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This page was generated on 2022-01-19 13:06:48 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for IVAS on tokay2


To the developers/maintainers of the IVAS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IVAS.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 972/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IVAS 2.14.0  (landing page)
Seonggyun Han
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/IVAS
git_branch: RELEASE_3_14
git_last_commit: cb2ad75
git_last_commit_date: 2021-10-26 12:18:38 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: IVAS
Version: 2.14.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IVAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings IVAS_2.14.0.tar.gz
StartedAt: 2022-01-18 21:37:09 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 21:43:52 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 403.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: IVAS.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IVAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings IVAS_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/IVAS.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IVAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IVAS' version '2.14.0'
* 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 'IVAS' can be installed ... WARNING
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/IVAS.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
ASdb-class  10.46   0.57   11.05
saveBplot    9.73   0.05    9.89
sQTLsFinder  9.23   0.06    9.30
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
saveBplot     11.25   0.11   11.47
ASdb-class    11.03   0.11   11.14
sQTLsFinder   10.73   0.07   10.80
RatioFromFPKM  5.16   0.01    5.17
* 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/IVAS.Rcheck/00check.log'
for details.



Installation output

IVAS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/IVAS_2.14.0.tar.gz && rm -rf IVAS.buildbin-libdir && mkdir IVAS.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IVAS.buildbin-libdir IVAS_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL IVAS_2.14.0.zip && rm IVAS_2.14.0.tar.gz IVAS_2.14.0.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
 20 77391   20 16138    0     0   192k      0 --:--:-- --:--:-- --:--:--  192k
100 77391  100 77391    0     0   696k      0 --:--:-- --:--:-- --:--:--  693k

install for i386

* installing *source* package 'IVAS' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: next used in wrong context: no loop is visible 
** help
*** installing help indices
  converting help for package 'IVAS'
    finding HTML links ... done
    ASdb-class                              html  
    CalSigSNP                               html  
    IVAS-deprecated                         html  
    IVAS-package                            html  
    MsqtlFinder                             html  
    RatioFromFPKM                           html  
    Splicingfinder                          html  
    calSignificant                          html  
    chrseparate                             html  
    finding level-2 HTML links ... done

    findAlternative                         html  
    findOversnp                             html  
    sQTLsFinder                             html  
    sampleexp                               html  
    samplesnp                               html  
    samplesnplocus                          html  
    saveBplot                               html  
    sqtlfinder                              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 'IVAS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IVAS' as IVAS_2.14.0.zip
* DONE (IVAS)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'IVAS' successfully unpacked and MD5 sums checked

Tests output


Example timings

IVAS.Rcheck/examples_i386/IVAS-Ex.timings

nameusersystemelapsed
ASdb-class10.46 0.5711.05
CalSigSNP3.670.143.81
RatioFromFPKM4.750.034.78
Splicingfinder2.930.012.95
chrseparate0.070.040.10
findAlternative0.600.000.61
findOversnp0.630.000.62
sQTLsFinder9.230.069.30
sampleexp000
samplesnp0.020.000.02
samplesnplocus000
saveBplot9.730.059.89

IVAS.Rcheck/examples_x64/IVAS-Ex.timings

nameusersystemelapsed
ASdb-class11.03 0.1111.14
CalSigSNP4.060.034.09
RatioFromFPKM5.160.015.17
Splicingfinder3.120.073.19
chrseparate0.100.010.11
findAlternative0.610.000.61
findOversnp0.640.000.64
sQTLsFinder10.73 0.0710.80
sampleexp0.000.010.01
samplesnp0.000.020.02
samplesnplocus000
saveBplot11.25 0.1111.47