BioC 2.13: CHECK report for SeqArray on perceval

Package: SeqArray

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SeqArray_1.2.1.tar.gz

StartedAt: 2014-04-05 04:16:24 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:26:56 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 631.9 seconds

RetCode: 0

Status:  OK

CheckDir: SeqArray.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/SeqArray.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 ‘SeqArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqArray’ version ‘1.2.1’
* 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 ‘SeqArray’ can be installed ... [38s/39s] 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
Unexported objects imported by ‘:::’ calls:
  ‘parallel:::recvOneData’ ‘parallel:::sendData’
  See the note in ?`:::` about the use of this operator.
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [28s/64s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
SeqArray-package 1.997  0.089  19.561
seqParallel      0.195  0.023  18.060
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test_asVCF.R’ [1s/1s]
  Running ‘test.R’ [251s/256s]
 [252s/257s] OK
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/SeqArray.Rcheck/00check.log’
for details.

* installing *source* package ‘SeqArray’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DCOREARRAY_NO_FORCEINLINE -DCOREARRAY_R_LINK -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreGDSLink.cpp -o CoreGDSLink.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DCOREARRAY_NO_FORCEINLINE -DCOREARRAY_R_LINK -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c SeqArray.cpp -o SeqArray.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 SeqArray.so CoreGDSLink.o SeqArray.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/SeqArray.Rcheck/SeqArray/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SeqArray)

name	user	system	elapsed
SeqArray-package	1.997	0.089	19.561
SeqVarGDSClass-class	0.592	0.033	0.631
seqApply	0.167	0.021	0.190
seqCompress.Option	2.134	0.053	2.263
seqDelete	1.115	0.028	1.190
seqExampleFileName	0.018	0.004	0.021
seqGDS2VCF	0.762	0.023	0.825
seqGetData	0.581	0.021	0.609
seqGetFilter	0.052	0.011	0.063
seqInfoNewVar	0.512	0.065	0.589
seqOpen	0.039	0.007	0.045
seqParallel	0.195	0.023	18.060
seqSetFilter	0.070	0.016	0.088
seqSlidingWindow	0.093	0.024	0.117
seqSummary	0.066	0.010	0.076
seqTranspose	1.175	0.036	1.215
seqVCF.Header	0.072	0.004	0.078
seqVCF.SampID	0.029	0.004	0.033
seqVCF2GDS	3.054	0.053	3.150