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BioC 3.5: CHECK report for simulatorZ on oaxaca

This page was generated on 2017-03-04 16:48:14 -0500 (Sat, 04 Mar 2017).

Package 1188/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simulatorZ 1.9.0
Yuqing Zhang
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/simulatorZ
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: simulatorZ
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings simulatorZ_1.9.0.tar.gz
StartedAt: 2017-03-04 09:16:01 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 09:20:00 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 239.2 seconds
RetCode: 0
Status:  OK 
CheckDir: simulatorZ.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings simulatorZ_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/simulatorZ.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.9.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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   15.825  0.425  16.325
getTrueModel  8.173  0.101   8.300
simBootstrap  6.980  0.088   7.071
zmatrix       6.930  0.083   7.016
simTime       6.576  0.081   6.657
simData       5.789  0.048   5.841
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/simulatorZ.Rcheck/00check.log’
for details.


simulatorZ.Rcheck/00install.out:

* installing *source* package ‘simulatorZ’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c coxformatrices.cpp -o coxformatrices.o
coxformatrices.cpp:79:17: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                NULL
                ^˜˜˜
                {   }
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stddef.h:72:18: note: expanded from macro 'NULL'
#    define NULL __null
                 ^˜˜˜˜˜
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o simulatorZ.so coxformatrices.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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
cvSubsets2.6120.0473.563
funCV2.3120.0272.339
geneFilter15.825 0.42516.325
getTrueModel8.1730.1018.300
masomenos1.4530.0101.464
plusMinus1.4070.0131.420
rowCoxTests0.7620.0230.785
simBootstrap6.9800.0887.071
simData5.7890.0485.841
simTime6.5760.0816.657
zmatrix6.9300.0837.016