iChip 1.14.0
Qianxing Mo
| 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/iChip | | 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/iChip.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 'iChip/DESCRIPTION' ... OK
* this is package 'iChip' version '1.14.0'
* 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 'iChip' can be installed ... [4s/4s] 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 ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
iChip2 13.28 0.075 13.643
iChip1 9.32 0.077 9.583
* 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 'iChip' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c iChip.c -o iChip.o
iChip.c:28:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
nprobe = (int *)R_alloc(*nrow, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜
iChip.c:29:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
position = (int *)R_alloc(*nrow, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜
iChip.c:30:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
score2 = (double *)R_alloc(*nrow, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜
iChip.c:24:69: warning: unused variable 'sdsignal' [-Wunused-variable]
double *score2,z0,z1,p,meanScore,varScore,sdScore,mean3sd,sdnoise,sdsignal;
^
iChip.c:24:61: warning: unused variable 'sdnoise' [-Wunused-variable]
double *score2,z0,z1,p,meanScore,varScore,sdScore,mean3sd,sdnoise,sdsignal;
^
iChip.c:193:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
score2 = (double *)R_alloc(*nrow,sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜
iChip.c:188:20: warning: unused variable 'j' [-Wunused-variable]
int sampleSize,i,j,r,nnoise,nsignal,state,nrowm1,sumxx,rm1;
^
iChip.c:404:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
x = (int **)R_alloc(*xrow,sizeof(int *));
˜˜˜˜˜˜˜ ^˜˜˜˜
iChip.c:405:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
y = (int **)R_alloc(*xrow,sizeof(int *));
˜˜˜˜˜˜˜ ^˜˜˜˜
iChip.c:411:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
x[i] = (int *)R_alloc(*xcol, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜
iChip.c:412:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
y[i] = (int *)R_alloc(*ycol, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜
iChip.c:466:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
J = (int *)R_alloc(*klen,sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜
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 iChip.so iChip.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/iChip.Rcheck/iChip/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iChip)