CGEN 2.2.0 William Wheeler
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/CGEN | 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 | WARNINGS | |
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 | WARNINGS | OK |
pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/CGEN.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 'CGEN/DESCRIPTION' ... OK
* this is package 'CGEN' version '2.2.0'
* 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 'CGEN' can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Components with restrictions not permitted:
GPL-2 + file LICENSE
* 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 ... WARNING
File '/Users/biocbuild/bbs-2.12-bioc/meat/CGEN.Rcheck/CGEN/libs/CGEN.so':
Found '_exit', possibly from 'exit' (C)
Objects: 'ccl.o', 'hcl.o'
Found '_printf', possibly from 'printf' (C)
Objects: 'Additive.o', 'CML.o', 'ccl.o', 'hcl.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 ... [77s/80s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getMatchedSets 37.700 0.986 39.216
snp.matched 33.519 0.163 34.520
* 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
WARNING: There was 1 warning.
NOTE: There was 1 note.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/CGEN.Rcheck/00check.log'
for details.
* installing *source* package 'CGEN' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c Additive.c -o Additive.o
Additive.c:515:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
m = (double **) malloc(n*sizeof(double *));
^˜
Additive.c:517:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
m[i] = (double *) malloc((i + 1)*sizeof(double));
˜˜^˜˜ ˜
Additive.c:543:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
l = (int *) R_alloc(n0, sizeof(int));
˜˜˜˜˜˜˜ ^˜
Additive.c:547:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
g = (double *) R_alloc(n0, sizeof(double));
˜˜˜˜˜˜˜ ^˜
Additive.c:548:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
t = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
Additive.c:549:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
X = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
Additive.c:550:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
c = (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 -ggdb -O0 -Wall -pedantic -Wconversion -c CML.c -o CML.o
CML.c:562:22: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
temp = 3* *D + 1 + value;
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
CML.c:680:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
m = (double **) malloc(n*sizeof(double *));
^˜
CML.c:682:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
m[i] = (double *) malloc((i + 1)*sizeof(double));
˜˜^˜˜ ˜
CML.c:708:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
l = (int *) R_alloc(n0, sizeof(int));
˜˜˜˜˜˜˜ ^˜
CML.c:712:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
g = (double *) R_alloc(n0, sizeof(double));
˜˜˜˜˜˜˜ ^˜
CML.c:713:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
t = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
CML.c:714:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
X = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
CML.c:715:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
c = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
CML.c:1198:13: warning: unused function 'print_dVec' [-Wunused-function]
static void print_dVec(vec, n, name)
^
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ccl.c -o ccl.o
ccl.c:134:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
*CONV = conv ;
˜ ^˜˜˜
ccl.c:413:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
new -> g = j ; new -> h = k ;
˜ ^
ccl.c:413:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
new -> g = j ; new -> h = k ;
˜ ^
ccl.c:386:13: warning: function 'tree_print' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void tree_print(tnode *node, int is_root)
^
4 warnings generated.
gfortran-4.2 -arch x86_64 -fPIC -g -O2 -Wall -pedantic -c csclust.f -o csclust.o
Warning: Nonconforming tab character in column 1 of line 46
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csclust.f:222.3:
650 RETURN
1
Warning: Label 650 at (1) defined but not used
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c fsclust.c -o fsclust.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c hcl.c -o hcl.o
hcl.c:128:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
*CONV = conv ;
˜ ^˜˜˜
hcl.c:402:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
new -> g = j ; new -> h = k ;
˜ ^
hcl.c:402:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
new -> g = j ; new -> h = k ;
˜ ^
hcl.c:375:13: warning: function 'tree_print' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void tree_print(tnode *node, int is_root)
^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c pmatch.c -o pmatch.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 CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/CGEN.Rcheck/CGEN/libs
** R
** data
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CGEN)