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BioC 3.1: CHECK report for sagenhaft on moscato2

This page was generated on 2015-10-09 09:27:22 -0700 (Fri, 09 Oct 2015).

Package 871/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sagenhaft 1.38.1
Tim Beissbarth
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/sagenhaft
Last Changed Rev: 105889 / Revision: 109384
Last Changed Date: 2015-07-07 14:52:07 -0700 (Tue, 07 Jul 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: sagenhaft
Version: 1.38.1
Command: rm -rf sagenhaft.buildbin-libdir sagenhaft.Rcheck && mkdir sagenhaft.buildbin-libdir sagenhaft.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sagenhaft.buildbin-libdir sagenhaft_1.38.1.tar.gz >sagenhaft.Rcheck\00install.out 2>&1 && cp sagenhaft.Rcheck\00install.out sagenhaft-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=sagenhaft.buildbin-libdir --install="check:sagenhaft-install.out" --force-multiarch --no-vignettes --timings sagenhaft_1.38.1.tar.gz
StartedAt: 2015-10-09 05:59:26 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 06:03:03 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 216.6 seconds
RetCode: 0
Status:  OK  
CheckDir: sagenhaft.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf sagenhaft.buildbin-libdir sagenhaft.Rcheck && mkdir sagenhaft.buildbin-libdir sagenhaft.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sagenhaft.buildbin-libdir sagenhaft_1.38.1.tar.gz >sagenhaft.Rcheck\00install.out 2>&1 && cp sagenhaft.Rcheck\00install.out sagenhaft-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=sagenhaft.buildbin-libdir --install="check:sagenhaft-install.out" --force-multiarch --no-vignettes --timings sagenhaft_1.38.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/sagenhaft.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 'sagenhaft/DESCRIPTION' ... OK
* this is package 'sagenhaft' version '1.38.1'
* 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 'sagenhaft' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   7.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'SparseM'
A package should be listed in only one of these fields.
* 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
sage.test: warning in dbinom(0:isize, p = (prob[i])[1], size = isize):
  partial argument match of 'p' to 'prob'
* 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' ... [89s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
error.correction     62.37   0.37   62.74
sagelibrary.simulate 21.40   0.03   21.44
** running examples for arch 'x64' ... [88s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
error.correction        61.14   0.55   61.68
sagelibrary.simulate    20.16   0.07   20.22
sage.library.comparison  5.07   0.03    5.10
* 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-bioc/meat/sagenhaft.Rcheck/00check.log'
for details.


sagenhaft.Rcheck/00install.out:


install for i386

* installing *source* package 'sagenhaft' ...
** 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 'sagenhaft' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sagenhaft' as sagenhaft_1.38.1.zip
* DONE (sagenhaft)

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

nameusersystemelapsed
error.correction62.37 0.3762.74
extract.lib000
sage.library0.640.020.66
sage.library.comparison3.350.013.37
sage.test0.020.000.01
sage.utilities000
sagelibrary.simulate21.40 0.0321.44

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

nameusersystemelapsed
error.correction61.14 0.5561.68
extract.lib000
sage.library0.700.010.72
sage.library.comparison5.070.035.10
sage.test0.010.000.01
sage.utilities000
sagelibrary.simulate20.16 0.0720.22