Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:57 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the vtpnet package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/vtpnet.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 2012/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
vtpnet 0.32.0 (landing page) VJ Carey
| 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: vtpnet |
Version: 0.32.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:vtpnet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings vtpnet_0.32.0.tar.gz |
StartedAt: 2021-10-15 01:10:54 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 01:17:19 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 384.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: vtpnet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:vtpnet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings vtpnet_0.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/vtpnet.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 ‘vtpnet/DESCRIPTION’ ... OK * this is package ‘vtpnet’ version ‘0.32.0’ * 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 ‘vtpnet’ can be installed ... OK * checking installed package size ... NOTE installed size is 20.1Mb sub-directories of 1Mb or more: data 20.0Mb * 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 'library' or 'require' calls to packages already attached by Depends: ‘doParallel’ ‘foreach’ Please remove these calls from your code. 'library' or 'require' call to ‘MotifDb’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘doParallel’ ‘foreach’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE rng2facHits: warning in dir(patt = "rda$"): partial argument match of 'patt' to 'pattern' runfimo: warning in dir(patt = "_out"): partial argument match of 'patt' to 'pattern' filterGWASbyMap: no visible global function definition for ‘as’ getMtags: no visible global function definition for ‘is’ getOneHits: no visible global function definition for ‘queryHits’ getOneHits: no visible global function definition for ‘subjectHits’ getOneHits: no visible global function definition for ‘metadata’ getOneHits: no visible global function definition for ‘metadata<-’ gwMatchPWM: no visible binding for global variable ‘Hsapiens’ gwMatchPWM: no visible global function definition for ‘is’ gwMatchPWM: no visible global function definition for ‘%dopar%’ gwMatchPWM: no visible global function definition for ‘foreach’ gwMatchPWM: no visible binding for global variable ‘i’ gwMatchPWM: no visible global function definition for ‘matchPWM’ gwMatchPWM: no visible global function definition for ‘PWMscoreStartingAt’ gwMatchPWM: no visible global function definition for ‘subject’ gwMatchPWM: no visible global function definition for ‘as’ rng2facHits: no visible global function definition for ‘as’ rng2facHits: no visible global function definition for ‘registerDoParallel’ rng2facHits: no visible global function definition for ‘%dopar%’ rng2facHits: no visible global function definition for ‘foreach’ rng2facHits: no visible binding for global variable ‘i’ runfimo: no visible global function definition for ‘%dopar%’ runfimo: no visible global function definition for ‘foreach’ runfimo: no visible binding for global variable ‘i’ setupGWPM: no visible global function definition for ‘registerDoParallel’ Undefined global functions or variables: %dopar% Hsapiens PWMscoreStartingAt as foreach i is matchPWM metadata metadata<- queryHits registerDoParallel subject subjectHits Consider adding importFrom("methods", "as", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: vtpnet-package.Rd:48-50: Dropping empty section \references prepare_Rd: vtpnet-package.Rd:53-54: Dropping empty section \seealso prepare_Rd: vtpnet-package.Rd:55-56: Dropping empty section \examples * 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 files in ‘vignettes’ ... OK * checking examples ... NONE * 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/vtpnet.Rcheck/00check.log’ for details.
vtpnet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL vtpnet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘vtpnet’ ... ** using staged installation ** R ** data ** 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 (vtpnet)