BioC 2.14: CHECK report for trigger on petty

Package: trigger

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch trigger_1.10.0.tar.gz

StartedAt: 2014-10-08 00:28:54 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:31:23 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 148.9 seconds

RetCode: 0

Status:  OK

CheckDir: trigger.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch trigger_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/trigger.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.10.0’
* 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 ... [5s/5s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [85s/86s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
trigger-export2cross 74.923  8.185  84.358
* 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/trigger.Rcheck/00check.log’
for details.

* installing *source* package ‘trigger’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c trigger.c -o trigger.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o trigger.so trigger.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/trigger.Rcheck/trigger/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘trigger’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (trigger)

name	user	system	elapsed
plot	0.002	0.000	0.002
trigger-build	0.001	0.001	0.002
trigger-eigenR2	0.000	0.000	0.001
trigger-export2cross	74.923	8.185	84.358
trigger-link	0.002	0.001	0.002
trigger-loclink	0.001	0.000	0.002
trigger-mlink	0.001	0.001	0.001
trigger-net	0.002	0.000	0.002
trigger-netPlot2ps	0.002	0.000	0.002
trigger-trait	0.001	0.000	0.001