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This page was generated on 2022-10-19 13:21:42 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 palomino3


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? 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 997/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IVAS 2.16.0  (landing page)
Seonggyun Han
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/IVAS
git_branch: RELEASE_3_15
git_last_commit: efada2b
git_last_commit_date: 2022-04-26 11:23:37 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: IVAS
Version: 2.16.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IVAS.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings IVAS_2.16.0.tar.gz
StartedAt: 2022-10-19 01:17:20 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 01:22:29 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 309.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: IVAS.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IVAS.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings IVAS_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/IVAS.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'IVAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IVAS' version '2.16.0'
* 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 'F:/biocbuild/bbs-3.15-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
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
ASdb-class    10.49   0.20   10.69
saveBplot     10.26   0.11   10.43
sQTLsFinder    9.81   0.12    9.93
RatioFromFPKM  5.57   0.03    5.60
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/IVAS.Rcheck/00check.log'
for details.



Installation output

IVAS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL IVAS
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* 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
** 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
* DONE (IVAS)

Tests output


Example timings

IVAS.Rcheck/IVAS-Ex.timings

nameusersystemelapsed
ASdb-class10.49 0.2010.69
CalSigSNP3.480.023.50
RatioFromFPKM5.570.035.60
Splicingfinder3.050.023.07
chrseparate0.090.010.11
findAlternative0.550.030.57
findOversnp0.660.020.68
sQTLsFinder9.810.129.93
sampleexp0.000.020.02
samplesnp000
samplesnplocus0.020.000.02
saveBplot10.26 0.1110.43