iSeq 1.12.0
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/iSeq | | 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/iSeq.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 'iSeq/DESCRIPTION' ... OK
* this is package 'iSeq' version '1.12.0'
* 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 'iSeq' can be installed ... [3s/3s] 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 ... [38s/39s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
iSeq1 12.469 0.234 13.097
peakreg 11.539 0.251 11.949
iSeq2 11.491 0.209 11.945
* 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 'iSeq' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c iSeq.c -o iSeq.o
iSeq.c:208:20: warning: unused variable 'j' [-Wunused-variable]
int sampleSize,i,j,r,n0,n1,state,nrowm1,sumxx;
^
iSeq.c:697:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
istart = (int *)R_alloc(*xrow,sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜
iSeq.c:698:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
iend = (int *)R_alloc(*xrow,sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜
iSeq.c:710:26: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
maxden1 = 1.0*count1[0]/(gend[0]-gstart[0]+1);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
iSeq.c:711:26: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
maxden2 = 1.0*count2[0]/(gend[0]-gstart[0]+1);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
iSeq.c:721:26: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
iden1 = 1.0*count1[i]/idist;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
iSeq.c:722:26: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
iden2 = 1.0*count2[i]/idist;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
iSeq.c:788:80: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
maxden1 = (1.0*count1[istart[j]]/idistC + 1.0*count1[istart[j]+1]/idistN)/2.0;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
iSeq.c:789:80: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
maxden2 = (1.0*count2[istart[j]]/idistC + 1.0*count2[istart[j]+1]/idistN)/2.0;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
iSeq.c:796:82: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
iden1 = (1.0*count1[i-1]/idistP + 1.0*count1[i]/idistC + 1.0*count1[i+1]/idistN)/3.0;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
iSeq.c:797:82: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
iden2 = (1.0*count2[i-1]/idistP + 1.0*count2[i]/idistC + 1.0*count2[i+1]/idistN)/3.0;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
iSeq.c:811:62: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
iden1 = (1.0*count1[i-1]/idistP + 1.0*count1[i]/idistC)/2.0;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
iSeq.c:812:62: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
iden2 = (1.0*count2[i-1]/idistP + 1.0*count2[i]/idistC)/2.0;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
iSeq.c:834:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
J = (int *)R_alloc(*klen,sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜
14 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 iSeq.so iSeq.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/iSeq.Rcheck/iSeq/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 (iSeq)