Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:55 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 TurboNorm package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 2085/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TurboNorm 1.47.0 (landing page) Maarten van Iterson
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: TurboNorm |
Version: 1.47.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TurboNorm.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings TurboNorm_1.47.0.tar.gz |
StartedAt: 2022-12-29 04:22:54 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 04:24:07 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 72.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TurboNorm.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TurboNorm.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings TurboNorm_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TurboNorm.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'TurboNorm/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'TurboNorm' version '1.47.0' * 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 'TurboNorm' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 12.2.0' * checking installed package size ... OK * 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: 'convert' 'limma' 'marray' 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 normalize.AffyBatch.pspline: no visible global function definition for 'intensity<-' pspline: no visible global function definition for 'as' pspline: no visible global function definition for 'maRb<-' pspline: no visible global function definition for 'maGb<-' pspline: no visible global function definition for 'maA' pspline: no visible global function definition for 'maM' pspline: no visible global function definition for 'layout' pspline: no visible global function definition for 'maM<-' pspline: no visible global function definition for 'lines' turbotrend: no visible global function definition for 'median' Undefined global functions or variables: as intensity<- layout lines maA maGb<- maM maM<- maRb<- median Consider adding importFrom("graphics", "layout", "lines") importFrom("methods", "as") importFrom("stats", "median") 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... 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/TurboNorm/libs/x64/TurboNorm.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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed normalize.pspline 17.25 0.81 18.12 panel.pspline 9.41 0.14 9.88 * 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 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TurboNorm.Rcheck/00check.log' for details.
TurboNorm.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL TurboNorm ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'TurboNorm' ... ** 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:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o Rinit.c:8:40: warning: missing braces around initializer [-Wmissing-braces] 8 | static const R_CMethodDef cMethods[] = { | ^ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c binners.c -o binners.o gcc -shared -s -static-libgcc -o TurboNorm.dll tmp.def Rinit.o binners.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/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-TurboNorm/00new/TurboNorm/libs/x64 ** R ** data ** 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 (TurboNorm)
TurboNorm.Rcheck/TurboNorm-Ex.timings
name | user | system | elapsed | |
methylation | 0.05 | 0.00 | 0.05 | |
normalize.pspline | 17.25 | 0.81 | 18.12 | |
panel.pspline | 9.41 | 0.14 | 9.88 | |
pspline | 2.34 | 0.24 | 2.57 | |
turbotrend | 0.92 | 0.03 | 0.96 | |