Package: GeneSelector

Version: 2.31.2

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneSelector.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GeneSelector_2.31.2.tar.gz

StartedAt: 2018-10-29 03:31:04 -0400 (Mon, 29 Oct 2018)

EndedAt: 2018-10-29 03:32:43 -0400 (Mon, 29 Oct 2018)

EllapsedTime: 99.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneSelector.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneSelector.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GeneSelector_2.31.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneSelector.Rcheck'
* using R Under development (unstable) (2018-10-22 r75479)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneSelector/DESCRIPTION' ... OK
* this is package 'GeneSelector' version '2.31.2'
* 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 'GeneSelector' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'GeneSelector' is deprecated and will be removed from
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneSelector.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'multtest' 'siggenes' 'samr' 'limma'
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' calls in package code:
  'limma' 'multtest' 'samr' 'siggenes'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  'limma' 'multtest'
  All declared Imports should be used.
':::' call which should be '::': 'siggenes:::qvalue.cal'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
HeatmapRankings,RepeatedRanking: warning in heatmap(Rmat[ind, , drop =
  FALSE], hclustfun = hclust, labCol = colnames(Rmat), scale = "none",
  labRow = character(), col = terrain.colors(20), mar = c(8, 8)):
  partial argument match of 'mar' to 'margins'
RankingBaldiLong,matrix-numeric: warning in rank(-abs(statistic), ties
  = "first"): partial argument match of 'ties' to 'ties.method'
RankingEbam,matrix-numeric: warning in rank(-posterior, ties =
  "first"): partial argument match of 'ties' to 'ties.method'
RankingFC,matrix-numeric: warning in rank(-abs(statistic), ties =
  "first"): partial argument match of 'ties' to 'ties.method'
RankingFoxDimmic,matrix-numeric: warning in rank(-abs(statistic), ties
  = "first"): partial argument match of 'ties' to 'ties.method'
RankingLimma,matrix-numeric: warning in rank(-abs(statistic), ties =
  "first"): partial argument match of 'ties' to 'ties.method'
RankingSam,matrix-numeric: warning in rank(-abs(statistic), ties =
  "first"): partial argument match of 'ties' to 'ties.method'
RankingShrinkageT,matrix-numeric: warning in rank(-abs(statistic), ties
  = "first"): partial argument match of 'ties' to 'ties.method'
RankingSoftthresholdT,matrix-numeric: warning in rank(-abs(statistic),
  ties = "first"): partial argument match of 'ties' to 'ties.method'
RankingTstat,matrix-numeric: warning in rank(-abs(statistic), ties =
  "first"): partial argument match of 'ties' to 'ties.method'
RankingWelchT,matrix-numeric: warning in rank(-abs(statistic), ties =
  "first"): partial argument match of 'ties' to 'ties.method'
AdjustPvalues: no visible global function definition for 'mt.rawp2adjp'
AdjustPvalues: no visible global function definition for 'pi0.est'
RankingEbam,matrix-numeric: no visible binding for global variable
  'quan.a0'
RankingLimma,matrix-numeric: no visible global function definition for
  'lmFit'
RankingLimma,matrix-numeric: no visible global function definition for
  'eBayes'
RankingPermutation,matrix-numeric: no visible binding for global
  variable 'test'
RankingPermutation,matrix-numeric : <anonymous>: no visible binding for
  global variable 'mt.sample.teststat'
RankingSam,matrix-numeric: no visible global function definition for
  'samr.pvalues.from.perms'
RepeatRanking,GeneRanking-BootMatrix-missing-missing-missing: no
  visible binding for global variable 'RankingBstat'
RepeatRanking,GeneRanking-FoldMatrix-ANY-missing-missing: no visible
  binding for global variable 'RankingBstat'
RepeatRanking,GeneRanking-missing-missing-ANY-ANY: no visible binding
  for global variable 'RankingBstat'
plot,RepeatedRanking-missing: no visible binding for global variable
  'xlab'
plot,RepeatedRanking-missing: no visible binding for global variable
  'ylab'
plot,RepeatedRanking-missing: no visible binding for global variable
  'cex'
plot,RepeatedRanking-missing: no visible binding for global variable
  'main'
Undefined global functions or variables:
  RankingBstat cex eBayes lmFit main mt.rawp2adjp mt.sample.teststat
  pi0.est quan.a0 samr.pvalues.from.perms test xlab ylab
* 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 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-3.9-bioc/R/library/GeneSelector/libs/i386/GeneSelector.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/GeneSelector/libs/x64/GeneSelector.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: 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneSelector.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GeneSelector_2.31.2.tar.gz && rm -rf GeneSelector.buildbin-libdir && mkdir GeneSelector.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneSelector.buildbin-libdir GeneSelector_2.31.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GeneSelector_2.31.2.zip && rm GeneSelector_2.31.2.tar.gz GeneSelector_2.31.2.zip
###
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install for i386

