cleanUpdTSeq 1.6.1
Sarah Sheppard ; Jianhong Ou ; Lihua Julie Zhu
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/cleanUpdTSeq | | Last Changed Rev: 103922 / Revision: 109384 | | Last Changed Date: 2015-05-18 08:00:31 -0700 (Mon, 18 May 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf cleanUpdTSeq.buildbin-libdir cleanUpdTSeq.Rcheck && mkdir cleanUpdTSeq.buildbin-libdir cleanUpdTSeq.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cleanUpdTSeq.buildbin-libdir cleanUpdTSeq_1.6.1.tar.gz >cleanUpdTSeq.Rcheck\00install.out 2>&1 && cp cleanUpdTSeq.Rcheck\00install.out cleanUpdTSeq-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=cleanUpdTSeq.buildbin-libdir --install="check:cleanUpdTSeq-install.out" --force-multiarch --no-vignettes --timings cleanUpdTSeq_1.6.1.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/cleanUpdTSeq.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-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 '1.6.1'
* 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 ... NOTE
Malformed Title field: should not end in a period.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BED2GRangesSeq: no visible global function definition for 'IRanges'
getDownstreamSequence: no visible global function definition for
'IRanges'
getDownstreamSequence: no visible global function definition for
'seqlengths'
getUpstreamSequence: no visible global function definition for
'IRanges'
getUpstreamSequence: no visible global function definition for
'seqlengths'
* 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' ... [75s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
predictTestSet 31.36 0.09 31.75
data.NaiveBayes 25.80 0.16 25.96
buildFeatureVector 6.53 0.00 6.73
** running examples for arch 'x64' ... [72s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
predictTestSet 31.08 0.07 31.13
data.NaiveBayes 25.08 0.22 25.30
buildFeatureVector 5.66 0.00 5.66
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [24s]
[24s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [21s]
[22s] OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: 'BiocStyle'
* 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
* DONE
Status: 4 NOTEs
See
'E:/biocbld/bbs-3.1-bioc/meat/cleanUpdTSeq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'cleanUpdTSeq' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
install for x64
* installing *source* package 'cleanUpdTSeq' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'cleanUpdTSeq' as cleanUpdTSeq_1.6.1.zip
* DONE (cleanUpdTSeq)