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CHECK report for ASEB on riesling1

This page was generated on 2020-10-21 12:13:43 -0400 (Wed, 21 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ASEB PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 87/1939HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASEB 1.33.0
Likun Wang
Snapshot Date: 2020-10-20 14:40:34 -0400 (Tue, 20 Oct 2020)
URL: https://git.bioconductor.org/packages/ASEB
Branch: master
Last Commit: 399b394
Last Changed Date: 2020-04-27 14:28:02 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ASEB
Version: 1.33.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASEB.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ASEB_1.33.0.tar.gz
StartedAt: 2020-10-20 20:10:03 -0400 (Tue, 20 Oct 2020)
EndedAt: 2020-10-20 20:11:10 -0400 (Tue, 20 Oct 2020)
EllapsedTime: 67.3 seconds
RetCode: 0
Status:  OK  
CheckDir: ASEB.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASEB.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ASEB_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/ASEB.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.33.0'
* 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-3.12-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-3.12-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-3.12-bioc/meat/ASEB.Rcheck/00check.log'
for details.



Installation output

ASEB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/ASEB_1.33.0.tar.gz && rm -rf ASEB.buildbin-libdir && mkdir ASEB.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASEB.buildbin-libdir ASEB_1.33.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ASEB_1.33.0.zip && rm ASEB_1.33.0.tar.gz ASEB_1.33.0.zip
###
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##############################################################################


  % 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  365k  100  365k    0     0  71.3M      0 --:--:-- --:--:-- --:--:-- 71.3M

install for i386

* installing *source* package 'ASEB' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.12-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-3.12-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.12-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-3.12-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-3.12-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.12-bioc/meat/ASEB.buildbin-libdir/ASEB/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ASEB' as ASEB_1.33.0.zip
* DONE (ASEB)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'ASEB' successfully unpacked and MD5 sums checked

Tests output


Example timings

ASEB.Rcheck/examples_i386/ASEB-Ex.timings

nameusersystemelapsed
SequenceInfo000
asebProteins0.850.010.87
asebSites0.610.030.65
drawEScurve0.650.020.69
drawStat0.800.000.82
readSequence0.310.000.32

ASEB.Rcheck/examples_x64/ASEB-Ex.timings

nameusersystemelapsed
SequenceInfo000
asebProteins0.670.030.72
asebSites0.480.000.55
drawEScurve0.520.000.53
drawStat0.670.000.70
readSequence0.310.000.31