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BioC experimental data: CHECK report for seqc on moscato2

This page was generated on 2015-10-07 16:21:29 -0700 (Wed, 07 Oct 2015).

Package 207/241HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqc 1.2.0
Yang Liao and Wei Shi
Snapshot Date: 2015-10-07 07:15:35 -0700 (Wed, 07 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs/seqc
Last Changed Rev: 3279 / Revision: 3442
Last Changed Date: 2015-04-16 13:16:53 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
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 

Summary

Package: seqc
Version: 1.2.0
Command: rm -rf seqc.buildbin-libdir seqc.Rcheck && mkdir seqc.buildbin-libdir seqc.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=seqc.buildbin-libdir seqc_1.2.0.tar.gz >seqc.Rcheck\00install.out 2>&1 && cp seqc.Rcheck\00install.out seqc-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=seqc.buildbin-libdir --install="check:seqc-install.out" --force-multiarch --no-vignettes --timings seqc_1.2.0.tar.gz
StartedAt: 2015-10-07 11:51:51 -0700 (Wed, 07 Oct 2015)
EndedAt: 2015-10-07 11:58:47 -0700 (Wed, 07 Oct 2015)
EllapsedTime: 416.2 seconds
RetCode: 0
Status:  OK  
CheckDir: seqc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf seqc.buildbin-libdir seqc.Rcheck && mkdir seqc.buildbin-libdir seqc.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=seqc.buildbin-libdir seqc_1.2.0.tar.gz >seqc.Rcheck\00install.out 2>&1 && cp seqc.Rcheck\00install.out seqc-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=seqc.buildbin-libdir --install="check:seqc-install.out" --force-multiarch --no-vignettes --timings seqc_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-data-experiment/meat/seqc.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 'seqc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'seqc' version '1.2.0'
* 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 'seqc' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 306.9Mb
  sub-directories of 1Mb or more:
    data  306.6Mb
* 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
.create.SEQC.gene.eSet: no visible global function definition for
  'ExpressionSet'
.create.SEQC.gene.eSet: no visible global function definition for
  'pData<-'
.create.SEQC.gene.eSet: no visible global function definition for
  'fData<-'
seqc.eSet: possible error in .create.SEQC.junction.eSet(platform,
  center): unused argument (center)
* checking Rd files ... NOTE
prepare_Rd: seqc.samples.Rd:14-15: Dropping empty section \details
* 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' ... [1s] OK
** running examples for arch 'x64' ... [1s] 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: 3 NOTEs
See
  'E:/biocbld/bbs-3.1-data-experiment/meat/seqc.Rcheck/00check.log'
for details.


seqc.Rcheck/00install.out:


install for i386

* installing *source* package 'seqc' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'seqc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqc' as seqc_1.2.0.zip
* DONE (seqc)

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

nameusersystemelapsed
FCData0.610.080.69
FCJunctions000
SEQC-package0.010.000.01
taqman0.020.000.02

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

nameusersystemelapsed
FCData0.540.060.62
FCJunctions0.020.000.02
SEQC-package000
taqman000