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CHECK report for SynExtend on tokay2

This page was generated on 2021-01-20 12:34:55 -0500 (Wed, 20 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE SynExtend PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1787/1932HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SynExtend 1.3.2
Nicholas Cooley
Snapshot Date: 2021-01-19 14:40:23 -0500 (Tue, 19 Jan 2021)
URL: https://git.bioconductor.org/packages/SynExtend
Branch: master
Last Commit: fe12ba7
Last Changed Date: 2020-12-16 14:16:05 -0500 (Wed, 16 Dec 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] NA 
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SynExtend
Version: 1.3.2
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SynExtend.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SynExtend_1.3.2.tar.gz
StartedAt: 2021-01-20 09:50:51 -0500 (Wed, 20 Jan 2021)
EndedAt: 2021-01-20 10:00:39 -0500 (Wed, 20 Jan 2021)
EllapsedTime: 587.7 seconds
RetCode: 0
Status:  OK  
CheckDir: SynExtend.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SynExtend.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SynExtend_1.3.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/SynExtend.Rcheck'
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SynExtend/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SynExtend' version '1.3.2'
* package encoding: UTF-8
* 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 'SynExtend' 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
* 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 ... NOTE
Package in Depends field not imported from: 'igraph'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
PairSummaries     93.67   0.47   94.14
NucleotideOverlap 89.66   1.72   92.82
gffToDataFrame    21.91   0.00   21.90
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
NucleotideOverlap 117.08   0.44  117.78
PairSummaries     108.87   0.14  109.09
gffToDataFrame     21.72   0.00   21.72
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/SynExtend.Rcheck/00check.log'
for details.



Installation output

SynExtend.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.13/bioc/src/contrib/SynExtend_1.3.2.tar.gz && rm -rf SynExtend.buildbin-libdir && mkdir SynExtend.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SynExtend.buildbin-libdir SynExtend_1.3.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SynExtend_1.3.2.zip && rm SynExtend_1.3.2.tar.gz SynExtend_1.3.2.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 1550k  100 1550k    0     0  23.9M      0 --:--:-- --:--:-- --:--:-- 27.5M

install for i386

* installing *source* package 'SynExtend' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SynExtend'
    finding HTML links ... done
    ExactSelect                             html  
REDIRECT:topic	 ExactSelect -> ExactSelect.html [ SUCCESS ]
    GlobalSelect                            html  
REDIRECT:topic	 GlobalSelect -> GlobalSelect.html [ SUCCESS ]
    LinkedPairs-class                       html  
REDIRECT:topic	 LinkedPairs-class -> LinkedPairs-class.html [ SUCCESS ]
REDIRECT:topic	 [.LinkedPairs -> LinkedPairs-class.html [ SUCCESS ]
REDIRECT:topic	 print.LinkedPairs -> LinkedPairs-class.html [ SUCCESS ]
    LocalSelect                             html  
REDIRECT:topic	 LocalSelect -> LocalSelect.html [ SUCCESS ]
    NucleotideOverlap                       html  
REDIRECT:topic	 NucleotideOverlap -> NucleotideOverlap.html [ SUCCESS ]
    finding level-2 HTML links ... done

    PairSummaries                           html  
REDIRECT:topic	 PairSummaries -> PairSummaries.html [ SUCCESS ]
    gffToDataFrame                          html  
REDIRECT:topic	 gffToDataFrame -> gffToDataFrame.html [ SUCCESS ]
** 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 'SynExtend' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SynExtend' as SynExtend_1.3.2.zip
* DONE (SynExtend)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'SynExtend' successfully unpacked and MD5 sums checked

Tests output


Example timings

SynExtend.Rcheck/examples_i386/SynExtend-Ex.timings

nameusersystemelapsed
ExactSelect000
GlobalSelect0.020.000.02
LocalSelect0.000.020.01
NucleotideOverlap89.66 1.7292.82
PairSummaries93.67 0.4794.14
gffToDataFrame21.91 0.0021.90

SynExtend.Rcheck/examples_x64/SynExtend-Ex.timings

nameusersystemelapsed
ExactSelect000
GlobalSelect0.000.010.01
LocalSelect000
NucleotideOverlap117.08 0.44117.78
PairSummaries108.87 0.14109.09
gffToDataFrame21.72 0.0021.72