BioC 2.12: CHECK report for reb on petty

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: 2013-10-08 23:38:28 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:42:02 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 214.4 seconds

RetCode: 0

Status:  OK

CheckDir: reb.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/reb.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 ... [17s/18s] 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'
  Found '_putchar', possibly from 'putchar' (C)
    Object: 'movbin.o'
  Found '_puts', possibly from 'printf' (C), 'puts' (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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [43s/46s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
cset2band      12.576  0.251  13.549
fromRevIsh      9.496  0.148  10.007
smoothByRegion  9.150  0.114   9.493
* 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.

* installing *source* package 'reb' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c movbin.c -o movbin.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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)

name	user	system	elapsed
absMax	0.005	0.002	0.007
buildChromCytoband	0.018	0.012	0.621
buildChromMap	0.015	0.003	0.018
cset2band	12.576	0.251	13.549
fromRevIsh	9.496	0.148	10.007
isAbnormal	0.023	0.005	0.028
mcr.eset	0.179	0.020	0.202
movbin	0.096	0.011	0.577
movt	1.295	0.027	1.862
naMean	0.030	0.003	0.037
regmap	0.034	0.004	0.047
revish	0.270	0.010	0.302
rmAmbigMappings	0.037	0.005	0.042
smoothByRegion	9.150	0.114	9.493
summarizeByRegion	0.061	0.011	0.074
tBinomTest	0.020	0.004	0.024
writeGFF3	0.296	0.007	0.338