Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:36:31 -0400 (Mon, 16 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 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 1637/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RBioinf 1.60.0 (landing page) Robert Gentleman
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the RBioinf package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RBioinf.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: RBioinf |
Version: 1.60.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RBioinf.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings RBioinf_1.60.0.tar.gz |
StartedAt: 2023-10-16 05:43:12 -0400 (Mon, 16 Oct 2023) |
EndedAt: 2023-10-16 05:43:42 -0400 (Mon, 16 Oct 2023) |
EllapsedTime: 30.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RBioinf.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RBioinf.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings RBioinf_1.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/RBioinf.Rcheck' * using R version 4.3.1 (2023-06-16 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.2.0 GNU Fortran (GCC) 12.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'RBioinf/DESCRIPTION' ... OK * this is package 'RBioinf' version '1.60.0' * 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 'RBioinf' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 12.2.0' * checking installed package size ... NOTE installed size is 12.4Mb sub-directories of 1Mb or more: extdata 12.3Mb * 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 dependencies in R code ... NOTE Packages in Depends field not imported from: 'graph' 'methods' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: 'methods:::.getMethodsTable' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE class2Graph: warning in matrix(0, nr = nN, nc = nN): partial argument match of 'nr' to 'nrow' class2Graph: warning in matrix(0, nr = nN, nc = nN): partial argument match of 'nc' to 'ncol' LPO: no visible global function definition for 'getClass' OLDcplList: no visible global function definition for 'getAllSuperClasses' OLDcplList: no visible global function definition for 'getClass' S4Help: no visible global function definition for 'isClass' S4Help: no visible global function definition for 'getAllSuperClasses' S4Help: no visible global function definition for 'getClass' S4Help: no visible global function definition for 'menu' S4Help: no visible global function definition for 'isGeneric' S4Help: no visible global function definition for 'getGeneric' S4Help: no visible binding for global variable 'help' candidateDirectSC: no visible global function definition for 'getClass' class2Graph: no visible global function definition for 'is' class2Graph: no visible global function definition for 'getClass' class2Graph: no visible global function definition for 'getAllSuperClasses' class2Graph: no visible global function definition for 'new' class2Graph: no visible global function definition for 'as' classList2Graph: no visible global function definition for 'join' computeClassLinearization: no visible global function definition for 'getClass' printWithNumbers: no visible global function definition for 'is' subClassNames: no visible global function definition for 'isClassDef' subClassNames: no visible global function definition for 'getClass' superClassNames: no visible global function definition for 'isClassDef' superClassNames: no visible global function definition for 'getClass' superClasses: no visible global function definition for 'is' traceMethods: no visible global function definition for 'isGeneric' traceMethods: no visible global function definition for 'showMethods' Undefined global functions or variables: as getAllSuperClasses getClass getGeneric help is isClass isClassDef isGeneric join menu new showMethods Consider adding importFrom("methods", "as", "getAllSuperClasses", "getClass", "getGeneric", "is", "isClass", "isClassDef", "isGeneric", "new", "showMethods") importFrom("utils", "help", "menu") 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.17-bioc/R/library/RBioinf/libs/x64/RBioinf.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking sizes of PDF files under 'inst/doc' ... 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: 4 NOTEs See 'F:/biocbuild/bbs-3.17-bioc/meat/RBioinf.Rcheck/00check.log' for details.
RBioinf.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL RBioinf ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'RBioinf' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rand.c -o rand.o gcc -shared -s -static-libgcc -o RBioinf.dll tmp.def Rinit.o rand.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-RBioinf/00new/RBioinf/libs/x64 ** 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 (RBioinf)
RBioinf.Rcheck/RBioinf-Ex.timings
name | user | system | elapsed | |
Rcal | 0 | 0 | 0 | |
S4Help | 0 | 0 | 0 | |
asSimpleVector | 0 | 0 | 0 | |
classList2Graph | 0.10 | 0.00 | 0.09 | |
computeClassLinearization | 0.03 | 0.00 | 0.03 | |
printWithNumbers | 0 | 0 | 0 | |
randDNA | 0 | 0 | 0 | |
simplePVect | 0 | 0 | 0 | |
simpleRand | 0 | 0 | 0 | |
simpleSort | 0 | 0 | 0 | |
subClassNames | 0 | 0 | 0 | |
superClasses | 0 | 0 | 0 | |
traceMethods | 0 | 0 | 0 | |