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Package 535/671HostnameOS / ArchBUILDCHECKBUILD BIN
reb 1.38.0
Karl J. Dykema
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/reb
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 

Summary

Package: reb
Version: 1.38.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch reb_1.38.0.tar.gz
StartedAt: 2013-05-01 10:01:05 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 10:04:13 -0700 (Wed, 01 May 2013)
EllapsedTime: 188.5 seconds
RetCode: 0
Status:  OK 
CheckDir: reb.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/reb.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 'reb/DESCRIPTION' ... OK
* this is package 'reb' version '1.38.0'
* 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 'reb' can be installed ... [15s/15s] 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
.MAP2chromLoc: warning in mget(subnames, env = chrEnv, ifnotfound =
  NA): partial argument match of 'env' to 'envir'
rmAmbigMappings: warning in ls(env = get(package)): partial argument
  match of 'env' to 'envir'
* 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 ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/reb.Rcheck/reb/libs/reb.so':
  Found '_printf', possibly from 'printf' (C)
    Object: 'movbin.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 ... [38s/40s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
cset2band      11.282  0.328  12.503
smoothByRegion  8.010  0.166   8.898
fromRevIsh      7.931  0.218   8.452
* 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/reb.Rcheck/00check.log'
for details.

reb.Rcheck/00install.out:

* installing *source* package 'reb' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c movbin.c -o movbin.o
movbin.c:62:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  for(c=0,i=s;i<=e;i++) {
           ˜^
movbin.c:120:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  im = (double *) calloc(nc*nr,sizeof(double));
                  ˜˜˜˜˜˜ ˜˜^˜˜
movbin.c:134:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  im_vec = (double *) calloc(nc,sizeof(double));
                      ˜˜˜˜˜˜ ^˜
movbin.c:152:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  sum_mx = (double *) calloc(nr*nc,sizeof(double));
                      ˜˜˜˜˜˜ ˜˜^˜˜
4 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 reb.so movbin.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/reb.Rcheck/reb/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 (reb)

reb.Rcheck/reb-Ex.timings:

nameusersystemelapsed
absMax0.0070.0020.009
buildChromCytoband0.0160.0110.109
buildChromMap0.0160.0030.020
cset2band11.282 0.32812.503
fromRevIsh7.9310.2188.452
isAbnormal0.0200.0060.027
mcr.eset0.1750.0260.205
movbin0.0910.0130.106
movt0.9370.0260.988
naMean0.0310.0050.036
regmap0.0290.0050.035
revish0.2230.0110.247
rmAmbigMappings0.0390.0060.044
smoothByRegion8.0100.1668.898
summarizeByRegion0.0660.0150.086
tBinomTest0.0200.0040.025
writeGFF30.2360.0090.256