Back to Build/check report for BioC 3.17 experimental data |
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This page was generated on 2023-10-12 14:51:35 -0400 (Thu, 12 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
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 219/421 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
MAQCsubset 1.38.0 (landing page) VJ Carey
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | |||||||
To the developers/maintainers of the MAQCsubset package: - 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: MAQCsubset |
Version: 1.38.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MAQCsubset.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MAQCsubset_1.38.0.tar.gz |
StartedAt: 2023-10-12 11:36:33 -0400 (Thu, 12 Oct 2023) |
EndedAt: 2023-10-12 11:42:07 -0400 (Thu, 12 Oct 2023) |
EllapsedTime: 334.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MAQCsubset.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MAQCsubset.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MAQCsubset_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-data-experiment/meat/MAQCsubset.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘MAQCsubset/DESCRIPTION’ ... OK * this is package ‘MAQCsubset’ version ‘1.38.0’ * 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 ‘MAQCsubset’ can be installed ... OK * checking installed package size ... NOTE installed size is 64.6Mb sub-directories of 1Mb or more: data 64.2Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Loading required package: methods Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ 'library' or 'require' call to ‘genefilter’ 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: ‘Biobase’ ‘affy’ ‘lumi’ ‘methods’ 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 ... WARNING Loading required package: methods Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... NOTE Loading required package: methods Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE proboscis: no visible global function definition for ‘rowttests’ proboscis: no visible global function definition for ‘exprs’ Undefined global functions or variables: exprs rowttests * checking Rd files ... NOTE checkRd: (-1) gehMAQCsubDef.Rd:14: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ checkRd: (-1) gehMAQCsubDef.Rd:15: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ checkRd: (-1) gehMAQCsubDef.Rd:16: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ * 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 ... NOTE Loading required package: methods Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 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 ... ‘maqcNotes.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 6 NOTEs See ‘/home/biocbuild/bbs-3.17-data-experiment/meat/MAQCsubset.Rcheck/00check.log’ for details.
MAQCsubset.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MAQCsubset ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘MAQCsubset’ ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package can be loaded from final location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package keeps a record of temporary installation path * DONE (MAQCsubset)
MAQCsubset.Rcheck/MAQCsubset-Ex.timings
name | user | system | elapsed | |
MAQCsubset | 1.668 | 0.052 | 1.719 | |
gehMAQCsubDef | 0.357 | 0.004 | 0.361 | |
gnfCerebHi | 0.005 | 0.000 | 0.006 | |
proboStruct-class | 1.082 | 0.032 | 1.114 | |
proboscis | 1.020 | 0.046 | 1.067 | |