Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-18 12:03:58 -0400 (Mon, 18 Oct 2021).

CHECK results for ASEB on riesling1

To the developers/maintainers of the ASEB package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ASEB.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 86/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASEB 1.37.0  (landing page)
Likun Wang
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/ASEB
git_branch: master
git_last_commit: c56fa99
git_last_commit_date: 2021-05-19 11:50:59 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ASEB
Version: 1.37.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASEB.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ASEB_1.37.0.tar.gz
StartedAt: 2021-10-17 23:52:33 -0400 (Sun, 17 Oct 2021)
EndedAt: 2021-10-17 23:56:37 -0400 (Sun, 17 Oct 2021)
EllapsedTime: 243.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ASEB.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASEB.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ASEB_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/ASEB.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ASEB/DESCRIPTION' ... OK
* this is package 'ASEB' version '1.37.0'
* 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 'ASEB' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
* 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
* 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 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
SequenceInfo: no visible global function definition for 'new'
drawEScurve,data.frame: no visible global function definition for 'pdf'
drawEScurve,data.frame: no visible global function definition for
  'jpeg'
drawEScurve,data.frame: no visible global function definition for
  'lines'
drawEScurve,data.frame: no visible global function definition for 'rgb'
drawEScurve,data.frame: no visible global function definition for
  'dev.off'
drawStat,data.frame: no visible global function definition for 'pdf'
drawStat,data.frame: no visible global function definition for 'jpeg'
drawStat,data.frame: no visible global function definition for 'lines'
drawStat,data.frame: no visible global function definition for
  'dev.off'
ids,SequenceInfo: no visible global function definition for 'slot'
ids<-,SequenceInfo-character: no visible global function definition for
  'slot<-'
sequences,SequenceInfo: no visible global function definition for
  'slot'
sequences<-,SequenceInfo-character: no visible global function
  definition for 'slot<-'
show,SequenceInfo: no visible global function definition for 'show'
Undefined global functions or variables:
  dev.off jpeg lines new pdf rgb show slot slot<-
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "pdf", "rgb")
  importFrom("graphics", "lines")
  importFrom("methods", "new", "show", "slot", "slot<-")
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 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 'D:/biocbuild/bbs-3.14-bioc/R/library/ASEB/libs/i386/ASEB.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'D:/biocbuild/bbs-3.14-bioc/R/library/ASEB/libs/x64/ASEB.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)

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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/ASEB.Rcheck/00check.log'
for details.



Installation output

ASEB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ASEB_1.37.0.tar.gz && rm -rf ASEB.buildbin-libdir && mkdir ASEB.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASEB.buildbin-libdir ASEB_1.37.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ASEB_1.37.0.zip && rm ASEB_1.37.0.tar.gz ASEB_1.37.0.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
 25  365k   25 94437    0     0   485k      0 --:--:-- --:--:-- --:--:--  482k
100  365k  100  365k    0     0  1574k      0 --:--:-- --:--:-- --:--:-- 1568k

install for i386

* installing *source* package 'ASEB' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c asebC.cpp -o asebC.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ASEB.dll tmp.def asebC.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/ASEB.buildbin-libdir/00LOCK-ASEB/00new/ASEB/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ASEB'
    finding HTML links ... done
    SequenceInfo                            html  
    asebProteins                            html  
    asebSites                               html  
    drawEScurve                             html  
    drawStat                                html  
    readSequence                            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

install for x64

* installing *source* package 'ASEB' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c asebC.cpp -o asebC.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ASEB.dll tmp.def asebC.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/ASEB.buildbin-libdir/ASEB/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ASEB' as ASEB_1.37.0.zip
* DONE (ASEB)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'ASEB' successfully unpacked and MD5 sums checked

Tests output


Example timings

ASEB.Rcheck/examples_i386/ASEB-Ex.timings

nameusersystemelapsed
SequenceInfo000
asebProteins1.040.021.09
asebSites0.620.000.64
drawEScurve0.640.010.65
drawStat0.880.000.90
readSequence0.410.000.41

ASEB.Rcheck/examples_x64/ASEB-Ex.timings

nameusersystemelapsed
SequenceInfo000
asebProteins0.780.030.89
asebSites0.590.000.61
drawEScurve0.600.030.64
drawStat0.760.020.81
readSequence0.420.000.42