BioC 2.13: CHECK report for seqCNA on perceval

Package: seqCNA

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch seqCNA_1.2.0.tar.gz

StartedAt: 2014-04-05 04:17:13 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:19:07 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 113.2 seconds

RetCode: 0

Status:  OK

CheckDir: seqCNA.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/seqCNA.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqCNA’ version ‘1.2.0’
* 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 ‘seqCNA’ can be installed ... [6s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘adehabitatLT’ ‘doSNOW’ ‘GLAD’ ‘methods’ ‘seqCNA.annot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... NOTE
File ‘/Users/biocbuild/bbs-2.13-bioc/meat/seqCNA.Rcheck/seqCNA/libs/seqCNA.so’:
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘seqCNA.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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘seqCNA.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [7s/57s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotCNProfile   1.616  0.081  11.495
applyThresholds 0.839  0.048  11.044
runSeqnorm      0.630  0.030   7.175
writeCNProfile  0.575  0.036  10.582
runGLAD         0.513  0.039  10.446
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/seqCNA.Rcheck/00check.log’
for details.

* installing *source* package ‘seqCNA’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c seqCNA.cpp -o seqCNA.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o seqCNA.so seqCNA.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/seqCNA.Rcheck/seqCNA/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 (seqCNA)

name	user	system	elapsed
SeqCNAInfo-class	0.111	0.002	0.115
applyFilters	0.367	0.024	3.336
applyThresholds	0.839	0.048	11.044
plotCNProfile	1.616	0.081	11.495
readSeqsumm	0.076	0.004	0.080
runGLAD	0.513	0.039	10.446
runSeqnorm	0.630	0.030	7.175
runSeqsumm	0.022	0.004	0.031
seqsumm_HCC1143	0.058	0.004	0.062
writeCNProfile	0.575	0.036	10.582