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CHECK report for gaga on tokay1

This page was generated on 2019-04-13 11:20:35 -0400 (Sat, 13 Apr 2019).

Package 567/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaga 2.28.1
David Rossell
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/gaga
Branch: RELEASE_3_8
Last Commit: 884f515
Last Changed Date: 2019-01-04 13:33:31 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  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: gaga
Version: 2.28.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gaga.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings gaga_2.28.1.tar.gz
StartedAt: 2019-04-13 02:21:53 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:24:10 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 136.5 seconds
RetCode: 0
Status:  OK  
CheckDir: gaga.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gaga.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings gaga_2.28.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/gaga.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '2.28.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.8-bioc/R/library/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 use Fortran I/O
nor system RNGs. 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 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-3.8-bioc/meat/gaga.Rcheck/00check.log'
for details.



Installation output

gaga.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/gaga_2.28.1.tar.gz && rm -rf gaga.buildbin-libdir && mkdir gaga.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gaga.buildbin-libdir gaga_2.28.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL gaga_2.28.1.zip && rm gaga_2.28.1.tar.gz gaga_2.28.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  125k  100  125k    0     0  2923k      0 --:--:-- --:--:-- --:--:-- 3208k

install for i386

* installing *source* package 'gaga' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c cseqdesma.c -o cseqdesma.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/gaga.buildbin-libdir/gaga/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gaga'
    finding HTML links ... done
    buildPatterns                           html  
    checkfit                                html  
    classpred                               html  
    dcgamma                                 html  
    findgenes                               html  
    fitGG                                   html  
    forwsimDiffExpr                         html  
    geneclus                                html  
    getpar                                  html  
    parest                                  html  
    plotForwSim                             html  
    posmeansGG                              html  
    powclasspred                            html  
    powfindgenes                            html  
    print.gagaclus                          html  
    print.gagafit                           html  
    print.gagahyp                           html  
    seqBoundariesGrid                       html  
    simGG                                   html  
    simnewsamples                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'gaga' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c cseqdesma.c -o cseqdesma.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/gaga.buildbin-libdir/gaga/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gaga' as gaga_2.28.1.zip
* DONE (gaga)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'gaga' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

gaga.Rcheck/examples_i386/gaga-Ex.timings

nameusersystemelapsed
buildPatterns000
classpred000
findgenes000
fitGG0.150.000.15
forwsimDiffExpr2.110.002.11
geneclus000
parest000
powfindgenes0.430.000.43
simGG000

gaga.Rcheck/examples_x64/gaga-Ex.timings

nameusersystemelapsed
buildPatterns000
classpred000
findgenes000
fitGG0.140.000.14
forwsimDiffExpr2.110.002.11
geneclus000
parest000
powfindgenes0.50.00.5
simGG000