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BioC 3.1: CHECK report for trigger on zin2

This page was generated on 2015-10-09 09:24:48 -0700 (Fri, 09 Oct 2015).

Package 988/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trigger 1.14.0
John D. Storey
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/trigger
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: trigger
Version: 1.14.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings trigger_1.14.0.tar.gz
StartedAt: 2015-10-09 06:09:02 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 06:11:25 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 143.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: trigger.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings trigger_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/trigger.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.14.0’
* 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 ‘trigger’ can be installed ... [11s/11s] 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 ... OK
* checking R code for possible problems ... NOTE
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 ... [39s/39s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
trigger-export2cross 33.61  0.163   33.84
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/trigger.Rcheck/00check.log’
for details.


trigger.Rcheck/00install.out:

* installing *source* package ‘trigger’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c trigger.c -o trigger.o
trigger.c: In function ‘mergeorder’:
trigger.c:25:20: warning: variable ‘n3’ set but not used [-Wunused-but-set-variable]
 int i1,i2,i3,n1,n2,n3;
                    ^
trigger.c: In function ‘sec_link_stat’:
trigger.c:81:10: warning: variable ‘nct’ set but not used [-Wunused-but-set-variable]
 int ntr, nct, i, j;
          ^
trigger.c: In function ‘sec_link_stat_x’:
trigger.c:153:10: warning: variable ‘nct’ set but not used [-Wunused-but-set-variable]
 int ntr, nct, i, j, k, nk;
          ^
trigger.c: In function ‘condi_indep_stat’:
trigger.c:233:10: warning: variable ‘nct’ set but not used [-Wunused-but-set-variable]
 int ntr, nct, i, j;
          ^
trigger.c: In function ‘condi_indep_stat_x’:
trigger.c:310:10: warning: variable ‘nct’ set but not used [-Wunused-but-set-variable]
 int ntr, nct, i, j, k, nk;
          ^
trigger.c: In function ‘condi_indep_stat_rx’:
trigger.c:393:10: warning: variable ‘nct’ set but not used [-Wunused-but-set-variable]
 int ntr, nct, i, j, k, nk;
          ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o trigger.so trigger.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/trigger.Rcheck/trigger/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (trigger)

trigger.Rcheck/trigger-Ex.timings:

nameusersystemelapsed
plot0.0000.0030.001
trigger-build000
trigger-eigenR20.0000.0000.001
trigger-export2cross33.610 0.16333.840
trigger-link0.0000.0000.001
trigger-loclink0.0010.0000.000
trigger-mlink0.0010.0000.001
trigger-net0.0000.0000.001
trigger-netPlot2ps0.0010.0000.000
trigger-trait0.0010.0000.001