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BioC 3.5: CHECK report for sagenhaft on tokay2

This page was generated on 2017-08-16 13:18:52 -0400 (Wed, 16 Aug 2017).

Package 1173/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sagenhaft 1.46.0
Tim Beissbarth
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/sagenhaft
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sagenhaft
Version: 1.46.0
Command: rm -rf sagenhaft.buildbin-libdir sagenhaft.Rcheck && mkdir sagenhaft.buildbin-libdir sagenhaft.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sagenhaft.buildbin-libdir sagenhaft_1.46.0.tar.gz >sagenhaft.Rcheck\00install.out 2>&1 && cp sagenhaft.Rcheck\00install.out sagenhaft-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=sagenhaft.buildbin-libdir --install="check:sagenhaft-install.out" --force-multiarch --no-vignettes --timings sagenhaft_1.46.0.tar.gz
StartedAt: 2017-08-16 02:43:05 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:45:44 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 159.1 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 && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sagenhaft.buildbin-libdir sagenhaft_1.46.0.tar.gz >sagenhaft.Rcheck\00install.out 2>&1 && cp sagenhaft.Rcheck\00install.out sagenhaft-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=sagenhaft.buildbin-libdir --install="check:sagenhaft-install.out" --force-multiarch --no-vignettes --timings sagenhaft_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/sagenhaft.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.46.0'
* 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 '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'
extract.lib.from.zip: no visible global function definition for
  'zip.unpack'
Undefined global functions or variables:
  zip.unpack
Consider adding
  importFrom("utils", "zip.unpack")
to your NAMESPACE file.
* 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' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
error.correction     39.76   0.89   40.65
sagelibrary.simulate 11.69   0.31   12.00
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
error.correction     40.41   0.47   40.88
sagelibrary.simulate  9.72   0.14    9.86
* 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
  'C:/Users/biocbuild/bbs-3.5-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_1.46.0.zip
* DONE (sagenhaft)

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

nameusersystemelapsed
error.correction39.76 0.8940.65
extract.lib000
sage.library0.530.020.55
sage.library.comparison3.160.113.27
sage.test0.010.000.01
sage.utilities000
sagelibrary.simulate11.69 0.3112.00

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

nameusersystemelapsed
error.correction40.41 0.4740.88
extract.lib000
sage.library0.380.050.43
sage.library.comparison2.610.092.70
sage.test0.010.000.01
sage.utilities000
sagelibrary.simulate9.720.149.86