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CHECK report for ASpediaFI on tokay1

This page was generated on 2020-08-09 12:18:28 -0400 (Sun, 09 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ASpediaFI PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 88/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpediaFI 1.3.0
Doyeong Yu
Snapshot Date: 2020-08-08 14:51:01 -0400 (Sat, 08 Aug 2020)
URL: https://git.bioconductor.org/packages/ASpediaFI
Branch: master
Last Commit: 1255415
Last Changed Date: 2020-04-27 15:31:42 -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
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ASpediaFI
Version: 1.3.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASpediaFI.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ASpediaFI_1.3.0.tar.gz
StartedAt: 2020-08-09 05:41:11 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 05:51:40 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 628.5 seconds
RetCode: 0
Status:  OK  
CheckDir: ASpediaFI.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASpediaFI.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ASpediaFI_1.3.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ASpediaFI.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ASpediaFI/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ASpediaFI' version '1.3.0'
* 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 'ASpediaFI' 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 ... OK
* 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 R/sysdata.rda ... 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
annotateASevents 49.49   0.66   50.68
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
annotateASevents 48.61   0.25   48.88
* 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: OK


Installation output

ASpediaFI.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ASpediaFI_1.3.0.tar.gz && rm -rf ASpediaFI.buildbin-libdir && mkdir ASpediaFI.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASpediaFI.buildbin-libdir ASpediaFI_1.3.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ASpediaFI_1.3.0.zip && rm ASpediaFI_1.3.0.tar.gz ASpediaFI_1.3.0.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 2089k  100 2089k    0     0  20.4M      0 --:--:-- --:--:-- --:--:-- 21.2M

install for i386

* installing *source* package 'ASpediaFI' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'as.table' in package 'ASpediaFI'
** help
*** installing help indices
  converting help for package 'ASpediaFI'
    finding HTML links ... done
    ASpediaFI-accessor                      html  
    ASpediaFI-class                         html  
    GSE114922.fpkm                          html  
    GSE114922.psi                           html  
    analyzeFI                               html  
    annotateASevents                        html  
    exportNetwork                           html  
    quantifyPSI                             html  
    visualize                               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 'ASpediaFI' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ASpediaFI' as ASpediaFI_1.3.0.zip
* DONE (ASpediaFI)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ASpediaFI' successfully unpacked and MD5 sums checked

Tests output


Example timings

ASpediaFI.Rcheck/examples_i386/ASpediaFI-Ex.timings

nameusersystemelapsed
ASpediaFI-accessor0.190.000.19
ASpediaFI-class0.040.000.05
GSE114922.fpkm0.030.040.06
GSE114922.psi0.130.000.12
analyzeFI0.360.040.41
annotateASevents49.49 0.6650.68
exportNetwork0.010.000.01
quantifyPSI0.020.000.02
visualize000

ASpediaFI.Rcheck/examples_x64/ASpediaFI-Ex.timings

nameusersystemelapsed
ASpediaFI-accessor0.130.000.13
ASpediaFI-class0.040.000.05
GSE114922.fpkm0.030.000.03
GSE114922.psi0.080.020.10
analyzeFI0.220.040.26
annotateASevents48.61 0.2548.88
exportNetwork0.040.000.06
quantifyPSI0.020.000.02
visualize000