BioC 2.14: CHECK report for RIPSeeker on moscato2

Package: RIPSeeker

Version: 1.4.0

Command: rm -rf RIPSeeker.buildbin-libdir && mkdir RIPSeeker.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.4.0.tar.gz >RIPSeeker-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.4.0.tar.gz

StartedAt: 2014-10-08 04:38:32 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 04:45:08 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 396.3 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf RIPSeeker.buildbin-libdir && mkdir RIPSeeker.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.4.0.tar.gz >RIPSeeker-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.4.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/RIPSeeker.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RIPSeeker/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RIPSeeker' version '1.4.0'
* 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 whether package 'RIPSeeker' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
'library' or 'require' call to 'Rsamtools' which was already attached by Depends.
  Please remove these calls from your code.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following files look like leftovers/mistakes:
  'SD.aux', 'nar.aux'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... [79s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              11.20   0.00   11.20
disambiguateMultihits  9.78   0.03    9.81
selectBinSize          5.13   0.17    5.31
combineRIP             3.48   0.04   18.76
** running examples for arch 'x64' ... [92s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              15.43   0.00   15.43
disambiguateMultihits 11.89   0.02   11.90
selectBinSize          5.91   0.16    6.06
combineRIP             3.09   0.17   18.73
* 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 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/RIPSeeker.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'RIPSeeker' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'RIPSeeker' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RIPSeeker' as RIPSeeker_1.4.0.zip
* DONE (RIPSeeker)

name	user	system	elapsed
RIPSeeker-package	0	0	0
addDummyProb	1.31	0.00	1.31
addPseudoAlignment	1.02	0.00	1.01
annotateRIP	0	0	0
binCount	1.81	0.00	1.81
combineAlignGals	0.41	0.00	0.41
combineRIP	3.48	0.04	18.76
computeLogOdd	2.60	0.00	2.61
computeRPKM	0	0	0
disambiguateMultihits	9.78	0.03	9.81
empiricalFDR	0	0	0
evalBinSize	1.00	0.02	1.01
exportGRanges	0.02	0.00	0.02
galp2gal	1.56	0.00	1.56
getAlignGal	0.22	0.00	0.22
logScoreWithControl	0	0	0
logScoreWithoutControl	0	0	0
mainSeek	11.2	0.0	11.2
mainSeekSingleChrom	2.44	0.02	2.45
nbh.GRanges	0	0	0
nbh	3.9	0.0	3.9
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.41	0.00	0.40
nbh_gen	0.01	0.00	0.02
nbh_init	2.84	0.00	2.84
nbh_vit	0.42	0.00	0.42
nbm_chk	0	0	0
nbm_em	0.41	0.00	0.41
plotCoverage	1.73	0.03	1.76
plotStrandedCoverage	2.93	0.00	2.93
randindx	0.22	0.01	0.24
ripSeek	0.02	0.00	0.01
rulebaseRIPSeek	0	0	0
scoreMergedBins	0.01	0.00	0.02
seekRIP	0	0	0
selectBinSize	5.13	0.17	5.31
statdis	0.41	0.00	0.40
viewRIP	0.01	0.00	0.02

name	user	system	elapsed
RIPSeeker-package	0.02	0.00	0.02
addDummyProb	1.59	0.00	1.59
addPseudoAlignment	0.87	0.00	0.92
annotateRIP	0.02	0.00	0.01
binCount	1.92	0.02	1.94
combineAlignGals	0.89	0.00	0.89
combineRIP	3.09	0.17	18.73
computeLogOdd	2.66	0.00	2.67
computeRPKM	0	0	0
disambiguateMultihits	11.89	0.02	11.90
empiricalFDR	0	0	0
evalBinSize	1.31	0.00	1.31
exportGRanges	0	0	0
galp2gal	2.33	0.00	2.33
getAlignGal	0.21	0.00	0.22
logScoreWithControl	0.02	0.00	0.01
logScoreWithoutControl	0	0	0
mainSeek	15.43	0.00	15.43
mainSeekSingleChrom	2.68	0.00	2.68
nbh.GRanges	0	0	0
nbh	4.48	0.00	4.50
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.5	0.0	0.5
nbh_gen	0.01	0.00	0.01
nbh_init	3.43	0.00	3.43
nbh_vit	0.5	0.0	0.5
nbm_chk	0	0	0
nbm_em	0.47	0.00	0.47
plotCoverage	1.95	0.00	1.95
plotStrandedCoverage	3.35	0.09	3.44
randindx	0.25	0.01	0.26
ripSeek	0	0	0
rulebaseRIPSeek	0	0	0
scoreMergedBins	0.02	0.00	0.02
seekRIP	0	0	0
selectBinSize	5.91	0.16	6.06
statdis	0.48	0.00	0.49
viewRIP	0	0	0