LVSmiRNA 1.10.0
Stefano Calza
| 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/LVSmiRNA | | 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/LVSmiRNA.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 'LVSmiRNA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LVSmiRNA' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rmpi'
* 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 'LVSmiRNA' can be installed ... [10s/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
NB: .Last.lib will not be used unless it is exported
File 'LVSmiRNA/R/zzz.R':
.Last.lib calls:
library.dynam.unload("LVSmiRNA", libpath)
Package detach functions should not call 'library.dynam.unload'.
See section 'Good practice' in '?.Last.lib'.
* 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 ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [4s/4s] 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 were 2 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/LVSmiRNA.Rcheck/00check.log'
for details.
* installing *source* package 'LVSmiRNA' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c basic_fns.c -o basic_fns.o
basic_fns.c:113:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ipiv = (int *) R_alloc(n, sizeof(int));
˜˜˜˜˜˜˜ ^
basic_fns.c:117:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
avals = (double *) R_alloc(n * n, sizeof(double));
˜˜˜˜˜˜˜ ˜˜^˜˜
basic_fns.c:124:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
work = (double *) R_alloc(4*n, sizeof(double));
˜˜˜˜˜˜˜ ˜^˜
basic_fns.c:151:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
basic_fns.c:151:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
basic_fns.c:146:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
basic_fns.c:343:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
basic_fns.c:343:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -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 -ggdb -O0 -Wall -pedantic -Wconversion -c lvs_rlm.c -o lvs_rlm.o
lvs_rlm.c:51:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmpBeta = (double *) R_alloc(cols, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜
lvs_rlm.c:52:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
old_beta = (double *) R_alloc(cols, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜
lvs_rlm.c:53:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pred = (double *) R_alloc(rows, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜
lvs_rlm.c:60:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
Xwt = (double *) R_alloc(cols*rows, sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜
lvs_rlm.c:61:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
A = (double *) R_alloc(cols*rows, sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜
lvs_rlm.c:62:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
B = (double *) R_alloc(cols, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜
6 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 LVSmiRNA.so basic_fns.o init.o lvs_rlm.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/LVSmiRNA.Rcheck/LVSmiRNA/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'boxplot' when loading 'graphics'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'boxplot' when loading 'graphics'
* DONE (LVSmiRNA)