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BioC 3.1: CHECK report for Sushi on moscato2

This page was generated on 2015-10-09 09:31:09 -0700 (Fri, 09 Oct 2015).

Package 960/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Sushi 1.4.0
Douglas H Phanstiel
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/Sushi
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Sushi
Version: 1.4.0
Command: rm -rf Sushi.buildbin-libdir Sushi.Rcheck && mkdir Sushi.buildbin-libdir Sushi.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Sushi.buildbin-libdir Sushi_1.4.0.tar.gz >Sushi.Rcheck\00install.out 2>&1 && cp Sushi.Rcheck\00install.out Sushi-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=Sushi.buildbin-libdir --install="check:Sushi-install.out" --force-multiarch --no-vignettes --timings Sushi_1.4.0.tar.gz
StartedAt: 2015-10-09 06:40:39 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 06:43:00 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 141.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Sushi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Sushi.buildbin-libdir Sushi.Rcheck && mkdir Sushi.buildbin-libdir Sushi.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Sushi.buildbin-libdir Sushi_1.4.0.tar.gz >Sushi.Rcheck\00install.out 2>&1 && cp Sushi.Rcheck\00install.out Sushi-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=Sushi.buildbin-libdir --install="check:Sushi-install.out" --force-multiarch --no-vignettes --timings Sushi_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/Sushi.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 'Sushi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Sushi' version '1.4.0'
* 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 'Sushi' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... WARNING
  Warning: large data file saved inefficiently:
                      size ASCII compress
  Sushi_5C.bedpe.rda 321Kb  TRUE     none
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                  old_size new_size compress
  Sushi_5C.bedpe.rda                 321Kb     62Kb       xz
  Sushi_ChIAPET_pol2.bedpe.rda       846Kb    451Kb       xz
  Sushi_ChIPExo_CTCF.bedgraph.rda     29Kb     13Kb       xz
  Sushi_ChIPSeq_CTCF.bedgraph.rda    160Kb     37Kb       xz
  Sushi_ChIPSeq_pol2.bedgraph.rda     28Kb     11Kb       xz
  Sushi_DNaseI.bedgraph.rda           23Kb     12Kb       xz
  Sushi_GWAS.bed.rda                 515Kb    242Kb       xz
  Sushi_HiC.matrix.rda                40Kb     31Kb       xz
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [7s] OK
** running examples for arch 'x64' ... [8s] 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 WARNING, 1 NOTE
See
  'E:/biocbld/bbs-3.1-bioc/meat/Sushi.Rcheck/00check.log'
for details.


Sushi.Rcheck/00install.out:


install for i386

* installing *source* package 'Sushi' ...
** 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 'Sushi' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'Sushi' as Sushi_1.4.0.zip
* DONE (Sushi)

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

nameusersystemelapsed
SushiColors0.010.000.02
addlegend0.440.000.43
labelgenome1.340.051.39
labelplot0.060.000.06
maptocolors000
maptolwd000
opaque000
plotBed0.320.000.31
plotBedgraph0.000.010.02
plotBedpe0.250.000.25
plotGenes0.030.000.03
plotHic0.410.000.40
plotManhattan0.400.000.41
zoombox0.110.000.11
zoomsregion0.080.000.08

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

nameusersystemelapsed
SushiColors0.000.020.02
addlegend0.510.000.51
labelgenome1.470.001.48
labelplot0.060.000.08
maptocolors000
maptolwd000
opaque000
plotBed0.370.000.37
plotBedgraph0.040.000.04
plotBedpe0.250.010.26
plotGenes0.030.000.03
plotHic0.50.00.5
plotManhattan0.430.000.44
zoombox0.100.020.11
zoomsregion0.070.000.08