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CHECK report for ASEB on malbec1

This page was generated on 2021-05-06 12:26:54 -0400 (Thu, 06 May 2021).

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 91/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASEB 1.34.0  (landing page)
Likun Wang
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ASEB
Branch: RELEASE_3_12
Last Commit: 21baac1
Last Changed Date: 2020-10-27 10:44:11 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: ASEB
Version: 1.34.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ASEB.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ASEB_1.34.0.tar.gz
StartedAt: 2021-05-05 23:05:52 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:06:17 -0400 (Wed, 05 May 2021)
EllapsedTime: 25.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ASEB.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ASEB.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ASEB_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ASEB.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ASEB/DESCRIPTION’ ... OK
* this is package ‘ASEB’ 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 ‘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
* 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 is not available
File ‘/home/biocbuild/bbs-3.12-bioc/R/library/ASEB/libs/ASEB.so’:
  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 ... 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/ASEB.Rcheck/00check.log’
for details.



Installation output

ASEB.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ASEB
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ASEB’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c asebC.cpp -o asebC.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o ASEB.so asebC.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-ASEB/00new/ASEB/libs
** R
** 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 (ASEB)

Tests output


Example timings

ASEB.Rcheck/ASEB-Ex.timings

nameusersystemelapsed
SequenceInfo0.0000.0000.001
asebProteins1.8040.0041.871
asebSites1.4160.0081.422
drawEScurve1.4880.0041.495
drawStat1.7520.0081.760
readSequence0.880.000.88