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BioC 3.0: CHECK report for Sushi on moscato1

This page was generated on 2015-04-10 09:50:24 -0700 (Fri, 10 Apr 2015).

Package 874/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Sushi 1.2.0
Douglas H Phanstiel
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/Sushi
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: Sushi
Version: 1.2.0
Command: rm -rf Sushi.buildbin-libdir Sushi.Rcheck && mkdir Sushi.buildbin-libdir Sushi.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Sushi.buildbin-libdir Sushi_1.2.0.tar.gz >Sushi.Rcheck\00install.out 2>&1 && cp Sushi.Rcheck\00install.out Sushi-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=Sushi.buildbin-libdir --install="check:Sushi-install.out" --force-multiarch --no-vignettes --timings Sushi_1.2.0.tar.gz
StartedAt: 2015-04-10 06:05:51 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 06:09:11 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 200.4 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 && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Sushi.buildbin-libdir Sushi_1.2.0.tar.gz >Sushi.Rcheck\00install.out 2>&1 && cp Sushi.Rcheck\00install.out Sushi-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=Sushi.buildbin-libdir --install="check:Sushi-install.out" --force-multiarch --no-vignettes --timings Sushi_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/Sushi.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-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 '1.2.0'
* 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 'Sushi' 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 ... 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    450Kb       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    241Kb       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' ... [10s] OK
** running examples for arch 'x64' ... [15s] 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

WARNING: There was 1 warning.
See
  'D:/biocbld/bbs-3.0-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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Sushi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Sushi' as Sushi_1.2.0.zip
* DONE (Sushi)

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

nameusersystemelapsed
SushiColors0.020.000.01
addlegend0.610.010.63
labelgenome1.410.021.43
labelplot0.050.000.05
maptocolors000
maptolwd000
opaque000
plotBed0.390.010.41
plotBedgraph0.010.000.02
plotBedpe0.300.020.31
plotGenes0.030.000.03
plotHic0.50.00.5
plotManhattan0.530.000.53
zoombox0.120.000.12
zoomsregion0.080.000.08

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

nameusersystemelapsed
SushiColors0.020.000.02
addlegend1.030.001.03
labelgenome1.980.053.34
labelplot0.060.000.06
maptocolors000
maptolwd000
opaque0.020.000.02
plotBed0.650.000.66
plotBedgraph0.070.000.32
plotBedpe0.590.000.60
plotGenes0.050.000.04
plotHic0.850.020.88
plotManhattan0.630.000.62
zoombox0.090.010.11
zoomsregion0.090.000.09