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CHECK report for trigger on malbec2

This page was generated on 2020-10-17 11:55:58 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE trigger PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1834/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trigger 1.34.0
John D. Storey
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/trigger
Branch: RELEASE_3_11
Last Commit: 6628294
Last Changed Date: 2020-04-27 14:27:54 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: trigger
Version: 1.34.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:trigger.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings trigger_1.34.0.tar.gz
StartedAt: 2020-10-17 06:12:53 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:15:59 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 185.8 seconds
RetCode: 0
Status:  OK 
CheckDir: trigger.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:trigger.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings trigger_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/trigger.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.34.0’
* 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 ... 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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
trigger-export2cross 26.855  0.144  27.012
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/trigger.Rcheck/00check.log’
for details.



Installation output

trigger.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL trigger
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘trigger’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-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 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o trigger.so trigger.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-trigger/00new/trigger/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (trigger)

Tests output


Example timings

trigger.Rcheck/trigger-Ex.timings

nameusersystemelapsed
plot000
trigger-build000
trigger-eigenR2000
trigger-export2cross26.855 0.14427.012
trigger-link000
trigger-loclink000
trigger-mlink000
trigger-net000
trigger-netPlot2ps000
trigger-trait0.0010.0000.000