trigger 1.12.0
John D. Storey
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/trigger | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | 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 trigger_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/trigger.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trigger/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trigger’ version ‘1.12.0’
* 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 ‘trigger’ can be installed ... [25s/26s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Packages in Depends field not imported from:
‘corpcor’ ‘qtl’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Calls with DUP != TRUE:
.C("condi_indep_stat", ni, trait, cistrait, geno2, ng, r, DUP = FALSE)
.C("condi_indep_stat_rx", ni, nexp, trait, cistrait, geno2, ng,
r, DUP = FALSE, PACKAGE = "trigger")
.C("condi_indep_stat_x", ni, nexp, trait, cistrait, geno2, ng,
r, DUP = FALSE)
.C("link_stat", ni, trait, geno2, ng, lik0, lik1, DUP = FALSE)
.C("link_stat_xx", ni, nexp, trait, ngeno, geno2, ng, lik0, lik1,
DUP = FALSE)
.C("mergeorder", n1, x1, n2, x2, out, DUP = FALSE)
.C("order_c", x, as.integer(length(x)), out, DUP = FALSE)
.C("sec_link_stat", ni, trait, cistrait, geno2, ng, lik0, lik1,
DUP = FALSE)
.C("sec_link_stat_x", ni, nexp, trait, cistrait, geno2, ng, lik0,
lik1, DUP = FALSE)
DUP = FALSE is deprecated and will be disabled in future versions of R.
* checking R code for possible problems ... NOTE
traitmap.fun: warning in unlist(lapply(condi, function(x, stat0) {:
partial argument match of 'use.name' to 'use.names'
traitmap.fun: warning in mean(stat0 <= x): partial argument match of
'use.name' to 'use.names'
traitmap.fun: warning in }, stat0 = stat0), use.name = FALSE): partial
argument match of 'use.name' to 'use.names'
exportdata.trigger: no visible global function definition for
‘read.cross’
exportdata.trigger: no visible global function definition for
‘jittermap’
exportdata.trigger: no visible global function definition for
‘rescalemap’
exportdata.trigger: no visible global function definition for
‘plot.map’
exportdata.trigger: no visible global function definition for
‘calc.genoprob’
find.cis.genes: no visible global function definition for ‘bayesint’
find.cis.genes: no visible global function definition for ‘lodint’
find.cis.genes: no visible global function definition for ‘find.marker’
trait.trigger: no visible global function definition for ‘nind’
trait.trigger: no visible global function definition for
‘calc.genoprob’
trait.trigger: no visible global function definition for ‘scanone’
trigger.export2cross,trigger: no visible global function definition for
‘read.cross’
trigger.export2cross,trigger: no visible global function definition for
‘jittermap’
trigger.export2cross,trigger: no visible global function definition for
‘rescalemap’
trigger.export2cross,trigger: no visible global function definition for
‘plot.map’
trigger.export2cross,trigger: no visible global function definition for
‘calc.genoprob’
trigger.trait,trigger: no visible global function definition for ‘nind’
trigger.trait,trigger: no visible global function definition for
‘calc.genoprob’
trigger.trait,trigger: no visible global function definition for
‘scanone’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'plot' and siglist 'trigger,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [79s/79s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
trigger-export2cross 65.494 1.94 67.574
* 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
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/trigger.Rcheck/00check.log’
for details.