gaga 2.6.0
David Rossell
| 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/gaga | | 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/gaga.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 'gaga/DESCRIPTION' ... OK
* this is package 'gaga' version '2.6.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: '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 'gaga' can be installed ... [15s/16s] 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 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 ... [13s/13s] OK
* 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/gaga.Rcheck/00check.log'
for details.
* installing *source* package 'gaga' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cseqdesma.c -o cseqdesma.o
cseqdesma.c:622:48: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
for (i=0; i<ncolxpred; i++) { groupspred[i]= floor(i/(*mpred)); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cseqdesma.c:918:48: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
for (i=0; i<ncolxpred; i++) { groupspred[i]= floor(i/(*mpred)); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cseqdesma.c:1926:17: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
Bburnin= 0.2*(*Bgibbs); //Gibbs samples to exclude from training sample
˜ ˜˜˜^˜˜˜˜˜˜˜˜˜
cseqdesma.c:3654:47: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
for (i=0; i<ncolpred; i++) { groupspred[i]= floor(i / (*deltat)); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cseqdesma.c:3838:47: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
for (i=0; i<ncolpred; i++) { groupspred[i]= floor(i / (*deltat)); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cseqdesma.c:4038:47: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
for (i=0; i<ncolpred; i++) { groupspred[i]= floor(i / (*deltat)); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cseqdesma.c:4524:14: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((*usesumx==0)) { //if suff stat not pre-computed
˜˜˜˜˜˜˜˜^˜˜
cseqdesma.c:4524:14: note: remove extraneous parentheses around the comparison to silence this warning
if ((*usesumx==0)) { //if suff stat not pre-computed
˜ ^ ˜
cseqdesma.c:4524:14: note: use '=' to turn this equality comparison into an assignment
if ((*usesumx==0)) { //if suff stat not pre-computed
^˜
=
cseqdesma.c:5836:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((*usel==0)) {
˜˜˜˜˜^˜˜
cseqdesma.c:5836:13: note: remove extraneous parentheses around the comparison to silence this warning
if ((*usel==0)) {
˜ ^ ˜
cseqdesma.c:5836:13: note: use '=' to turn this equality comparison into an assignment
if ((*usel==0)) {
^˜
=
cseqdesma.c:6070:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((*usel==0)) {
˜˜˜˜˜^˜˜
cseqdesma.c:6070:13: note: remove extraneous parentheses around the comparison to silence this warning
if ((*usel==0)) {
˜ ^ ˜
cseqdesma.c:6070:13: note: use '=' to turn this equality comparison into an assignment
if ((*usel==0)) {
^˜
=
cseqdesma.c:6340:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((*usel==0)) { //If l values have to be generated
˜˜˜˜˜^˜˜
cseqdesma.c:6340:13: note: remove extraneous parentheses around the comparison to silence this warning
if ((*usel==0)) { //If l values have to be generated
˜ ^ ˜
cseqdesma.c:6340:13: note: use '=' to turn this equality comparison into an assignment
if ((*usel==0)) { //If l values have to be generated
^˜
=
10 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cstat.c -o cstat.o
cstat.c:571:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
a = (double ***) malloc(n1 * sizeof(double **));
^˜ ˜
cstat.c:574:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
a[0] = (double **) malloc(n1 * n2 * sizeof(double *));
˜˜˜^˜˜˜ ˜
cstat.c:578:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
a[0][0] = (double *) malloc(n1 * n2 * n3 * sizeof(double));
˜˜˜˜˜˜˜˜^˜˜˜ ˜
cstat.c:648:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
a = (int ***) malloc(n1 * sizeof(int **));
^˜ ˜
cstat.c:651:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
a[0] = (int **) malloc(n1 * n2 * sizeof(int *));
˜˜˜^˜˜˜ ˜
cstat.c:655:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
a[0][0] = (int *) malloc(n1 * n2 * n3 * sizeof(int));
˜˜˜˜˜˜˜˜^˜˜˜ ˜
cstat.c:1311:11: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort (v, size, sizeof (double), dcompare);
˜˜˜˜˜ ^˜˜˜
cstat.c:1410:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
r= i + (popsize - i - 1)*runif();
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cstat.c:1421:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
r= i + (popsize - i - 1)*runif();
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cstat.c:1461:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
return(min + runif()*(max+1-min));
˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cstat.c:1838:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
if(abs(ndf - 2.0) < eps) { /* df ˜= 2 */
˜˜˜ ˜˜˜˜^˜˜˜˜
cstat.c:2669:9: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
n = (long)(*a - 1.25e0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
12 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 gaga.so cseqdesma.o cstat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/gaga.Rcheck/gaga/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gaga)