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This page was generated on 2021-11-26 15:05:02 -0500 (Fri, 26 Nov 2021).

CHECK results for RiboDiPA on nebbiolo2

To the developers/maintainers of the RiboDiPA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RiboDiPA.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 1605/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RiboDiPA 1.2.0  (landing page)
Ji-Ping Wang
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/RiboDiPA
git_branch: RELEASE_3_14
git_last_commit: 0b22a63
git_last_commit_date: 2021-10-26 13:06:31 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RiboDiPA
Version: 1.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:RiboDiPA.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings RiboDiPA_1.2.0.tar.gz
StartedAt: 2021-11-25 10:55:11 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 11:01:46 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 394.5 seconds
RetCode: 0
Status:   OK  
CheckDir: RiboDiPA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:RiboDiPA.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings RiboDiPA_1.2.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/RiboDiPA.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RiboDiPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RiboDiPA’ version ‘1.2.0’
* 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 ‘RiboDiPA’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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
PsiteMapping        20.118  0.323  78.861
diffPatternTestExon  6.221  0.160   6.381
data.binned          4.953  0.180   5.133
DataBinning          2.451  0.204  57.235
data.psite           0.691  0.070  21.288
* 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-3.14-bioc/meat/RiboDiPA.Rcheck/00check.log’
for details.



Installation output

RiboDiPA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL RiboDiPA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘RiboDiPA’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c centerCPP.cpp -o centerCPP.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o RiboDiPA.so RcppExports.o centerCPP.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RiboDiPA/00new/RiboDiPA/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (RiboDiPA)

Tests output


Example timings

RiboDiPA.Rcheck/RiboDiPA-Ex.timings

nameusersystemelapsed
DataBinning 2.451 0.20457.235
PsiteMapping20.118 0.32378.861
RiboDiPA000
data.binned4.9530.1805.133
data.psite 0.691 0.07021.288
diffPatternTest3.6910.1003.791
diffPatternTestExon6.2210.1606.381
normFactor0.0040.0000.004
plotTest0.8460.0080.854
plotTrack2.4480.0522.499
psitecal0.0010.0000.001
result.pst2.5030.0192.523