BioC 2.14: CHECK report for cleanUpdTSeq on moscato2
This page was generated on 2014-10-08 08:55:45 -0700 (Wed, 08 Oct 2014).
cleanUpdTSeq 1.2.0 Sarah Sheppard ; Jianhong Ou ; Lihua Julie Zhu
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/cleanUpdTSeq | Last Changed Rev: 88838 / Revision: 95116 | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
Summary
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
|
Command output
##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################
* 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.
cleanUpdTSeq.Rcheck/00install.out:
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)
cleanUpdTSeq.Rcheck/examples_i386/cleanUpdTSeq-Ex.timings:
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 |
|
cleanUpdTSeq.Rcheck/examples_x64/cleanUpdTSeq-Ex.timings:
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 |
|