Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2021-11-30 13:55:17 -0500 (Tue, 30 Nov 2021).

CHECK results for trigger on riesling1

To the developers/maintainers of the trigger package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/trigger.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1987/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trigger 1.41.0  (landing page)
John D. Storey
Snapshot Date: 2021-11-29 14:50:17 -0500 (Mon, 29 Nov 2021)
git_url: https://git.bioconductor.org/packages/trigger
git_branch: master
git_last_commit: dcf2dad
git_last_commit_date: 2021-10-26 12:01:26 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: trigger
Version: 1.41.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:trigger.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings trigger_1.41.0.tar.gz
StartedAt: 2021-11-30 04:23:25 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 04:29:03 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 337.7 seconds
RetCode: 0
Status:   OK  
CheckDir: trigger.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:trigger.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings trigger_1.41.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/trigger.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.41.0'
* 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
* 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/trigger/libs/x64/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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
trigger-export2cross 19.64   1.51   21.16
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/trigger.Rcheck/00check.log'
for details.



Installation output

trigger.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.15/bioc/src/contrib/trigger_1.41.0.tar.gz && rm -rf trigger.buildbin-libdir && mkdir trigger.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=trigger.buildbin-libdir trigger_1.41.0.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL trigger_1.41.0.zip && rm trigger_1.41.0.tar.gz trigger_1.41.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1516k  100 1516k    0     0  3133k      0 --:--:-- --:--:-- --:--:-- 3133k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'trigger' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o trigger.dll tmp.def trigger.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/meat/trigger.buildbin-libdir/00LOCK-trigger/00new/trigger/libs/x64
** R
** data
** inst
** byte-compile and prepare 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'trigger' as trigger_1.41.0.zip
* DONE (trigger)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'trigger' successfully unpacked and MD5 sums checked

Tests output


Example timings

trigger.Rcheck/trigger-Ex.timings

nameusersystemelapsed
plot000
trigger-build000
trigger-eigenR2000
trigger-export2cross19.64 1.5121.16
trigger-link000
trigger-loclink000
trigger-mlink000
trigger-net000
trigger-netPlot2ps000
trigger-trait000