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BioC 3.3: CHECK report for BioQC on zin2

This page was generated on 2016-10-13 12:46:12 -0700 (Thu, 13 Oct 2016).

Package 115/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioQC 1.0.0
Jitao David Zhang
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/BioQC
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BioQC
Version: 1.0.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings BioQC_1.0.0.tar.gz
StartedAt: 2016-10-12 23:54:27 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:55:01 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 34.0 seconds
RetCode: 0
Status:  OK 
CheckDir: BioQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings BioQC_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/BioQC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioQC’ version ‘1.0.0’
* 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 ‘BioQC’ 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 loading without being on the library search path ... 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
rankSumTestWithCorrelation: no visible global function definition for
  ‘pt’
wmw.test: no visible global function definition for ‘wilcox.test’
wmwTest: no visible global function definition for ‘is’
Undefined global functions or variables:
  is pt wilcox.test
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "pt", "wilcox.test")
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 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 ... 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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-3.3-bioc/meat/BioQC.Rcheck/00check.log’
for details.


BioQC.Rcheck/00install.out:

* installing *source* package ‘BioQC’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG `/home/biocbuild/bbs-3.3-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include    -fpic  -g -O2  -Wall -c bioqc.c -o bioqc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG `/home/biocbuild/bbs-3.3-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include    -fpic  -g -O2  -Wall -c gini.c -o gini.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG `/home/biocbuild/bbs-3.3-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include    -fpic  -g -O2  -Wall -c read_gmt.cpp -o read_gmt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG `/home/biocbuild/bbs-3.3-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include    -fpic  -g -O2  -Wall -c stat_rank.c -o stat_rank.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG `/home/biocbuild/bbs-3.3-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include    -fpic  -g -O2  -Wall -c wmw_test_R.c -o wmw_test_R.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o BioQC.so bioqc.o gini.o read_gmt.o stat_rank.o wmw_test_R.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/BioQC.Rcheck/BioQC/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 (BioQC)

BioQC.Rcheck/BioQC-Ex.timings:

nameusersystemelapsed
absLog10p0.0020.0010.001
entropy0.0190.0000.019
filterPmat0.0020.0000.002
gini0.0010.0000.001
readGmt0.0230.0000.023
wmwTest0.2430.0040.247