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BioC 3.5: CHECK report for gaga on tokay2

This page was generated on 2017-08-16 13:19:48 -0400 (Wed, 16 Aug 2017).

Package 487/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaga 2.22.0
David Rossell
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/gaga
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gaga
Version: 2.22.0
Command: rm -rf gaga.buildbin-libdir gaga.Rcheck && mkdir gaga.buildbin-libdir gaga.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gaga.buildbin-libdir gaga_2.22.0.tar.gz >gaga.Rcheck\00install.out 2>&1 && cp gaga.Rcheck\00install.out gaga-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=gaga.buildbin-libdir --install="check:gaga-install.out" --force-multiarch --no-vignettes --timings gaga_2.22.0.tar.gz
StartedAt: 2017-08-15 23:50:44 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:52:39 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 115.5 seconds
RetCode: 0
Status:  OK  
CheckDir: gaga.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gaga.buildbin-libdir gaga.Rcheck && mkdir gaga.buildbin-libdir gaga.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gaga.buildbin-libdir gaga_2.22.0.tar.gz >gaga.Rcheck\00install.out 2>&1 && cp gaga.Rcheck\00install.out gaga-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=gaga.buildbin-libdir --install="check:gaga-install.out" --force-multiarch --no-vignettes --timings gaga_2.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/gaga.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gaga/DESCRIPTION' ... OK
* this is package 'gaga' version '2.22.0'
* 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 'gaga' 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
* 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 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
adjustfitNN: no visible global function definition for 'predict'
checkfit.gagafit: no visible global function definition for 'is'
checkfit.gagafit: no visible global function definition for 'density'
checkfit.gagafit: no visible global function definition for 'plot'
checkfit.gagafit: no visible global function definition for 'lines'
checkfit.gagafit: no visible global function definition for 'legend'
checkfit.gagafit: no visible global function definition for 'quantile'
checkfit.gagafit: no visible global function definition for 'points'
classpred.gagafit: no visible global function definition for 'is'
findgenes.gagafit: no visible global function definition for 'is'
findgenes.gagafit: no visible global function definition for 'kmeans'
fitGG: no visible global function definition for 'is'
fitGG: no visible global function definition for 'quantile'
fitGG: no visible global function definition for 'var'
fitGG: no visible global function definition for 'kmeans'
fitNN: no visible global function definition for 'is'
fitNNSingleHyp: no visible global function definition for 'is'
forwsimDiffExpr.gagafit: no visible global function definition for 'is'
forwsimDiffExpr.nnfit: no visible global function definition for 'is'
forwsimDiffExpr.nnfit: no visible global function definition for
  'quantile'
makeEBarraysSingleHyp: no visible global function definition for 'new'
parest.gagafit: no visible global function definition for 'is'
parest.gagafit: no visible binding for global variable 'quantile'
parest.gagafit: no visible global function definition for 'quantile'
plotForwSim: no visible global function definition for 'plot'
plotForwSim: no visible global function definition for 'lines'
posmeansGG.gagafit: no visible global function definition for 'is'
powclasspred.gagafit: no visible global function definition for 'is'
powfindgenes.gagafit: no visible global function definition for 'is'
powfindgenes.nnfit: no visible global function definition for 'is'
powfindgenes.nnfit: no visible global function definition for 'sd'
powsimprior.nnfit: no visible global function definition for 'sd'
ppGG: no visible global function definition for 'is'
sigmaPriorEst: no visible global function definition for 'is'
sigmaPriorEst: no visible binding for global variable 'var'
sigmaPriorEst: no visible global function definition for 'var'
simGG: no visible global function definition for 'rgamma'
simGG: no visible global function definition for 'new'
simNN: no visible global function definition for 'runif'
simNN: no visible global function definition for 'rnorm'
simNN: no visible global function definition for 'rgamma'
simNN: no visible global function definition for 'new'
simnewsamples.gagafit: no visible global function definition for 'is'
simnewsamples.gagafit: no visible global function definition for 'new'
simnewsamples.nnfit: no visible global function definition for 'is'
simnewsamples.nnfit: no visible global function definition for 'runif'
simnewsamples.nnfit: no visible global function definition for 'rgamma'
simnewsamples.nnfit: no visible global function definition for 'rnorm'
simnewsamples.nnfit: no visible global function definition for
  'model.matrix'
simnewsamples.nnfit: no visible global function definition for 'new'
Undefined global functions or variables:
  density is kmeans legend lines model.matrix new plot points predict
  quantile rgamma rnorm runif sd var
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("methods", "is", "new")
  importFrom("stats", "density", "kmeans", "model.matrix", "predict",
             "quantile", "rgamma", "rnorm", "runif", "sd", "var")
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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/gaga.buildbin-libdir/gaga/libs/i386/gaga.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' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/gaga.Rcheck/00check.log'
for details.


gaga.Rcheck/00install.out:


install for i386

* installing *source* package 'gaga' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c cseqdesma.c -o cseqdesma.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c cstat.c -o cstat.o
cstat.c: In function 'qnormC':
cstat.c:1638:3: warning: 'x' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return y; 
   ^
cstat.c: In function 'pnormC':
cstat.c:1552:5: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized]
     p, q, mean,sd,bound,x,z; 
     ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o gaga.dll tmp.def cseqdesma.o cstat.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/gaga.buildbin-libdir/gaga/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 'gaga' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c cseqdesma.c -o cseqdesma.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c cstat.c -o cstat.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o gaga.dll tmp.def cseqdesma.o cstat.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/gaga.buildbin-libdir/gaga/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gaga' as gaga_2.22.0.zip
* DONE (gaga)

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

nameusersystemelapsed
buildPatterns0.020.000.01
classpred000
findgenes0.020.000.02
fitGG0.320.000.32
forwsimDiffExpr3.050.003.05
geneclus0.020.000.02
parest000
powfindgenes0.470.000.47
simGG000

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

nameusersystemelapsed
buildPatterns0.010.000.02
classpred000
findgenes000
fitGG0.180.000.19
forwsimDiffExpr2.830.002.83
geneclus000
parest000
powfindgenes0.420.000.42
simGG000