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This page was generated on 2023-10-16 11:37:27 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1715/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RiboDiPA 1.8.0  (landing page)
Ji-Ping Wang
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/RiboDiPA
git_branch: RELEASE_3_17
git_last_commit: 49cff9b
git_last_commit_date: 2023-04-25 11:26:15 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for RiboDiPA on merida1


To the developers/maintainers of the RiboDiPA package:
- 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 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: RiboDiPA
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RiboDiPA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RiboDiPA_1.8.0.tar.gz
StartedAt: 2023-10-16 06:05:04 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 06:30:49 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 1544.7 seconds
RetCode: 0
Status:   OK  
CheckDir: RiboDiPA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RiboDiPA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RiboDiPA_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/RiboDiPA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RiboDiPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RiboDiPA’ version ‘1.8.0’
* 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
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
binTrack            39.723  1.039  70.289
PsiteMapping        39.487  0.685 222.633
diffPatternTestExon  5.839  0.113  10.659
diffPatternTest      4.603  0.125   7.903
data.binned          3.843  0.070   5.815
result.pst           3.157  0.051   5.459
DataBinning          2.492  0.349 392.598
data.psite           0.672  0.105 181.943
* 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: OK


Installation output

RiboDiPA.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RiboDiPA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘RiboDiPA’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c centerCPP.cpp -o centerCPP.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o RiboDiPA.so RcppExports.o centerCPP.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 2.492 0.349392.598
PsiteMapping 39.487 0.685222.633
RiboDiPA0.0000.0000.009
binTrack39.723 1.03970.289
bpTrack0.7040.0271.159
data.binned3.8430.0705.815
data.psite 0.672 0.105181.943
diffPatternTest4.6030.1257.903
diffPatternTestExon 5.839 0.11310.659
exonTrack0.0940.0050.154
normFactor0.0060.0020.010
plotTest1.3310.0282.200
plotTrack2.4720.0644.792
psitecal0.0000.0010.000
result.exon0.1100.0040.218
result.pst3.1570.0515.459