trigger 1.10.0 John D. Storey
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/trigger | 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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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings trigger_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/trigger.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.10.0’
* 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 ... [2s/2s] 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.
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 ... NOTE
Calls with DUP = FALSE:
.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 may 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'
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/36s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
trigger-export2cross 34.262 1.004 35.52
* 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
‘/home/biocbuild/bbs-2.14-bioc/meat/trigger.Rcheck/00check.log’
for details.