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CHECK report for GeneSelector on malbec2

This page was generated on 2018-10-29 10:07:03 -0400 (Mon, 29 Oct 2018).

Package 606/1642HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneSelector 2.31.2
Martin Slawski
Snapshot Date: 2018-10-28 16:46:29 -0400 (Sun, 28 Oct 2018)
URL: https://git.bioconductor.org/packages/GeneSelector
Branch: master
Last Commit: 772f876
Last Changed Date: 2018-10-18 08:07:29 -0400 (Thu, 18 Oct 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneSelector
Version: 2.31.2
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GeneSelector.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GeneSelector_2.31.2.tar.gz
StartedAt: 2018-10-29 03:18:49 -0400 (Mon, 29 Oct 2018)
EndedAt: 2018-10-29 03:19:51 -0400 (Mon, 29 Oct 2018)
EllapsedTime: 62.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GeneSelector.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GeneSelector.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GeneSelector_2.31.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GeneSelector.Rcheck’
* using R Under development (unstable) (2018-10-16 r75448)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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 ‘/home/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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/GeneSelector.Rcheck/00check.log’
for details.



Installation output

GeneSelector.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GeneSelector
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘GeneSelector’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c kendall.c -o kendall.o
kendall.c: In function ‘kendall’:
kendall.c:7:10: warning: ‘tau’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   res[0] = tau;
   ˜˜˜˜˜˜˜^˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c mcfour.c -o mcfour.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c mct.c -o mct.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o GeneSelector.so kendall.o mcfour.o mct.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/GeneSelector/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (GeneSelector)

Tests output


Example timings

GeneSelector.Rcheck/GeneSelector-Ex.timings

nameusersystemelapsed
AggregateMC0.1460.0000.147
AggregatePenalty0.6590.0000.662
AggregateSVD0.0930.0040.098
AggregateSimple0.1060.0040.111
GeneSelector2.7650.0562.837
GenerateBootMatrix0.0400.0040.044
GenerateFoldMatrix0.0130.0040.017
GetStabilityDistance0.0950.0120.107
GetStabilityOverlap0.1380.0000.139
GetStabilityUnion0.1610.0000.162
HeatmapRankings1.2680.0161.289
MergeMethods1.0790.0471.132
RankingBaldiLong0.0320.0000.033
RankingEbam0.2610.0040.268
RankingFC0.0090.0000.009
RankingFoxDimmic0.0230.0000.023
RankingLimma0.3140.0040.321
RankingPermutation0.3950.0040.402
RankingSam0.7210.0040.730
RankingShrinkageT0.030.000.03
RankingSoftthresholdT0.0800.0000.081
RankingTstat0.0090.0000.010
RankingWelchT0.0090.0000.010
RankingWilcEbam0.1160.0000.116
RankingWilcoxon0.0980.0040.103
RepeatRanking0.7100.0000.713
toydata0.0070.0000.007