Package: GeneSelector

Version: 2.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneSelector.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneSelector_2.32.0.tar.gz

StartedAt: 2019-04-16 00:10:05 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:11:13 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 68.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneSelector.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneSelector.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneSelector_2.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GeneSelector.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneSelector/DESCRIPTION’ ... OK
* this is package ‘GeneSelector’ version ‘2.32.0’
* 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 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 ‘/Users/biocbuild/bbs-3.8-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 sizes of PDF files under ‘inst/doc’ ... OK
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/GeneSelector.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneSelector
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘GeneSelector’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c kendall.c -o kendall.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mcfour.c -o mcfour.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mct.c -o mct.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GeneSelector.so kendall.o mcfour.o mct.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/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)

name	user	system	elapsed
AggregateMC	0.176	0.044	0.221
AggregatePenalty	0.721	0.031	0.762
AggregateSVD	0.146	0.028	0.176
AggregateSimple	0.125	0.030	0.156
GeneSelector	3.109	0.244	3.373
GenerateBootMatrix	0.059	0.004	0.064
GenerateFoldMatrix	0.018	0.002	0.020
GetStabilityDistance	0.113	0.031	0.144
GetStabilityOverlap	0.198	0.032	0.229
GetStabilityUnion	0.209	0.036	0.245
HeatmapRankings	1.770	0.191	1.972
MergeMethods	1.287	0.166	1.459
RankingBaldiLong	0.038	0.005	0.042
RankingEbam	0.346	0.032	0.379
RankingFC	0.011	0.002	0.012
RankingFoxDimmic	0.019	0.001	0.019
RankingLimma	0.255	0.006	0.262
RankingPermutation	0.482	0.012	0.500
RankingSam	1.050	0.137	1.193
RankingShrinkageT	0.049	0.002	0.052
RankingSoftthresholdT	0.092	0.002	0.095
RankingTstat	0.016	0.003	0.021
RankingWelchT	0.008	0.002	0.009
RankingWilcEbam	0.122	0.004	0.127
RankingWilcoxon	0.094	0.004	0.098
RepeatRanking	0.832	0.104	0.941
toydata	0.008	0.003	0.011