Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-19 11:40 -0400 (Mon, 19 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 1200/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metaSeq 1.45.0 (landing page) Koki Tsuyuzaki
| nebbiolo2 | Linux (Ubuntu 22.04.3 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 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the metaSeq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metaSeq.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: metaSeq |
Version: 1.45.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metaSeq.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings metaSeq_1.45.0.tar.gz |
StartedAt: 2024-08-19 02:31:20 -0400 (Mon, 19 Aug 2024) |
EndedAt: 2024-08-19 02:32:38 -0400 (Mon, 19 Aug 2024) |
EllapsedTime: 77.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metaSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metaSeq.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings metaSeq_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/metaSeq.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'metaSeq/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'metaSeq' version '1.45.0' * 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 whether package 'metaSeq' can be installed ... OK * checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: data 5.7Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 ... NOTE Unexported objects imported by ':::' calls: 'NOISeq:::busca' 'NOISeq:::n.menor' See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: 'oneside.noiseq' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File 'metaSeq/R/Accelerate.NOISeq.R': assignInNamespace("busca", busca, ns = "NOISeq", envir = env) assignInNamespace("n.menor", nmenor, ns = "NOISeq", envir = env) assignInNamespace("busca", busca, ns = "NOISeq", envir = env) assignInNamespace("n.menor", nmenor, ns = "NOISeq", envir = env) File 'metaSeq/R/Reset.Accelerate.NOISeq.R': assignInNamespace("busca", original.busca, ns = "NOISeq", envir = env) assignInNamespace("n.menor", original.n.menor, ns = "NOISeq", envir = env) File 'metaSeq/R/oneside.noiseq.R': assignInNamespace("probdeg", custom.probdeg, ns = "NOISeq", envir = env) assignInNamespace("MD", custom.MD, ns = "NOISeq", envir = env) assignInNamespace("probdeg", original.probdeg, ns = "NOISeq", envir = env) assignInNamespace("MD", original.MD, ns = "NOISeq", envir = env) Accelerate.NOISeq: no visible global function definition for 'data' Accelerate.NOISeq: no visible binding for global variable 'text.n.menor_unix' Accelerate.NOISeq: no visible binding for global variable 'text.busca_unix' Accelerate.NOISeq: no visible global function definition for 'assignInNamespace' Accelerate.NOISeq: no visible binding for global variable 'busca' Accelerate.NOISeq: no visible binding for global variable 'nmenor' Accelerate.NOISeq: no visible binding for global variable 'text.n.menor_win' Accelerate.NOISeq: no visible binding for global variable 'text.busca_win' Reset.Accelerate.NOISeq: no visible global function definition for 'assignInNamespace' custom.MD: no visible global function definition for 'combn' custom.probdeg: no visible global function definition for 'na.omit' each.Fisher.ignore.test: no visible global function definition for 'pchisq' each.Fisher.test: no visible global function definition for 'pchisq' each.Stouffer.ignore.test: no visible global function definition for 'qnorm' each.Stouffer.ignore.test: no visible global function definition for 'pnorm' each.Stouffer.test: no visible global function definition for 'qnorm' each.Stouffer.test: no visible global function definition for 'pnorm' oneside.noiseq: no visible global function definition for 'assignInNamespace' original.MD: no visible global function definition for 'combn' original.probdeg: no visible global function definition for 'na.omit' original.probdeg: no visible binding for global variable 'n.menor' original.probdeg: no visible binding for global variable 'busca' Undefined global functions or variables: assignInNamespace busca combn data n.menor na.omit nmenor pchisq pnorm qnorm text.busca_unix text.busca_win text.n.menor_unix text.n.menor_win Consider adding importFrom("stats", "na.omit", "pchisq", "pnorm", "qnorm") importFrom("utils", "assignInNamespace", "combn", "data") 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 data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... NOTE The following files should probably not be installed: 'Fig1.jpeg', 'Fig2.png' Consider the use of a .Rinstignore file: see 'Writing R Extensions', or move the vignette sources from 'inst/doc' to 'vignettes'. * checking files in 'vignettes' ... OK * checking examples ... 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: 5 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/metaSeq.Rcheck/00check.log' for details.
metaSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL metaSeq ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'metaSeq' ... ** using staged installation ** R ** data ** 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 (metaSeq)
metaSeq.Rcheck/metaSeq-Ex.timings
name | user | system | elapsed | |
BreastCancer | 0.06 | 0.02 | 0.08 | |
Fisher.test | 1.23 | 0.03 | 1.27 | |
Result.Meta | 0.13 | 0.00 | 0.13 | |
Stouffer.test | 1.01 | 0.05 | 1.06 | |
StudyA | 0.09 | 0.03 | 0.13 | |
meta.oneside.noiseq | 1.35 | 0.02 | 1.36 | |
meta.readData | 1.22 | 0.09 | 1.31 | |
other.oneside.pvalues | 0 | 0 | 0 | |
pvals | 1.11 | 0.03 | 1.15 | |