmix.so':
Found '__ZSt4cerr', possibly from 'std::cerr' (C++)
Object: 'updates_BGmix.o'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... [81s/95s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
BGmix 13.365 0.494 16.714
FDRforTailPP 11.898 1.400 15.225
EstimatePi0 6.107 0.539 7.727
BGmix-package 6.105 0.304 7.660
FDRplotTailPP 5.482 0.903 7.284
histTailPP 5.492 0.404 7.203
TailPP 5.444 0.361 6.658
plotMixDensity 5.471 0.304 7.318
* 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/BGmix.Rcheck/00check.log'
for details.
* installing *source* package 'BGmix' ...
checking for gcc... clang
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for clang option to accept ISO C99... none needed
checking for cos in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -DUSING_R -c BGmix_main.cpp -o BGmix_main.o
In file included from BGmix_main.cpp:25:
In file included from ./updates_BGmix.h:1:
In file included from ./rand.hh:32:
In file included from ../boostIncl/boost/random.hpp:36:
In file included from ../boostIncl/boost/random/linear_congruential.hpp:25:
In file included from ../boostIncl/boost/random/detail/const_mod.hpp:22:
../boostIncl/boost/integer_traits.hpp:164:66: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
public detail::integer_traits_base< ::boost::long_long_type, LLONG_MIN, LLONG_MAX>
^
/usr/include/i386/limits.h:86:21: note: expanded from macro 'LLONG_MIN'
#define LLONG_MIN (-0x7fffffffffffffffLL-1) /* min signed long long */
^
In file included from BGmix_main.cpp:25:
In file included from ./updates_BGmix.h:1:
In file included from ./rand.hh:32:
In file included from ../boostIncl/boost/random.hpp:36:
In file included from ../boostIncl/boost/random/linear_congruential.hpp:25:
In file included from ../boostIncl/boost/random/detail/const_mod.hpp:22:
../boostIncl/boost/integer_traits.hpp:164:77: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
public detail::integer_traits_base< ::boost::long_long_type, LLONG_MIN, LLONG_MAX>
^
/usr/include/i386/limits.h:85:19: note: expanded from macro 'LLONG_MAX'
#define LLONG_MAX 0x7fffffffffffffffLL /* max signed long long */
^
In file included from BGmix_main.cpp:25:
In file included from ./updates_BGmix.h:1:
In file included from ./rand.hh:32:
In file included from ../boostIncl/boost/random.hpp:36:
In file included from ../boostIncl/boost/random/linear_congruential.hpp:25:
In file included from ../boostIncl/boost/random/detail/const_mod.hpp:22:
../boostIncl/boost/integer_traits.hpp:170:70: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
public detail::integer_traits_base< ::boost::ulong_long_type, 0, ULLONG_MAX>
^
/usr/include/i386/limits.h:84:20: note: expanded from macro 'ULLONG_MAX'
#define ULLONG_MAX 0xffffffffffffffffULL /* max unsigned long long */
^
In file included from BGmix_main.cpp:25:
In file included from ./updates_BGmix.h:1:
In file included from ./rand.hh:32:
In file included from ../boostIncl/boost/random.hpp:41:
../boostIncl/boost/random/lagged_fibonacci.hpp:112:22: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
minstd_rand0 gen(value);
˜˜˜ ^˜˜˜˜
../boostIncl/boost/random/lagged_fibonacci.hpp:289:25: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
minstd_rand0 intgen(value);
˜˜˜˜˜˜ ^˜˜˜˜
In file included from BGmix_main.cpp:25:
In file included from ./updates_BGmix.h:1:
In file included from ./rand.hh:32:
In file included from ../boostIncl/boost/random.hpp:42:
In file included from ../boostIncl/boost/random/ranlux.hpp:20:
../boostIncl/boost/random/subtract_with_carry.hpp:97:74: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
random::linear_congruential<int32_t, 40014, 0, 2147483563, 0> intgen(value);
˜˜˜˜˜˜ ^˜˜˜˜
../boostIncl/boost/random/subtract_with_carry.hpp:287:71: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
random::linear_congruential<int32_t, 40014, 0, 2147483563, 0> gen(value);
˜˜˜ ^˜˜˜˜
BGmix_main.cpp:38:18: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define PRINTF(...) Rprintf((char*) __VA_ARGS__)
^
BGmix_main.cpp:490:13: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
Random rand(seed);
˜˜˜˜ ^˜˜˜
In file included from BGmix_main.cpp:25:
In file included from ./updates_BGmix.h:1:
In file included from ./rand.hh:32:
In file included from ../boostIncl/boost/random.hpp:41:
../boostIncl/boost/random/lagged_fibonacci.hpp:289:25: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
minstd_rand0 intgen(value);
˜˜˜˜˜˜ ^˜˜˜˜
../boostIncl/boost/random/lagged_fibonacci.hpp:269:66: note: in instantiation of member function 'boost::random::lagged_fibonacci_01<double, 48, 4423, 2098>::seed' requested here
explicit lagged_fibonacci_01(uint32_t value) { init_modulus(); seed(value); }
^
./rand.hh:48:31: note: in instantiation of member function 'boost::random::lagged_fibonacci_01<double, 48, 4423, 2098>::lagged_fibonacci_01' requested here
Boost_Wrap(uint32_t seed) : Engine(seed), U01(), Generator(Engine,U01) {}
^
./rand.hh:60:35: note: in instantiation of member function 'Boost_Wrap<boost::random::lagged_fibonacci_01<double, 48, 4423, 2098>, double>::Boost_Wrap' requested here
Rand(uint32_t seed=643774788) : unif(seed), GM_a1(0), GM_a2(0) {}
^