* installing *source* package 'GeneSelector' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c kendall.c -o kendall.o
kendall.c: In function 'kendall':
kendall.c:6:14: warning: 'tau' may be used uninitialized in this function [-Wmaybe-uninitialized]
          tau = tau + w[i] * w[j] * (((r[i] - r[j]) * (rprime[i] - rprime[j])) < 0); 
              ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c mcfour.c -o mcfour.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c mct.c -o mct.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o GeneSelector.dll tmp.def kendall.o mcfour.o mct.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneSelector.buildbin-libdir/GeneSelector/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GeneSelector'
    finding HTML links ... done
    AggregateMC                             html  
    AggregatePenalty                        html  
    AggregateSVD                            html  
    AggregateSimple                         html  
    AggregatedRanking-class                 html  
    BootMatrix-class                        html  
    FoldMatrix-class                        html  
    GeneRanking-class                       html  
    GeneSelector-package                    html  
    GeneSelector                            html  
    GeneSelectorOutput-class                html  
    GenerateBootMatrix                      html  
    GenerateFoldMatrix                      html  
    GetStabilityDistance                    html  
    GetStabilityOverlap                     html  
    GetStabilityUnion                       html  
    HeatmapRankings                         html  
    MergeMethods                            html  
    RankingBaldiLong                        html  
    RankingEbam                             html  
    RankingFC                               html  
    RankingFoxDimmic                        html  
    RankingLimma                            html  
    RankingPermutation                      html  
    RankingSam                              html  
    RankingShrinkageT                       html  
    RankingSoftthresholdT                   html  
    RankingTstat                            html  
    RankingWelchT                           html  
    RankingWilcEbam                         html  
    RankingWilcoxon                         html  
    RepeatRanking                           html  
    RepeatedRanking-class                   html  
    StabilityDistance-class                 html  
    StabilityOverlap-class                  html  
    StabilityUnion-class                    html  
    dispersion,RepeatedRanking              html  
    internals                               html  
    samplingcontrol                         html  
    toplist-methods                         html  
    toydata                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'GeneSelector' is deprecated and will be removed from
  Bioconductor version 3.9
In R CMD INSTALL

install for x64

* installing *source* package 'GeneSelector' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c kendall.c -o kendall.o
kendall.c: In function 'kendall':
kendall.c:6:14: warning: 'tau' may be used uninitialized in this function [-Wmaybe-uninitialized]
          tau = tau + w[i] * w[j] * (((r[i] - r[j]) * (rprime[i] - rprime[j])) < 0); 
              ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c mcfour.c -o mcfour.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c mct.c -o mct.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o GeneSelector.dll tmp.def kendall.o mcfour.o mct.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneSelector.buildbin-libdir/GeneSelector/libs/x64
** testing if installed package can be loaded
Warning: Package 'GeneSelector' is deprecated and will be removed from
  Bioconductor version 3.9
* MD5 sums
packaged installation of 'GeneSelector' as GeneSelector_2.31.2.zip
* DONE (GeneSelector)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GeneSelector' successfully unpacked and MD5 sums checked
In R CMD INSTALL