BioC 2.14: CHECK report for cleanUpdTSeq on moscato2

Package: cleanUpdTSeq

Version: 1.2.0

Command: rm -rf cleanUpdTSeq.buildbin-libdir && mkdir cleanUpdTSeq.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cleanUpdTSeq.buildbin-libdir cleanUpdTSeq_1.2.0.tar.gz >cleanUpdTSeq-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=cleanUpdTSeq.buildbin-libdir --install="check:cleanUpdTSeq-install.out" --force-multiarch --no-vignettes --timings cleanUpdTSeq_1.2.0.tar.gz

StartedAt: 2014-10-07 23:51:37 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:56:55 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 318.2 seconds

RetCode: 0

Status:  OK

CheckDir: cleanUpdTSeq.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf cleanUpdTSeq.buildbin-libdir && mkdir cleanUpdTSeq.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cleanUpdTSeq.buildbin-libdir cleanUpdTSeq_1.2.0.tar.gz >cleanUpdTSeq-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=cleanUpdTSeq.buildbin-libdir --install="check:cleanUpdTSeq-install.out" --force-multiarch --no-vignettes --timings cleanUpdTSeq_1.2.0.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/cleanUpdTSeq.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 'cleanUpdTSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cleanUpdTSeq' version '1.2.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'BSgenome' 'BSgenome.Drerio.UCSC.danRer7'
  'GenomicRanges' 'seqinr' 'e1071'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'cleanUpdTSeq' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [68s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
predictTestSet     31.15   0.18   32.28
data.NaiveBayes    22.03   0.08   22.12
buildFeatureVector  6.34   0.11    6.55
** running examples for arch 'x64' ... [63s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
predictTestSet     26.82   0.14   26.96
data.NaiveBayes    21.62   0.14   21.77
buildFeatureVector  6.44   0.13    6.57
* 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
  'E:/biocbld/bbs-2.14-bioc/meat/cleanUpdTSeq.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'cleanUpdTSeq' ...
** R
** data
** 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 'cleanUpdTSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cleanUpdTSeq' as cleanUpdTSeq_1.2.0.zip
* DONE (cleanUpdTSeq)

name	user	system	elapsed
BED2GRangesSeq	0.04	0.00	0.05
buildFeatureVector	6.34	0.11	6.55
cleanUpdTSeq-package	0	0	0
data.NaiveBayes	22.03	0.08	22.12
getDownstreamSequence	1.13	0.01	1.16
getUpstreamSequence	0.96	0.02	0.96
predictTestSet	31.15	0.18	32.28

name	user	system	elapsed
BED2GRangesSeq	0.03	0.00	0.03
buildFeatureVector	6.44	0.13	6.57
cleanUpdTSeq-package	0.02	0.00	0.01
data.NaiveBayes	21.62	0.14	21.77
getDownstreamSequence	1.11	0.02	1.12
getUpstreamSequence	0.93	0.00	0.93
predictTestSet	26.82	0.14	26.96