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CHECK report for RnaSeqSampleSize on malbec1

This page was generated on 2019-04-16 11:51:02 -0400 (Tue, 16 Apr 2019).

Package 1333/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnaSeqSampleSize 1.14.1
Shilin Zhao
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/RnaSeqSampleSize
Branch: RELEASE_3_8
Last Commit: 9d55430
Last Changed Date: 2019-01-04 13:47:31 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RnaSeqSampleSize
Version: 1.14.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RnaSeqSampleSize.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RnaSeqSampleSize_1.14.1.tar.gz
StartedAt: 2019-04-16 02:42:10 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:44:06 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 116.6 seconds
RetCode: 0
Status:  OK 
CheckDir: RnaSeqSampleSize.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RnaSeqSampleSize.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RnaSeqSampleSize_1.14.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/RnaSeqSampleSize.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RnaSeqSampleSize/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RnaSeqSampleSize’ version ‘1.14.1’
* 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 ‘RnaSeqSampleSize’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
convertIdOneToOne: no visible global function definition for
  ‘flush.console’
est_power_root: no visible global function definition for ‘qnbinom’
est_power_root: no visible global function definition for ‘pnbinom’
est_power_root: no visible global function definition for ‘dnbinom’
generateModel: no visible global function definition for ‘plot’
generateModel: no visible global function definition for ‘points’
generateModel: no visible global function definition for ‘polygon’
generateModel: no visible global function definition for ‘rainbow’
generateModel: no visible global function definition for ‘legend’
generateModel: no visible global function definition for ‘lm’
generateModel: no visible global function definition for ‘abline’
modelPower: no visible global function definition for ‘qnbinom’
modelPower: no visible global function definition for ‘pnbinom’
modelPower: no visible global function definition for ‘dnbinom’
nb_pvalue_store: no visible global function definition for ‘dnbinom’
pCutoffMatrix: no visible global function definition for ‘qbeta’
plot_power_curve: no visible global function definition for ‘plot’
plot_power_curve: no visible global function definition for ‘legend’
plot_power_curve: no visible global function definition for ‘abline’
plot_power_curve: no visible global function definition for ‘lines’
sample_size: no visible global function definition for ‘qnorm’
selectDistribution: no visible global function definition for ‘data’
selectDistribution: no visible global function definition for ‘is’
Undefined global functions or variables:
  abline data dnbinom flush.console is legend lines lm plot pnbinom
  points polygon qbeta qnbinom qnorm rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "plot", "points",
             "polygon")
  importFrom("methods", "is")
  importFrom("stats", "dnbinom", "lm", "pnbinom", "qbeta", "qnbinom",
             "qnorm")
  importFrom("utils", "data", "flush.console")
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 ... NOTE
Note: information on .o files is not available
* 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
convertIdOneToOne 0.392  0.004   12.01
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/RnaSeqSampleSize.Rcheck/00check.log’
for details.



Installation output

RnaSeqSampleSize.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL RnaSeqSampleSize
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘RnaSeqSampleSize’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RnaSeqSampleSize.c -o RnaSeqSampleSize.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c bd0.c -o bd0.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c cumsumBorder.cpp -o cumsumBorder.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c stirlerr.c -o stirlerr.o
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o RnaSeqSampleSize.so RcppExports.o RnaSeqSampleSize.o bd0.o cumsumBorder.o stirlerr.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/RnaSeqSampleSize/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘RnaSeqSampleSize.Rnw’ 
** testing if installed package can be loaded
* DONE (RnaSeqSampleSize)

Tests output


Example timings

RnaSeqSampleSize.Rcheck/RnaSeqSampleSize-Ex.timings

nameusersystemelapsed
convertIdOneToOne 0.392 0.00412.010
est_count_dispersion0.1920.0040.197
est_power2.3040.0122.319
est_power_curve000
est_power_distribution0.0000.0000.001
optimize_parameter2.3240.0122.339
plot_power_curve0.760.000.76
sample_size1.4280.0001.426
sample_size_distribution0.0000.0000.001