Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:11 -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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings metaSeq_1.32.0.tar.gz |
StartedAt: 2021-10-15 01:39:09 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 01:40:49 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 100.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metaSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings metaSeq_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/metaSeq.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * 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 ... OK * checking for portable file names ... OK * checking whether package 'metaSeq' can be installed ... OK * checking installed package size ... NOTE installed size is 6.3Mb 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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: 5 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/metaSeq.Rcheck/00check.log' for details.
metaSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/metaSeq_1.32.0.tar.gz && rm -rf metaSeq.buildbin-libdir && mkdir metaSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metaSeq.buildbin-libdir metaSeq_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL metaSeq_1.32.0.zip && rm metaSeq_1.32.0.tar.gz metaSeq_1.32.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 6245k 0 6535 0 0 80341 0 0:01:19 --:--:-- 0:01:19 80679 100 6245k 100 6245k 0 0 6598k 0 --:--:-- --:--:-- --:--:-- 6601k install for i386 * installing *source* package 'metaSeq' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'metaSeq' finding HTML links ... done Accelerate.NOISeq html BreastCancer html Fisher.test html Reset.Accelerate.NOISeq html Result.Meta html Stouffer.test html StudyA html meta.oneside.noiseq html meta.readData html metaSeq-package html other.oneside.pvalues html pvals html text.busca_unix html text.busca_win html text.n.menor_unix html text.n.menor_win html ** 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 install for x64 * installing *source* package 'metaSeq' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'metaSeq' as metaSeq_1.32.0.zip * DONE (metaSeq) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'metaSeq' successfully unpacked and MD5 sums checked
metaSeq.Rcheck/examples_i386/metaSeq-Ex.timings
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metaSeq.Rcheck/examples_x64/metaSeq-Ex.timings
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