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This page was generated on 2024-06-14 12:02 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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

Package 1051/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IVAS 2.25.0  (landing page)
Seonggyun Han
Snapshot Date: 2024-06-13 14:00 -0400 (Thu, 13 Jun 2024)
git_url: https://git.bioconductor.org/packages/IVAS
git_branch: devel
git_last_commit: 6650399
git_last_commit_date: 2024-04-30 10:41:26 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for IVAS on nebbiolo2

To the developers/maintainers of the IVAS package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: IVAS
Version: 2.25.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:IVAS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings IVAS_2.25.0.tar.gz
StartedAt: 2024-06-14 00:48:57 -0400 (Fri, 14 Jun 2024)
EndedAt: 2024-06-14 00:54:25 -0400 (Fri, 14 Jun 2024)
EllapsedTime: 327.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: IVAS.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:IVAS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings IVAS_2.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/IVAS.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘IVAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IVAS’ version ‘2.25.0’
* 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 ‘IVAS’ can be installed ... WARNING
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/home/biocbuild/bbs-3.20-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 code 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 loading without being on the library search path ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
saveBplot     11.440  0.148  11.567
ASdb-class    10.850  0.268  11.118
sQTLsFinder   10.012  0.120  10.132
RatioFromFPKM  5.811  0.104   5.916
CalSigSNP      4.915  0.140   5.054
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/IVAS.Rcheck/00check.log’
for details.


Installation output

IVAS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL IVAS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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-class10.850 0.26811.118
CalSigSNP4.9150.1405.054
RatioFromFPKM5.8110.1045.916
Splicingfinder3.4640.0643.528
chrseparate0.0810.0080.089
findAlternative0.4940.0200.514
findOversnp0.4960.0040.500
sQTLsFinder10.012 0.12010.132
sampleexp0.0040.0000.003
samplesnp0.0020.0000.002
samplesnplocus0.0010.0000.001
saveBplot11.440 0.14811.567