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CHECK report for CancerMutationAnalysis on malbec2

This page was generated on 2018-07-19 10:33:56 -0400 (Thu, 19 Jul 2018).

Package 185/1560HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerMutationAnalysis 1.22.0
Simina M. Boca
Snapshot Date: 2018-07-18 16:45:10 -0400 (Wed, 18 Jul 2018)
URL: https://git.bioconductor.org/packages/CancerMutationAnalysis
Branch: RELEASE_3_7
Last Commit: ad61308
Last Changed Date: 2018-04-30 10:35:24 -0400 (Mon, 30 Apr 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CancerMutationAnalysis
Version: 1.22.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CancerMutationAnalysis.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CancerMutationAnalysis_1.22.0.tar.gz
StartedAt: 2018-07-18 22:52:25 -0400 (Wed, 18 Jul 2018)
EndedAt: 2018-07-18 22:54:23 -0400 (Wed, 18 Jul 2018)
EllapsedTime: 117.8 seconds
RetCode: 0
Status:  OK 
CheckDir: CancerMutationAnalysis.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CancerMutationAnalysis.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CancerMutationAnalysis_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/CancerMutationAnalysis.Rcheck’
* using R version 3.5.1 RC (2018-06-24 r74929)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CancerMutationAnalysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CancerMutationAnalysis’ version ‘1.22.0’
* 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 ‘CancerMutationAnalysis’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
* 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
Package in Depends field not imported from: ‘qvalue’
  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
ebfdr: no visible global function definition for ‘density’
ebfdr: no visible global function definition for ‘plot’
ebfdr: no visible global function definition for ‘text’
ebfdr: no visible global function definition for ‘abline’
ebfdr: no visible global function definition for ‘rug’
ebfdr: no visible global function definition for ‘hist’
p2q: no visible global function definition for ‘qvalue’
perm.null.het.p.values: no visible global function definition for
  ‘dhyper’
perm.null.p.values: no visible global function definition for ‘dhyper’
Undefined global functions or variables:
  abline density dhyper hist plot qvalue rug text
Consider adding
  importFrom("graphics", "abline", "hist", "plot", "rug", "text")
  importFrom("stats", "density", "dhyper")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
cma.set.sim 32.976  0.172  33.185
cma.fdr     19.360  0.104  19.490
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/CancerMutationAnalysis.Rcheck/00check.log’
for details.



Installation output

CancerMutationAnalysis.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL CancerMutationAnalysis
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘CancerMutationAnalysis’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c get.cdf.het.berns.c -o get.cdf.het.berns.o
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o CancerMutationAnalysis.so get.cdf.het.berns.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/CancerMutationAnalysis/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CancerMutationAnalysis)

Tests output


Example timings

CancerMutationAnalysis.Rcheck/CancerMutationAnalysis-Ex.timings

nameusersystemelapsed
cma.fdr19.360 0.10419.490
cma.scores0.6440.0120.696
cma.set.sim32.976 0.17233.185
cma.set.stat1.3760.0001.374
combine.sims0.0000.0000.001
extract.sims.method0.0000.0000.002