Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 404/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CODEX 1.38.0 (landing page) Yuchao Jiang
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the CODEX package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CODEX.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: CODEX |
Version: 1.38.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CODEX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CODEX_1.38.0.tar.gz |
StartedAt: 2024-12-20 15:14:29 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 15:19:36 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 307.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CODEX.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CODEX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CODEX_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CODEX.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CODEX/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CODEX’ version ‘1.38.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'Rsamtools', 'GenomeInfoDb', 'BSgenome.Hsapiens.UCSC.hg19', 'IRanges', 'Biostrings', 'S4Vectors' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘CODEX’ 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 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 ... NOTE choiceofK: no visible global function definition for ‘pdf’ choiceofK: no visible global function definition for ‘par’ choiceofK: no visible global function definition for ‘dev.off’ getbambed: no visible global function definition for ‘read.table’ normalize : <anonymous>: no visible global function definition for ‘smooth.spline’ normalize : <anonymous>: no visible global function definition for ‘predict’ normalize: no visible global function definition for ‘glm’ normalize: no visible binding for global variable ‘poisson’ normalize: no visible global function definition for ‘lm’ normalize2 : <anonymous>: no visible global function definition for ‘smooth.spline’ normalize2 : <anonymous>: no visible global function definition for ‘predict’ normalize2: no visible global function definition for ‘glm’ normalize2: no visible binding for global variable ‘poisson’ normalize2: no visible global function definition for ‘lm’ Undefined global functions or variables: dev.off glm lm par pdf poisson predict read.table smooth.spline Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "par") importFrom("stats", "glm", "lm", "poisson", "predict", "smooth.spline") importFrom("utils", "read.table") to your NAMESPACE file. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed normalize 18.653 0.630 20.138 normalize2 16.019 0.416 16.938 getcoverage 11.952 0.481 12.838 * 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/CODEX.Rcheck/00check.log’ for details.
CODEX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CODEX ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘CODEX’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (CODEX)
CODEX.Rcheck/CODEX-Ex.timings
name | user | system | elapsed | |
bambedObjDemo | 0.000 | 0.001 | 0.001 | |
choiceofK | 0.026 | 0.004 | 0.030 | |
coverageObjDemo | 0.000 | 0.001 | 0.000 | |
gcDemo | 0.001 | 0.000 | 0.002 | |
getbambed | 0.026 | 0.004 | 0.034 | |
getcoverage | 11.952 | 0.481 | 12.838 | |
getgc | 1.657 | 0.054 | 1.816 | |
getmapp | 0.044 | 0.005 | 0.069 | |
mappDemo | 0 | 0 | 0 | |
mapp_ref | 0.013 | 0.001 | 0.017 | |
mappability | 0.001 | 0.001 | 0.001 | |
normObjDemo | 0.000 | 0.000 | 0.002 | |
normalize | 18.653 | 0.630 | 20.138 | |
normalize2 | 16.019 | 0.416 | 16.938 | |
qc | 0.021 | 0.001 | 0.022 | |
qcObjDemo | 0.000 | 0.000 | 0.001 | |
segment | 0.161 | 0.031 | 0.195 | |