XBSeq 1.1.0
Yuanhang Liu
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/XBSeq | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf XBSeq.buildbin-libdir XBSeq.Rcheck && mkdir XBSeq.buildbin-libdir XBSeq.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=XBSeq.buildbin-libdir XBSeq_1.1.0.tar.gz >XBSeq.Rcheck\00install.out 2>&1 && cp XBSeq.Rcheck\00install.out XBSeq-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=XBSeq.buildbin-libdir --install="check:XBSeq-install.out" --force-multiarch --no-vignettes --timings XBSeq_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/XBSeq.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'XBSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'XBSeq' version '1.1.0'
* 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 'XBSeq' 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 ... NOTE
MAplot: no visible binding for global variable 'baseMean'
MAplot: no visible binding for global variable 'log2FoldChange'
XBSeqDataSet: no visible global function definition for 'DataFrame'
XBSeqDataSet: no visible global function definition for
'SummarizedExperiment'
XBSeqTestForMatrices : <anonymous>: no visible binding for global
variable 'bgcounts'
XBplot: no visible binding for global variable 'Sample'
XBplot: no visible binding for global variable 'Group'
XBplot: no visible binding for global variable '..count..'
adjustScv: no visible binding for global variable
'scvBiasCorrectionFits'
counts,XBSeqDataSet: no visible global function definition for 'assays'
counts,XBSeqDataSet: no visible global function definition for 'assay'
estimateRealCount,XBSeqDataSet: no visible global function definition
for 'assay'
estimateRealCount,XBSeqDataSet: no visible global function definition
for 'assay<-'
Undefined global functions or variables:
..count.. DataFrame Group Sample SummarizedExperiment assay assay<-
assays baseMean bgcounts log2FoldChange scvBiasCorrectionFits
* 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' ... [412s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MAplot 135.61 0.91 136.64
XBSeq 128.15 0.48 128.64
XBSeqTest 125.91 0.27 126.17
** running examples for arch 'x64' ... [370s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MAplot 117.29 0.50 117.80
XBSeq 113.77 0.34 114.13
XBSeqTest 113.39 0.21 113.60
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [145s]
[145s] OK
** running tests for arch 'x64' ...
Running 'testthat.R' [139s]
[139s] 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
* DONE
Status: 1 NOTE
See
'c:/biocbld/bbs-3.3-bioc/meat/XBSeq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'XBSeq' ...
** 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 'XBSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'XBSeq' as XBSeq_1.1.0.zip
* DONE (XBSeq)