Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:42 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the metaSeq package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1092/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metaSeq 1.32.0 (landing page) Koki Tsuyuzaki
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: metaSeq |
Version: 1.32.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metaSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metaSeq_1.32.0.tar.gz |
StartedAt: 2021-10-14 20:53:27 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:54:59 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 91.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metaSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metaSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metaSeq_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/metaSeq.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘metaSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘metaSeq’ version ‘1.32.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... 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 5.8Mb * 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 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 ... 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 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: 6 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/metaSeq.Rcheck/00check.log’ for details.
metaSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL metaSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 | 0.121 | 0.011 | 0.133 | |
Fisher.test | 2.016 | 0.030 | 2.047 | |
Result.Meta | 0.209 | 0.004 | 0.213 | |
Stouffer.test | 2.280 | 0.029 | 2.311 | |
StudyA | 0.194 | 0.006 | 0.199 | |
meta.oneside.noiseq | 1.959 | 0.014 | 1.974 | |
meta.readData | 2.222 | 0.014 | 2.237 | |
other.oneside.pvalues | 0.022 | 0.001 | 0.023 | |
pvals | 1.740 | 0.028 | 1.770 | |