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BioC 3.0: CHECK report for MIMOSA on moscato1

This page was generated on 2015-04-10 09:50:04 -0700 (Fri, 10 Apr 2015).

Package 552/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MIMOSA 1.2.0
Greg Finak
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/MIMOSA
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: MIMOSA
Version: 1.2.0
Command: rm -rf MIMOSA.buildbin-libdir MIMOSA.Rcheck && mkdir MIMOSA.buildbin-libdir MIMOSA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MIMOSA.buildbin-libdir MIMOSA_1.2.0.tar.gz >MIMOSA.Rcheck\00install.out 2>&1 && cp MIMOSA.Rcheck\00install.out MIMOSA-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=MIMOSA.buildbin-libdir --install="check:MIMOSA-install.out" --force-multiarch --no-vignettes --timings MIMOSA_1.2.0.tar.gz
StartedAt: 2015-04-10 03:06:11 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:10:04 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 233.2 seconds
RetCode: 0
Status:  OK  
CheckDir: MIMOSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MIMOSA.buildbin-libdir MIMOSA.Rcheck && mkdir MIMOSA.buildbin-libdir MIMOSA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MIMOSA.buildbin-libdir MIMOSA_1.2.0.tar.gz >MIMOSA.Rcheck\00install.out 2>&1 && cp MIMOSA.Rcheck\00install.out MIMOSA-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=MIMOSA.buildbin-libdir --install="check:MIMOSA-install.out" --force-multiarch --no-vignettes --timings MIMOSA_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/MIMOSA.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MIMOSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MIMOSA' version '1.2.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'MIMOSA' 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
* 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
MIMOSAExpressionSet: no visible global function definition for
  'ExpressionSet'
MIMOSAExpressionSet: no visible global function definition for
  'AnnotatedDataFrame'
boxplotMIMOSAResultList: no visible global function definition for
  'ldply'
boxplotMIMOSAResultList: no visible global function definition for
  'aes'
boxplotMIMOSAResultList: no visible global function definition for
  'geom_boxplot'
boxplotMIMOSAResultList: no visible global function definition for
  'coord_trans'
boxplotMIMOSAResultList: no visible global function definition for
  'facet_wrap'
boxplotMIMOSAResultList: no visible global function definition for
  'ggtitle'
boxplotMIMOSAResultList: no visible global function definition for
  'geom_jitter'
boxplotMIMOSAResultList: no visible global function definition for
  'position_jitter'
boxplotMIMOSAResultList: no visible global function definition for
  'geom_line'
boxplotMIMOSAResultList: no visible global function definition for
  'scale_fill_brewer'
boxplotMIMOSAResultList: no visible global function definition for
  'scale_color_brewer'
huberFilter: no visible global function definition for 'huber'
refactorPData: no visible global function definition for 'pData<-'
setpData.icsdata: no visible global function definition for 'pData<-'
volcanoPlot.MIMOSAResultList: no visible global function definition for
  'is.formula'
volcanoPlot.MIMOSAResultList: no visible global function definition for
  'facet_grid'
pData<-,BetaMixResult-data.frame: no visible global function definition
  for 'pData<-'
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.0-bioc/meat/MIMOSA.buildbin-libdir/MIMOSA/libs/i386/MIMOSA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.0-bioc/meat/MIMOSA.buildbin-libdir/MIMOSA/libs/x64/MIMOSA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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' ... [23s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
MIMOSA-accessors 7.17      0    7.18
** running examples for arch 'x64' ... [30s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
MIMOSA-accessors 9.16   0.02    9.18
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R' [7s]
 [8s] OK
** running tests for arch 'x64' ...
  Running 'test-all.R' [7s]
 [7s] 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/MIMOSA.Rcheck/00check.log'
for details.

MIMOSA.Rcheck/00install.out:


install for i386

* installing *source* package 'MIMOSA' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c BetaMix.cpp -o BetaMix.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c MCMC.cpp -o MCMC.o
MCMC.cpp: In function 'SEXPREC* fitMCMC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MCMC.cpp:73:23: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
MCMC.cpp:88:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:188:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:191:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:267:16: warning: null argument where non-null required (argument 1) [-Wnonnull]
MCMC.cpp:351:16: warning: null argument where non-null required (argument 1) [-Wnonnull]
MCMC.cpp:526:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:545:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:548:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp: In function 'double lkbeta(const std::vector<double, std::allocator<double> >&)':
MCMC.cpp:630:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp: In function 'void simZ(double&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<bool>&, int, int)':
MCMC.cpp:680:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp: In function 'double normconstIBeta(double, double, double, double)':
MCMC.cpp:812:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp: In function 'double nc(double, double, double, double, double)':
MCMC.cpp:890:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c MIMOSA_init.c -o MIMOSA_init.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c betaintegral.c -o betaintegral.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c betaintegralRcpp.cpp -o betaintegralRcpp.o
g++ -m32 -shared -s -static-libgcc -o MIMOSA.dll tmp.def BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -lm -lstdc++ -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lRlapack -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lRblas -lgfortran -ID:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/MIMOSA.buildbin-libdir/MIMOSA/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'MIMOSA'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'MIMOSA' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c BetaMix.cpp -o BetaMix.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c MCMC.cpp -o MCMC.o
MCMC.cpp: In function 'SEXPREC* fitMCMC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MCMC.cpp:73:23: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
MCMC.cpp:88:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:188:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:191:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:267:16: warning: null argument where non-null required (argument 1) [-Wnonnull]
MCMC.cpp:351:16: warning: null argument where non-null required (argument 1) [-Wnonnull]
MCMC.cpp:526:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:545:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp:548:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp: In function 'double lkbeta(const std::vector<double, std::allocator<double> >&)':
MCMC.cpp:630:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp: In function 'void simZ(double&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<bool>&, int, int)':
MCMC.cpp:680:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp: In function 'double normconstIBeta(double, double, double, double)':
MCMC.cpp:812:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
MCMC.cpp: In function 'double nc(double, double, double, double, double)':
MCMC.cpp:890:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c MIMOSA_init.c -o MIMOSA_init.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c betaintegral.c -o betaintegral.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I"D:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c betaintegralRcpp.cpp -o betaintegralRcpp.o
g++ -m64 -shared -s -static-libgcc -o MIMOSA.dll tmp.def BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -lm -lstdc++ -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lRlapack -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lRblas -lgfortran -ID:/biocbld/bbs-3.0-bioc/R/library/RcppArmadillo/include -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/MIMOSA.buildbin-libdir/MIMOSA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MIMOSA' as MIMOSA_1.2.0.zip
* DONE (MIMOSA)

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

nameusersystemelapsed
ConstructMIMOSAExpressionSet0.450.000.59
MIMOSA-accessors7.170.007.18
MIMOSA3.320.003.33
MIMOSAExpressionSet0.350.000.34
countsTable3.160.003.17
fdr3.220.003.21
volcanoPlot3.440.003.45

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

nameusersystemelapsed
ConstructMIMOSAExpressionSet0.580.000.57
MIMOSA-accessors9.160.029.18
MIMOSA3.760.003.76
MIMOSAExpressionSet0.450.000.45
countsTable4.820.004.82
fdr4.660.004.66
volcanoPlot4.010.004.03