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This page was generated on 2021-10-15 15:05:47 -0400 (Fri, 15 Oct 2021).

CHECK results for ORFhunteR on nebbiolo1

To the developers/maintainers of the ORFhunteR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ORFhunteR.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 1322/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFhunteR 1.0.0  (landing page)
Vasily V. Grinev
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/ORFhunteR
git_branch: RELEASE_3_13
git_last_commit: aacc377
git_last_commit_date: 2021-05-19 12:59:25 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ORFhunteR
Version: 1.0.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ORFhunteR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ORFhunteR_1.0.0.tar.gz
StartedAt: 2021-10-14 10:54:00 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:59:28 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 328.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ORFhunteR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ORFhunteR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ORFhunteR_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ORFhunteR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ORFhunteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ORFhunteR’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘ORFhunteR’ can be installed ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
annotateORFs 7.074  0.948 110.353
findPTCs     1.288  0.141  32.852
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/ORFhunteR.Rcheck/00check.log’
for details.



Installation output

ORFhunteR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ORFhunteR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘ORFhunteR’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getBaoMetrics.cpp -o getBaoMetrics.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getCorrelationFactors.cpp -o getCorrelationFactors.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getPatternCount_V.cpp -o getPatternCount_V.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o ORFhunteR.so RcppExports.o getBaoMetrics.o getCorrelationFactors.o getPatternCount_V.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-ORFhunteR/00new/ORFhunteR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ORFhunteR)

Tests output


Example timings

ORFhunteR.Rcheck/ORFhunteR-Ex.timings

nameusersystemelapsed
annotateORFs 7.074 0.948110.353
classifyORFsCandidates0.0000.0000.002
codonStartStop0.0220.0200.043
findORFs0.0160.0000.016
findPTCs 1.288 0.14132.852
getSeqORFs0.0110.0140.097
loadTrExper0.0100.0010.010
predictORF0.0010.0000.001
translateORFs0.2080.0470.447
vectorizeORFs0.0380.0120.060