SMAP 1.24.0
Robin Andersson
| 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/SMAP | | 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/SMAP.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 'SMAP/DESCRIPTION' ... OK
* this is package 'SMAP' version '1.24.0'
* 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 'SMAP' can be installed ... [4s/5s] 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 ... OK
* 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 ... [16s/16s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
smap 11.795 0.169 12.202
* 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
* installing *source* package 'SMAP' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c gradient.c -o gradient.o
gradient.c:227:48: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
eta_change(&eta->Pi[i], &work_grad->Pi[i], sign(prod), e_change, e_same, e_min,
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:335:15: note: expanded from macro 'sign'
#define sign Rf_sign
^
gradient.c:232:54: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
eta_change(&eta->A[i][j], &work_grad->A[i][j], sign(prod), e_change, e_same,
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:335:15: note: expanded from macro 'sign'
#define sign Rf_sign
^
gradient.c:237:48: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
eta_change(&eta->mu[i], &work_grad->mu[i], sign(prod), e_change, e_same, e_min, e_max);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:335:15: note: expanded from macro 'sign'
#define sign Rf_sign
^
gradient.c:240:54: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
eta_change(&eta->sigma[i], &work_grad->sigma[i], sign(prod), e_change, e_same,
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:335:15: note: expanded from macro 'sign'
#define sign Rf_sign
^
gradient.c:247:10: warning: unused variable 'tmp' [-Wunused-variable]
double tmp;
^
gradient.c:302:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double **W_A = (double**) R_alloc(N, sizeof(double*));
˜˜˜˜˜˜˜ ^
gradient.c:312:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
W_A[i] = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c overlap.c -o overlap.o
overlap.c:9:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->ids = (int*) R_alloc(n, sizeof(int));
˜˜˜˜˜˜˜ ^
overlap.c:10:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->olaps = (double*) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
overlap.c:47:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
o_struct **overlap = (o_struct**) R_alloc(t, sizeof(o_struct*));
˜˜˜˜˜˜˜ ^
overlap.c:64:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *olap = (double*) R_alloc(i - prev_zero, sizeof(double));
˜˜˜˜˜˜˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
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 prob.c -o prob.o
prob.c:9:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->A = (double**) R_alloc(N, sizeof(double*));
˜˜˜˜˜˜˜ ^
prob.c:10:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->Pi = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
prob.c:11:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->mu = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
prob.c:12:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->sigma = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
prob.c:15:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->Z = (double**) R_alloc(N, sizeof(double*));
˜˜˜˜˜˜˜ ^
prob.c:16:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->Y = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
prob.c:23:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->A[i] = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
prob.c:26:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->Z[i] = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c viterbi.c -o viterbi.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o SMAP.so gradient.o init.o overlap.o prob.o viterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/SMAP.Rcheck/SMAP/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'SMAP'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SMAP)