BGmix_main.cpp:490:8: note: in instantiation of member function 'Rand<Boost_Wrap<boost::random::lagged_fibonacci_01<double, 48, 4423, 2098>, double>, double>::Rand' requested here
Random rand(seed);
^
10 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -DUSING_R -c rundir.cpp -o rundir.o
rundir.cpp:28:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
reverse=digit+48;
˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜
rundir.cpp:33:21: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
reverse+=digit+48;
˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -DUSING_R -c updates_BGmix.cpp -o updates_BGmix.o
In file included from updates_BGmix.cpp:3:
In file included from ./updates_BGmix.h:1:
In file included from ./rand.hh:32:
In file included from ../boostIncl/boost/random.hpp:36:
In file included from ../boostIncl/boost/random/linear_congruential.hpp:25:
In file included from ../boostIncl/boost/random/detail/const_mod.hpp:22:
../boostIncl/boost/integer_traits.hpp:164:66: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
public detail::integer_traits_base< ::boost::long_long_type, LLONG_MIN, LLONG_MAX>
^
/usr/include/i386/limits.h:86:21: note: expanded from macro 'LLONG_MIN'
#define LLONG_MIN (-0x7fffffffffffffffLL-1) /* min signed long long */
^
In file included from updates_BGmix.cpp:3:
In file included from ./updates_BGmix.h:1:
In file included from ./rand.hh:32:
In file included from ../boostIncl/boost/random.hpp:36:
In file included from ../boostIncl/boost/random/linear_congruential.hpp:25:
In file included from ../boostIncl/boost/random/detail/const_mod.hpp:22:
../boostIncl/boost/integer_traits.hpp:164:77: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
public detail::integer_traits_base< ::boost::long_long_type, LLONG_MIN, LLONG_MAX>
^
/usr/include/i386/limits.h:85:19: note: expanded from macro 'LLONG_MAX'
#define LLONG_MAX 0x7fffffffffffffffLL /* max signed long long */
^
In file included from updates_BGmix.cpp:3:
In file included from ./updates_BGmix.h:1:
In file included from ./rand.hh:32:
In file included from ../boostIncl/boost/random.hpp:36:
In file included from ../boostIncl/boost/random/linear_congruential.hpp:25:
In file included from ../boostIncl/boost/random/detail/const_mod.hpp:22:
../boostIncl/boost/integer_traits.hpp:170:70: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
public detail::integer_traits_base< ::boost::ulong_long_type, 0, ULLONG_MAX>
^
/usr/include/i386/limits.h:84:20: note: expanded from macro 'ULLONG_MAX'
#define ULLONG_MAX 0xffffffffffffffffULL /* max unsigned long long */
^
In file included from updates_BGmix.cpp:3:
In file included from ./updates_BGmix.h:1:
In file included from ./rand.hh:32:
In file included from ../boostIncl/boost/random.hpp:41:
../boostIncl/boost/random/lagged_fibonacci.hpp:112:22: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
minstd_rand0 gen(value);
˜˜˜ ^˜˜˜˜
../boostIncl/boost/random/lagged_fibonacci.hpp:289:25: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
minstd_rand0 intgen(value);
˜˜˜˜˜˜ ^˜˜˜˜
In file included from updates_BGmix.cpp:3:
In file included from ./updates_BGmix.h:1:
In file included from ./rand.hh:32:
In file included from ../boostIncl/boost/random.hpp:42:
In file included from ../boostIncl/boost/random/ranlux.hpp:20:
../boostIncl/boost/random/subtract_with_carry.hpp:97:74: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
random::linear_congruential<int32_t, 40014, 0, 2147483563, 0> intgen(value);
˜˜˜˜˜˜ ^˜˜˜˜
../boostIncl/boost/random/subtract_with_carry.hpp:287:71: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
random::linear_congruential<int32_t, 40014, 0, 2147483563, 0> gen(value);
˜˜˜ ^˜˜˜˜
updates_BGmix.cpp:564:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
std::valarray<double> dumvector(0.0,ncomps);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
updates_BGmix.cpp:565:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
for(int j=0; j<ncomps; ++j) dumvector[j] = nalloc[j]+nu[j];
˜˜˜˜˜˜˜˜˜ ^
updates_BGmix.cpp:569:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
for(int j=0; j<ncomps; ++j) wtc[j] = dumvector[j];
˜˜˜˜˜˜˜˜˜ ^
In file included from updates_BGmix.cpp:3:
In file included from ./updates_BGmix.h:1:
./rand.hh:334:7: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
a[i]=this->Gamma(a[i]);
˜ ^
updates_BGmix.cpp:567:6: note: in instantiation of member function 'Rand<Boost_Wrap<boost::random::lagged_fibonacci_01<double, 48, 4423, 2098>, double>, double>::Dirichlet' requested here
rand.Dirichlet(dumvector,ncomps);
^
In file included from updates_BGmix.cpp:3:
In file included from ./updates_BGmix.h:1:
./rand.hh:334:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
a[i]=this->Gamma(a[i]);
˜ ^
./rand.hh:335:14: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
sum += a[i];
˜ ^
./rand.hh:338:7: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
a[i]=a[i]/sum;
˜ ^
./rand.hh:338:12: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
a[i]=a[i]/sum;
˜ ^
15 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 BGmix.so BGmix_main.o rundir.o updates_BGmix.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
rm -r ../boostIncl
installing to /Users/biocbuild/bbs-2.12-bioc/meat/BGmix.Rcheck/BGmix/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
* DONE (BGmix)