Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:06 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 1762/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RiboDiPA 1.17.1 (landing page) Ji-Ping Wang
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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. |
Package: RiboDiPA |
Version: 1.17.1 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RiboDiPA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RiboDiPA_1.17.1.tar.gz |
StartedAt: 2025-08-09 01:58:29 -0400 (Sat, 09 Aug 2025) |
EndedAt: 2025-08-09 02:16:26 -0400 (Sat, 09 Aug 2025) |
EllapsedTime: 1077.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RiboDiPA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RiboDiPA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RiboDiPA_1.17.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RiboDiPA.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘RiboDiPA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RiboDiPA’ version ‘1.17.1’ * 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 ... NOTE .pMappingChr: no visible global function definition for ‘pcoverageByTranscript’ Undefined global functions or variables: pcoverageByTranscript * 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 PsiteMapping 30.557 1.177 121.197 binTrack 29.733 0.939 30.672 diffPatternTestExon 5.841 0.243 6.085 DataBinning 2.865 0.460 194.967 data.psite 0.639 0.092 81.692 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/RiboDiPA.Rcheck/00check.log’ for details.
RiboDiPA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL RiboDiPA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘RiboDiPA’ ... ** this is package ‘RiboDiPA’ version ‘1.17.1’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c centerCPP.cpp -o centerCPP.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o RiboDiPA.so RcppExports.o centerCPP.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-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)
RiboDiPA.Rcheck/RiboDiPA-Ex.timings
name | user | system | elapsed | |
DataBinning | 2.865 | 0.460 | 194.967 | |
PsiteMapping | 30.557 | 1.177 | 121.197 | |
RiboDiPA | 0 | 0 | 0 | |
binTrack | 29.733 | 0.939 | 30.672 | |
bpTrack | 0.548 | 0.063 | 0.610 | |
data.binned | 3.021 | 0.060 | 3.081 | |
data.psite | 0.639 | 0.092 | 81.692 | |
diffPatternTest | 2.781 | 0.030 | 2.812 | |
diffPatternTestExon | 5.841 | 0.243 | 6.085 | |
exonTrack | 0.062 | 0.000 | 0.062 | |
normFactor | 0.005 | 0.000 | 0.005 | |
plotTest | 0.980 | 0.009 | 0.989 | |
plotTrack | 1.435 | 0.028 | 1.464 | |
psitecal | 0 | 0 | 0 | |
result.exon | 0.075 | 0.001 | 0.077 | |
result.pst | 1.544 | 0.009 | 1.552 | |