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This page was generated on 2024-05-15 13:46:35 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 1047/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IVAS 2.25.0  (landing page)
Seonggyun Han
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for IVAS on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: IVAS
Version: 2.24.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:IVAS.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings IVAS_2.24.0.tar.gz
StartedAt: 2024-05-09 08:46:16 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 08:52:46 -0000 (Thu, 09 May 2024)
EllapsedTime: 389.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: IVAS.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:IVAS.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings IVAS_2.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/IVAS.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IVAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IVAS’ version ‘2.24.0’
* 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-3.19-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      16.416  0.143  16.579
ASdb-class     15.368  0.384  15.781
sQTLsFinder    14.670  0.116  14.810
RatioFromFPKM   8.328  0.140   8.483
CalSigSNP       6.810  0.135   6.957
Splicingfinder  5.080  0.048   5.136
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/IVAS.Rcheck/00check.log’
for details.


Installation output

IVAS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL IVAS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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-class15.368 0.38415.781
CalSigSNP6.8100.1356.957
RatioFromFPKM8.3280.1408.483
Splicingfinder5.0800.0485.136
chrseparate0.1290.0080.137
findAlternative0.7850.0240.810
findOversnp0.8370.0200.858
sQTLsFinder14.670 0.11614.810
sampleexp0.0000.0030.004
samplesnp0.0020.0000.003
samplesnplocus0.0010.0000.002
saveBplot16.416 0.14316.579