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BioC 3.2: CHECK report for Sushi on windows1.bioconductor.org

This page was generated on 2015-10-27 17:31:12 -0400 (Tue, 27 Oct 2015).

Package 1033/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Sushi 1.8.0
Douglas H Phanstiel
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Sushi
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Sushi
Version: 1.8.0
Command: rm -rf Sushi.buildbin-libdir Sushi.Rcheck && mkdir Sushi.buildbin-libdir Sushi.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Sushi.buildbin-libdir Sushi_1.8.0.tar.gz >Sushi.Rcheck\00install.out 2>&1 && cp Sushi.Rcheck\00install.out Sushi-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Sushi.buildbin-libdir --install="check:Sushi-install.out" --force-multiarch --no-vignettes --timings Sushi_1.8.0.tar.gz
StartedAt: 2015-10-27 06:00:15 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 06:02:04 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 109.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Sushi.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Sushi.buildbin-libdir Sushi.Rcheck && mkdir Sushi.buildbin-libdir Sushi.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Sushi.buildbin-libdir Sushi_1.8.0.tar.gz >Sushi.Rcheck\00install.out 2>&1 && cp Sushi.Rcheck\00install.out Sushi-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Sushi.buildbin-libdir --install="check:Sushi-install.out" --force-multiarch --no-vignettes --timings Sushi_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/Sushi.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.8.0'
* 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 ... WARNING
Undocumented arguments in documentation object 'plotBedpe'
  'border'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... [6s] OK
** running examples for arch 'x64' ... [7s] 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: 2 WARNINGs, 1 NOTE
See
  'C:/biocbld/bbs-3.2-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_1.8.0.zip
* DONE (Sushi)

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

nameusersystemelapsed
SushiColors0.010.000.01
addlegend0.330.000.33
labelgenome0.880.000.88
labelplot0.030.020.04
maptocolors000
maptolwd000
opaque0.000.010.02
plotBed0.230.000.23
plotBedgraph0.030.000.04
plotBedpe0.280.020.29
plotGenes0.040.000.03
plotHic0.310.000.32
plotManhattan0.220.010.23
zoombox0.150.040.19
zoomsregion0.080.000.08

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

nameusersystemelapsed
SushiColors0.010.000.01
addlegend0.390.000.39
labelgenome1.270.011.28
labelplot0.050.000.05
maptocolors000
maptolwd000
opaque000
plotBed0.400.010.42
plotBedgraph0.030.000.03
plotBedpe0.240.000.23
plotGenes0.030.000.03
plotHic0.380.000.38
plotManhattan0.480.020.50
zoombox0.080.000.08
zoomsregion0.060.000.06