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BioC 3.1: CHECK report for prot2D on moscato2

This page was generated on 2015-10-09 09:30:24 -0700 (Fri, 09 Oct 2015).

Package 749/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
prot2D 1.6.0
Sebastien Artigaud
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/prot2D
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  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: prot2D
Version: 1.6.0
Command: rm -rf prot2D.buildbin-libdir prot2D.Rcheck && mkdir prot2D.buildbin-libdir prot2D.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=prot2D.buildbin-libdir prot2D_1.6.0.tar.gz >prot2D.Rcheck\00install.out 2>&1 && cp prot2D.Rcheck\00install.out prot2D-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=prot2D.buildbin-libdir --install="check:prot2D-install.out" --force-multiarch --no-vignettes --timings prot2D_1.6.0.tar.gz
StartedAt: 2015-10-09 05:00:40 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 05:02:22 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 102.3 seconds
RetCode: 0
Status:  OK  
CheckDir: prot2D.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf prot2D.buildbin-libdir prot2D.Rcheck && mkdir prot2D.buildbin-libdir prot2D.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=prot2D.buildbin-libdir prot2D_1.6.0.tar.gz >prot2D.Rcheck\00install.out 2>&1 && cp prot2D.Rcheck\00install.out prot2D-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=prot2D.buildbin-libdir --install="check:prot2D-install.out" --force-multiarch --no-vignettes --timings prot2D_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/prot2D.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 'prot2D/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'prot2D' version '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'fdrtool' 'st' 'samr' 'Biobase' 'limma' 'Mulcom' 'impute' 'MASS'
  'qvalue'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'prot2D' 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'fdrtool' 'limma' 'samr' 'st'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'MASS' 'Mulcom' 'impute'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Norm.qt: no visible global function definition for 'normalizeQuantiles'
Norm.vsn: no visible global function definition for 'normalizeVSN'
robust.fdr : lts.rank.regr: no visible global function definition for
  'ltsreg'
* 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' ... [8s] OK
** running examples for arch 'x64' ... [9s] 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: 4 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/prot2D.Rcheck/00check.log'
for details.


prot2D.Rcheck/00install.out:


install for i386

* installing *source* package 'prot2D' ...
** 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 'prot2D' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'prot2D' as prot2D_1.6.0.zip
* DONE (prot2D)

prot2D.Rcheck/examples_i386/prot2D-Ex.timings:

nameusersystemelapsed
ES.prot0.180.010.19
Norm.qt0.070.020.25
Norm.vsn0.420.000.42
RIplot0.050.000.05
Sim.Prot.2D1.440.011.53
prot2D-package1.570.021.59
variousT1.560.011.58

prot2D.Rcheck/examples_x64/prot2D-Ex.timings:

nameusersystemelapsed
ES.prot0.230.000.23
Norm.qt0.110.000.11
Norm.vsn0.480.000.48
RIplot0.040.000.04
Sim.Prot.2D1.610.001.61
prot2D-package1.750.001.75
variousT2.200.012.21