GeneSelector 2.14.0
Martin Slawski
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/GeneSelector | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneSelector_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/GeneSelector.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneSelector/DESCRIPTION’ ... OK
* this is package ‘GeneSelector’ version ‘2.14.0’
* 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 ... [5s/5s] OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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'
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'
RankingPermutation,matrix-numeric: no visible binding for global
variable ‘test’
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’
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/15s] 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
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/GeneSelector.Rcheck/00check.log’
for details.
* installing *source* package ‘GeneSelector’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c kendall.c -o kendall.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c mcfour.c -o mcfour.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c mct.c -o mct.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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 /Users/biocbuild/bbs-2.14-bioc/meat/GeneSelector.Rcheck/GeneSelector/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneSelector)