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BioC 3.3: CHECK report for BioQC on moscato2

This page was generated on 2016-10-13 12:54:38 -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: rm -rf BioQC.buildbin-libdir BioQC.Rcheck && mkdir BioQC.buildbin-libdir BioQC.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioQC.buildbin-libdir BioQC_1.0.0.tar.gz >BioQC.Rcheck\00install.out 2>&1 && cp BioQC.Rcheck\00install.out BioQC-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=BioQC.buildbin-libdir --install="check:BioQC-install.out" --force-multiarch --no-vignettes --timings BioQC_1.0.0.tar.gz
StartedAt: 2016-10-13 01:28:31 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:30:10 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 98.2 seconds
RetCode: 0
Status:  OK  
CheckDir: BioQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BioQC.buildbin-libdir BioQC.Rcheck && mkdir BioQC.buildbin-libdir BioQC.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioQC.buildbin-libdir BioQC_1.0.0.tar.gz >BioQC.Rcheck\00install.out 2>&1 && cp BioQC.Rcheck\00install.out BioQC-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=BioQC.buildbin-libdir --install="check:BioQC-install.out" --force-multiarch --no-vignettes --timings BioQC_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/BioQC.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.3-bioc/meat/BioQC.buildbin-libdir/BioQC/libs/i386/BioQC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/BioQC.Rcheck/00check.log'
for details.


BioQC.Rcheck/00install.out:


install for i386

* installing *source* package 'BioQC' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG `E:/biocbld/BBS-3˜1.3-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c bioqc.c -o bioqc.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG `E:/biocbld/BBS-3˜1.3-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c gini.c -o gini.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG `E:/biocbld/BBS-3˜1.3-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c read_gmt.cpp -o read_gmt.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG `E:/biocbld/BBS-3˜1.3-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stat_rank.c -o stat_rank.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG `E:/biocbld/BBS-3˜1.3-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c wmw_test_R.c -o wmw_test_R.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o BioQC.dll tmp.def bioqc.o gini.o read_gmt.o stat_rank.o wmw_test_R.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/BioQC.buildbin-libdir/BioQC/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'BioQC' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG `E:/biocbld/BBS-3˜1.3-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bioqc.c -o bioqc.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG `E:/biocbld/BBS-3˜1.3-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c gini.c -o gini.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG `E:/biocbld/BBS-3˜1.3-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c read_gmt.cpp -o read_gmt.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG `E:/biocbld/BBS-3˜1.3-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stat_rank.c -o stat_rank.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG `E:/biocbld/BBS-3˜1.3-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c wmw_test_R.c -o wmw_test_R.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o BioQC.dll tmp.def bioqc.o gini.o read_gmt.o stat_rank.o wmw_test_R.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/BioQC.buildbin-libdir/BioQC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioQC' as BioQC_1.0.0.zip
* DONE (BioQC)

BioQC.Rcheck/examples_i386/BioQC-Ex.timings:

nameusersystemelapsed
absLog10p000
entropy0.010.020.03
filterPmat0.020.000.02
gini000
readGmt0.030.000.03
wmwTest0.310.000.31

BioQC.Rcheck/examples_x64/BioQC-Ex.timings:

nameusersystemelapsed
absLog10p000
entropy0.040.000.05
filterPmat000
gini000
readGmt0.050.000.05
wmwTest0.480.000.48