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BioC 3.2: CHECK report for XBSeq on moscato1

This page was generated on 2016-04-23 10:22:07 -0700 (Sat, 23 Apr 2016).

Package 1096/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XBSeq 1.0.2
Yuanhang Liu
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/XBSeq
Last Changed Rev: 113335 / Revision: 116712
Last Changed Date: 2016-02-05 13:58:31 -0800 (Fri, 05 Feb 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: XBSeq
Version: 1.0.2
Command: rm -rf XBSeq.buildbin-libdir XBSeq.Rcheck && mkdir XBSeq.buildbin-libdir XBSeq.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=XBSeq.buildbin-libdir XBSeq_1.0.2.tar.gz >XBSeq.Rcheck\00install.out 2>&1 && cp XBSeq.Rcheck\00install.out XBSeq-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=XBSeq.buildbin-libdir --install="check:XBSeq-install.out" --force-multiarch --no-vignettes --timings XBSeq_1.0.2.tar.gz
StartedAt: 2016-04-23 08:35:26 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 09:04:46 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 1759.9 seconds
RetCode: 0
Status:  OK  
CheckDir: XBSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf XBSeq.buildbin-libdir XBSeq.Rcheck && mkdir XBSeq.buildbin-libdir XBSeq.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=XBSeq.buildbin-libdir XBSeq_1.0.2.tar.gz >XBSeq.Rcheck\00install.out 2>&1 && cp XBSeq.Rcheck\00install.out XBSeq-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=XBSeq.buildbin-libdir --install="check:XBSeq-install.out" --force-multiarch --no-vignettes --timings XBSeq_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/XBSeq.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.0.2'
* 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'
XBSeqTest: no visible global function definition for 'dispTable'
XBSeqTest: no visible global function definition for 'conditions'
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 : .local: no visible global function definition for
  'assays'
counts,XBSeqDataSet : .local: 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<-'
estimateSCV,XBSeqDataSet : .local: no visible global function
  definition for 'conditions'
estimateSCV,XBSeqDataSet : .local: no visible global function
  definition for 'dispTable<-'
* 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' ... [556s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
MAplot    183.44   0.74  184.33
XBSeq     172.38   0.29  172.69
XBSeqTest 171.41   0.18  171.60
** running examples for arch 'x64' ... [503s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
MAplot    160.14   0.50  160.73
XBSeq     155.83   0.10  155.94
XBSeqTest 155.04   0.13  155.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R' [198s]
 [199s] OK
** running tests for arch 'x64' ...
  Running 'testthat.R' [187s]
 [188s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/XBSeq.Rcheck/00check.log'
for details.


XBSeq.Rcheck/00install.out:


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_1.0.2.zip
* DONE (XBSeq)

XBSeq.Rcheck/examples_i386/XBSeq-Ex.timings:

nameusersystemelapsed
MAplot183.44 0.74184.33
XBSeq172.38 0.29172.69
XBSeqDataSet-class0.220.000.22
XBSeqTest171.41 0.18171.60
XBplot0.50.00.5
conditions0.150.010.17
counts0.150.000.16
dispEst3.060.003.06
dispTable3.280.023.29
estimateRealCount0.170.000.17
estimateSCV3.000.013.01
fitInfo3.010.003.01
getSignalVars2.170.002.17
plotSCVEsts3.340.023.35

XBSeq.Rcheck/examples_x64/XBSeq-Ex.timings:

nameusersystemelapsed
MAplot160.14 0.50160.73
XBSeq155.83 0.10155.94
XBSeqDataSet-class0.180.010.20
XBSeqTest155.04 0.13155.16
XBplot0.510.010.53
conditions0.170.000.17
counts0.160.000.16
dispEst3.710.003.71
dispTable3.720.003.72
estimateRealCount0.170.000.17
estimateSCV4.050.034.09
fitInfo3.70.03.7
getSignalVars2.90.02.9
plotSCVEsts4.020.024.04