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CHECK report for trigger on tokay1

This page was generated on 2018-04-12 13:21:25 -0400 (Thu, 12 Apr 2018).

Package 1421/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trigger 1.24.0
John D. Storey
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/trigger
Branch: RELEASE_3_6
Last Commit: 15ac215
Last Changed Date: 2017-10-30 12:39:37 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: trigger
Version: 1.24.0
Command: rm -rf trigger.buildbin-libdir trigger.Rcheck && mkdir trigger.buildbin-libdir trigger.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=trigger.buildbin-libdir trigger_1.24.0.tar.gz >trigger.Rcheck\00install.out 2>&1 && cp trigger.Rcheck\00install.out trigger-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=trigger.buildbin-libdir --install="check:trigger-install.out" --force-multiarch --no-vignettes --timings trigger_1.24.0.tar.gz
StartedAt: 2018-04-12 03:41:20 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:45:38 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 257.9 seconds
RetCode: 0
Status:  OK  
CheckDir: trigger.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf trigger.buildbin-libdir trigger.Rcheck && mkdir trigger.buildbin-libdir trigger.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=trigger.buildbin-libdir trigger_1.24.0.tar.gz >trigger.Rcheck\00install.out 2>&1 && cp trigger.Rcheck\00install.out trigger-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=trigger.buildbin-libdir --install="check:trigger-install.out" --force-multiarch --no-vignettes --timings trigger_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/trigger.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'trigger/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'trigger' version '1.24.0'
* 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 whether package 'trigger' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
initialize,trigger: no visible global function definition for
  'callNextMethod'
Undefined global functions or variables:
  callNextMethod
Consider adding
  importFrom("methods", "callNextMethod")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/trigger.buildbin-libdir/trigger/libs/i386/trigger.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
trigger-export2cross 32.56   1.71    34.3
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
trigger-export2cross 32.18   1.44   33.64
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/trigger.Rcheck/00check.log'
for details.



Installation output

trigger.Rcheck/00install.out


install for i386

* installing *source* package 'trigger' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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;
          ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o trigger.dll tmp.def trigger.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/trigger.buildbin-libdir/trigger/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'trigger'
    finding HTML links ... done
    plot                                    html  
    trigger-build                           html  
    trigger-class                           html  
    trigger-eigenR2                         html  
    trigger-export2cross                    html  
    trigger-link                            html  
    trigger-loclink                         html  
    trigger-mlink                           html  
    trigger-net                             html  
    trigger-netPlot2ps                      html  
    trigger-trait                           html  
    yeast                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'trigger' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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;
          ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o trigger.dll tmp.def trigger.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/trigger.buildbin-libdir/trigger/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'trigger' as trigger_1.24.0.zip
* DONE (trigger)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

trigger.Rcheck/examples_i386/trigger-Ex.timings

nameusersystemelapsed
plot000
trigger-build000
trigger-eigenR2000
trigger-export2cross32.56 1.7134.30
trigger-link000
trigger-loclink000
trigger-mlink000
trigger-net000
trigger-netPlot2ps000
trigger-trait000

trigger.Rcheck/examples_x64/trigger-Ex.timings

nameusersystemelapsed
plot000
trigger-build000
trigger-eigenR2000
trigger-export2cross32.18 1.4433.64
trigger-link000
trigger-loclink000
trigger-mlink000
trigger-net000
trigger-netPlot2ps000
trigger-trait000