Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1433/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
nuCpos 1.24.0 (landing page) Hiroaki Kato
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the nuCpos package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/nuCpos.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: nuCpos |
Version: 1.24.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nuCpos.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nuCpos_1.24.0.tar.gz |
StartedAt: 2024-11-20 00:42:15 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 00:46:33 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 258.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: nuCpos.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nuCpos.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nuCpos_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/nuCpos.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘nuCpos/DESCRIPTION’ ... OK * this is package ‘nuCpos’ version ‘1.24.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘nuCpos’ 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 R/sysdata.rda ... NOTE Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress sysdata.rda 2.2Mb 998Kb xz * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test_HBA.R’ Running ‘test_localHBA.R’ OK * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/nuCpos.Rcheck/00check.log’ for details.
nuCpos.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL nuCpos ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘nuCpos’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (nuCpos)
nuCpos.Rcheck/tests/test_HBA.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > test_HBA <- function(){ + load(system.file("extdata","inseq.RData",package="nuCpos")) + load(system.file("extdata","INSEQ_DNAString.RData",package="nuCpos")) + inseq.N <- gsub(pattern = "A", replacement = "N", inseq) + mm.HBA <- -5.108546 + sc.HBA <- -2.460025 + sp.HBA <- -2.627370 + expect_equal(unname(HBA(inseq, species = "mm", silent = TRUE)), + mm.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(inseq, species = "sc", silent = TRUE)), + sc.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(inseq, species = "sp", silent = TRUE)), + sp.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(INSEQ, species = "mm", silent = TRUE)), + mm.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(INSEQ, species = "sc", silent = TRUE)), + sc.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(INSEQ, species = "sp", silent = TRUE)), + sp.HBA, tolerance = 1.0e-6) + expect_true(is.na(HBA("AAA", species = "mm", silent = TRUE))) + expect_true(is.na(HBA(123, species = "mm", silent = TRUE))) + expect_true(is.na(HBA(inseq.N, species = "mm", silent = TRUE))) + } > > proc.time() user system elapsed 0.157 0.060 0.220
nuCpos.Rcheck/tests/test_localHBA.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > test_localHBA <- function(){ + load(system.file("extdata","inseq.RData",package="nuCpos")) + load(system.file("extdata","INSEQ_DNAString.RData",package="nuCpos")) + inseq.N <- gsub(pattern = "A", replacement = "N", inseq) + mm.lHBA <- c(-1.26144039, -1.60878614, 0.04168163, + 0.67028283, 0.64609413, -2.04965343, -2.87359702, + -0.23010702, -0.45807823, -0.46043330, -0.45175477, + 0.02487367, -0.30991794) + sc.lHBA <- c(-1.56140949, -1.62502354, 0.48885990, + 2.37615568, 2.90458625, -1.35195919, -3.13228907, + -0.32208031, 0.27650871, 0.01922002, 0.49787625, + -0.17151500, -1.27186158) + sp.lHBA <- c(-1.566757163, -2.249651890, 1.188983606, + 1.808008192, 2.304915648, -0.290338951, -1.741081053, + -0.093952092, 0.119058916, -1.335654721, -0.001721381, + 0.244317796, -0.968842314) + expect_equal(unname(localHBA(inseq, species = "mm", silent = TRUE)), + mm.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(inseq, species = "sc", silent = TRUE)), + sc.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(inseq, species = "sp", silent = TRUE)), + sp.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(INSEQ, species = "mm", silent = TRUE)), + mm.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(INSEQ, species = "sc", silent = TRUE)), + sc.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(INSEQ, species = "sp", silent = TRUE)), + sp.lHBA, tolerance = 1.0e-6) + expect_true(is.na(localHBA("AAA", species = "mm", silent = TRUE))) + expect_true(is.na(localHBA(123, species = "mm", silent = TRUE))) + expect_true(is.na(localHBA(inseq.N, species = "mm", silent = TRUE))) + } > > proc.time() user system elapsed 0.160 0.061 0.227
nuCpos.Rcheck/nuCpos-Ex.timings
name | user | system | elapsed | |
HBA | 1.968 | 0.104 | 2.099 | |
localHBA | 0.015 | 0.002 | 0.017 | |
nuCpos-package | 0.006 | 0.001 | 0.006 | |