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BioC 3.4: CHECK report for GENESIS on tokay1

This page was generated on 2017-04-15 16:19:44 -0400 (Sat, 15 Apr 2017).

Package 496/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GENESIS 2.4.0
Matthew P. Conomos
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/GENESIS
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  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: GENESIS
Version: 2.4.0
Command: rm -rf GENESIS.buildbin-libdir GENESIS.Rcheck && mkdir GENESIS.buildbin-libdir GENESIS.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GENESIS.buildbin-libdir GENESIS_2.4.0.tar.gz >GENESIS.Rcheck\00install.out 2>&1 && cp GENESIS.Rcheck\00install.out GENESIS-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GENESIS.buildbin-libdir --install="check:GENESIS-install.out" --force-multiarch --no-vignettes --timings GENESIS_2.4.0.tar.gz
StartedAt: 2017-04-14 22:31:44 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:43:03 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 678.9 seconds
RetCode: 0
Status:  OK  
CheckDir: GENESIS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GENESIS.buildbin-libdir GENESIS.Rcheck && mkdir GENESIS.buildbin-libdir GENESIS.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GENESIS.buildbin-libdir GENESIS_2.4.0.tar.gz >GENESIS.Rcheck\00install.out 2>&1 && cp GENESIS.Rcheck\00install.out GENESIS-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GENESIS.buildbin-libdir --install="check:GENESIS-install.out" --force-multiarch --no-vignettes --timings GENESIS_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/GENESIS.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GENESIS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GENESIS' version '2.4.0'
* 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 'GENESIS' 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 ... NOTE
Unexported object imported by a ':::' call: 'survey:::saddle'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
pcairPartition: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
assocTestMM 17.08   0.84   19.92
fitNullMM   12.54   0.55   13.09
varCompCI   12.48   0.54   13.03
pcrelate    11.92   0.50   12.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
assocTestMM 16.14   0.82   18.55
pcrelate    13.86   0.52   14.37
fitNullMM   13.09   0.38   13.47
varCompCI   11.23   0.83   12.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/GENESIS.Rcheck/00check.log'
for details.


GENESIS.Rcheck/00install.out:


install for i386

* installing *source* package 'GENESIS' ...
** 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 'GENESIS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GENESIS' as GENESIS_2.4.0.zip
* DONE (GENESIS)

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

nameusersystemelapsed
assocTestMM17.08 0.8419.92
assocTestSeqWindow1.440.111.86
fitNullMM12.54 0.5513.09
king2mat0.270.000.27
pcair0.650.110.77
pcairPartition0.070.000.06
pcrelate11.92 0.5012.42
plot.pcair1.110.081.19
varCompCI12.48 0.5413.03

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

nameusersystemelapsed
assocTestMM16.14 0.8218.55
assocTestSeqWindow1.500.052.06
fitNullMM13.09 0.3813.47
king2mat0.320.000.32
pcair0.650.070.73
pcairPartition0.750.020.77
pcrelate13.86 0.5214.37
plot.pcair1.240.181.42
varCompCI11.23 0.8312.06