CHECK report for GeneSelector on merida2
This page was generated on 2018-10-29 10:39:10 -0400 (Mon, 29 Oct 2018).
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 | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
Summary
Command output
##############################################################################
##############################################################################
###
### Running 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_2.31.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneSelector.Rcheck’
* using R Under development (unstable) (2018-04-05 r74542)
* 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 ‘2.31.2’
* 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 ‘/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
* 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-3.9-bioc/meat/GeneSelector.Rcheck/00check.log’
for details.
Installation output
GeneSelector.Rcheck/00install.out
Tests output
Example timings
GeneSelector.Rcheck/GeneSelector-Ex.timings