Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:05:40 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the myvariant package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/myvariant.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1260/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
myvariant 1.24.0 (landing page) Adam Mark, Chunlei Wu
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: myvariant |
Version: 1.24.0 |
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:myvariant.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings myvariant_1.24.0.tar.gz |
StartedAt: 2022-04-12 08:25:28 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 08:29:26 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 238.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: myvariant.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:myvariant.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings myvariant_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/myvariant.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘myvariant/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘myvariant’ version ‘1.24.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘myvariant’ can be installed ... OK * checking installed package size ... OK * 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 package 'methods' is used but not declared * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .convertColumn4csv: no visible binding for global variable ‘is’ .df2DF: no visible binding for global variable ‘as’ .getIndels: no visible binding for global variable ‘REF’ .getIndels: no visible binding for global variable ‘ALT’ .unnest.df : <anonymous>: no visible global function definition for ‘is’ .unnest.df : <anonymous>: no visible global function definition for ‘setNames’ MyVariant: no visible global function definition for ‘new’ formatHgvs: no visible global function definition for ‘seqlevelsStyle<-’ validMyVariantObject: no visible global function definition for ‘slot’ .request.get,MyVariant: no visible global function definition for ‘capture.output’ .request.post,MyVariant: no visible global function definition for ‘capture.output’ Undefined global functions or variables: ALT REF as capture.output is new seqlevelsStyle<- setNames slot Consider adding importFrom("methods", "as", "is", "new", "slot") importFrom("stats", "setNames") importFrom("utils", "capture.output") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/myvariant.Rcheck/00check.log’ for details.
myvariant.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL myvariant ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘myvariant’ ... ** using staged installation ** R ** 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 (myvariant)
myvariant.Rcheck/myvariant-Ex.timings
name | user | system | elapsed | |
MyVariant-class | 0.002 | 0.000 | 0.001 | |
MyVariant | 0.002 | 0.000 | 0.002 | |
formatHgvs | 0.821 | 0.060 | 0.882 | |
formatSingleHgvs | 0.001 | 0.000 | 0.001 | |
getVariant | 0.043 | 0.040 | 0.499 | |
getVariants | 0.075 | 0.008 | 0.479 | |
metadata | 0.018 | 0.004 | 0.111 | |
queryVariant | 0.111 | 0.016 | 0.850 | |
queryVariants | 0 | 0 | 0 | |