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This page was generated on 2024-05-18 11:36:58 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 1083/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IVAS 2.24.0  (landing page)
Seonggyun Han
Snapshot Date: 2024-05-17 14:00:11 -0400 (Fri, 17 May 2024)
git_url: https://git.bioconductor.org/packages/IVAS
git_branch: RELEASE_3_19
git_last_commit: 9312880
git_last_commit_date: 2024-04-30 10:41:26 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for IVAS on palomino3


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: 2.24.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IVAS.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings IVAS_2.24.0.tar.gz
StartedAt: 2024-05-18 03:17:59 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 03:23:42 -0400 (Sat, 18 May 2024)
EllapsedTime: 343.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: IVAS.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IVAS.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings IVAS_2.24.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/IVAS.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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-3.19-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 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    13.22   0.27   13.48
saveBplot     12.59   0.16   12.84
sQTLsFinder   12.28   0.10   12.37
RatioFromFPKM  8.09   0.10    8.19
CalSigSNP      5.83   0.06    5.91
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/IVAS.Rcheck/00check.log'
for details.


Installation output

IVAS.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL IVAS
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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-class13.22 0.2713.48
CalSigSNP5.830.065.91
RatioFromFPKM8.090.108.19
Splicingfinder4.080.074.16
chrseparate0.090.000.09
findAlternative0.630.050.67
findOversnp0.650.030.69
sQTLsFinder12.28 0.1012.37
sampleexp000
samplesnp0.000.010.01
samplesnplocus0.010.000.02
saveBplot12.59 0.1612.84