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BioC 3.5: CHECK report for simulatorZ on malbec2

This page was generated on 2017-08-16 13:16:03 -0400 (Wed, 16 Aug 2017).

Package 1228/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simulatorZ 1.10.0
Yuqing Zhang
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/simulatorZ
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  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: simulatorZ
Version: 1.10.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings simulatorZ_1.10.0.tar.gz
StartedAt: 2017-08-16 02:20:18 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:23:26 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 188.1 seconds
RetCode: 0
Status:  OK 
CheckDir: simulatorZ.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings simulatorZ_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/simulatorZ.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘simulatorZ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘simulatorZ’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘simulatorZ’ 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
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘IRanges’ ‘S4Vectors’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘BiocGenerics’ ‘methods’
  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
fastCox: no visible global function definition for ‘pnorm’
fastCox: no visible global function definition for ‘new’
geneFilter: no visible global function definition for ‘cor’
getMatrix: no visible global function definition for ‘is’
masomenos: no visible global function definition for ‘is’
plusMinus: no visible binding for global variable ‘sd’
plusMinus: no visible binding for global variable ‘quantile’
plusMinus: no visible global function definition for ‘new’
rowCoxTests: no visible global function definition for ‘pnorm’
simData: no visible global function definition for ‘is’
simTime: no visible global function definition for ‘runif’
Undefined global functions or variables:
  cor is new pnorm quantile runif sd
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "cor", "pnorm", "quantile", "runif", "sd")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
geneFilter   13.808  0.096  13.950
getTrueModel  7.380  0.092   7.478
simBootstrap  6.764  0.068   6.836
zmatrix       6.684  0.048   6.739
simTime       6.232  0.092   6.328
simData       5.532  0.096   5.630
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/simulatorZ.Rcheck/00check.log’
for details.


simulatorZ.Rcheck/00install.out:

* installing *source* package ‘simulatorZ’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c coxformatrices.cpp -o coxformatrices.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o simulatorZ.so coxformatrices.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/simulatorZ.Rcheck/simulatorZ/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (simulatorZ)

simulatorZ.Rcheck/simulatorZ-Ex.timings:

nameusersystemelapsed
cvSubsets2.6480.0243.351
funCV2.1160.0122.128
geneFilter13.808 0.09613.950
getTrueModel7.3800.0927.478
masomenos1.5040.0121.516
plusMinus1.5800.0241.605
rowCoxTests0.9040.0000.906
simBootstrap6.7640.0686.836
simData5.5320.0965.630
simTime6.2320.0926.328
zmatrix6.6840.0486.739