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CHECK report for flowType on malbec1

This page was generated on 2019-04-16 11:49:14 -0400 (Tue, 16 Apr 2019).

Package 550/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowType 2.20.1
Nima Aghaeepour
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/flowType
Branch: RELEASE_3_8
Last Commit: ffccd19
Last Changed Date: 2019-01-04 13:33:07 -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  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowType
Version: 2.20.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:flowType.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings flowType_2.20.1.tar.gz
StartedAt: 2019-04-15 23:59:21 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-16 00:00:47 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 85.6 seconds
RetCode: 0
Status:  OK 
CheckDir: flowType.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:flowType.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings flowType_2.20.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/flowType.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 ‘flowType/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowType’ version ‘2.20.1’
* 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 ‘flowType’ 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
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘BH’ ‘Rcpp’
  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
flowType: no visible global function definition for ‘new’
plot,Phenotypes-flowFrame: no visible global function definition for
  ‘density’
Undefined global functions or variables:
  density new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "density")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/flowType.Rcheck/00check.log’
for details.



Installation output

flowType.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL flowType
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘flowType’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c countsAndMeans.cpp -o countsAndMeans.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c flowType.cpp -o flowType.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c numberGenerator.cpp -o numberGenerator.o
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o flowType.so countsAndMeans.o flowType.o numberGenerator.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/flowType/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 (flowType)

Tests output


Example timings

flowType.Rcheck/flowType-Ex.timings

nameusersystemelapsed
DLBCLExample0.0080.0000.011
HIVData0.1400.0040.144
HIVMetaData0.0040.0000.002
Phenotypes0.0000.0000.001
calcNumPops0.0000.0000.001
decodePhenotype-methods0.0000.0000.001
encodePhenotype0.0000.0000.001
flowType-package0.1200.0120.131
flowType0.1240.0040.127
getLabels000
plot000
summary-methods000