tweeDEseq 1.6.1
Juan R Gonzalez
| 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/tweeDEseq | | Last Changed Rev: 75805 / Revision: 76155 | | Last Changed Date: 2013-04-19 03:38:05 -0700 (Fri, 19 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/tweeDEseq.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 'tweeDEseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tweeDEseq' version '1.6.1'
* 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 'tweeDEseq' can be installed ... [6s/6s] 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 ... [17s/17s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
glmPT 6.972 0.046 7.081
* 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 'tweeDEseq' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c cov_wt_C.c -o cov_wt_C.o
cov_wt_C.c:6:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
res = (double *)malloc(n*sizeof(double));
^˜
cov_wt_C.c:35:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
xc = (double *)malloc((n)*sizeof(double));
^ ˜
cov_wt_C.c:52:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
y = (double *)malloc((*n)*sizeof(double));
^˜ ˜
cov_wt_C.c:53:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
res = (double *)malloc((*p*2)*sizeof(double));
˜˜^˜ ˜
cov_wt_C.c:88:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
resk3 = (double *)malloc(n*sizeof(double));
^˜
cov_wt_C.c:119:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
y = (double *)malloc((*n)*sizeof(double));
^˜ ˜
6 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_tweeDEseq.c -o init_tweeDEseq.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c loglikGlm.c -o loglikGlm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c logprobs.c -o logprobs.o
logprobs.c:28:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
newC = (double*)realloc(newC, k*sizeof(double));
^˜
logprobs.c:54:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
oldC = (double*)realloc(oldC, (k+1)*sizeof(double));
˜^˜ ˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c permtest.c -o permtest.o
permtest.c:43:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
permtest.c:53:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
rnd = floor(runif(0,n-i));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
permtest.c:65:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
x1 = (double *)malloc(n1*sizeof(double));
^˜˜
permtest.c:66:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
x2 = (double *)malloc(n2*sizeof(double));
^˜˜
permtest.c:101:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
pvalreals = (double *)malloc((*n)*sizeof(double));
^˜ ˜
permtest.c:102:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
pvalperms = (double **)malloc((*nperm)*sizeof(double *));
^˜˜˜˜˜ ˜
permtest.c:104:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
pvalperms[i] = (double *)malloc((*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 probs.c -o probs.o
probs.c:7:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
C = (double **)malloc(n*sizeof(double *));
^˜
probs.c:9:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
C[i] = (double *)malloc((i+1)*sizeof(double));
˜^˜ ˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c zhu2.c -o zhu2.o
zhu2.c:18:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
r = (double *)malloc((*n)*sizeof(double));
^˜ ˜
zhu2.c:30:14: warning: ordered comparison between pointer and zero ('double *' and 'int') is an extension [-Wpedantic]
if((tol>0)&&(res[i+1]<=*tol)&&(res[i+1]<res[i])){
˜˜˜^˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c zhu3.c -o zhu3.o
zhu3.c:7:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
res = (double *)malloc((n+1)*sizeof(double));
˜^˜ ˜
zhu3.c:16:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
r = (double *)malloc((n)*sizeof(double));
^ ˜
2 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 tweeDEseq.so cov_wt_C.o init_tweeDEseq.o loglikGlm.o logprobs.o permtest.o probs.o zhu2.o zhu3.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/tweeDEseq.Rcheck/tweeDEseq/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 (tweeDEseq)