Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:39 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 224/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
blima 1.41.0 (landing page) Vojtěch Kulvait
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the blima package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/blima.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: blima |
Version: 1.41.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:blima.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings blima_1.41.0.tar.gz |
StartedAt: 2024-12-23 20:12:35 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 20:18:50 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 375.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: blima.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:blima.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings blima_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/blima.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘blima/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘blima’ version ‘1.41.0’ * package encoding: UTF-8 * 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 ‘blima’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 code 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE nonParametricEstimator: no visible global function definition for ‘var’ performXieCorrection: no visible global function definition for ‘dnorm’ performXieCorrection: no visible global function definition for ‘pnorm’ vstFromLumi: no visible global function definition for ‘lm’ vstFromLumi: no visible global function definition for ‘predict’ Undefined global functions or variables: dnorm lm pnorm predict var Consider adding importFrom("stats", "dnorm", "lm", "pnorm", "predict", "var") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) createSummarizedMatrix.Rd:11: Lost braces; missing escapes or markup? 11 | \item{channelInclude}{This field allows user to set channel with weights which have to be from {0,1}. | ^ checkRd: (-1) doProbeTTests.Rd:12: Lost braces; missing escapes or markup? 12 | \item{channelInclude}{This field allows user to set channel with weights which have to be {0,1}. | ^ checkRd: (-1) doTTests.Rd:12: Lost braces; missing escapes or markup? 12 | \item{channelInclude}{This field allows user to set channel with weights which have to be {0,1}. | ^ checkRd: (-1) meanDistribution.Rd:15: Lost braces; missing escapes or markup? 15 | \item{channelInclude}{This field allows user to set channel with weights which have to be in {0,1}. | ^ checkRd: (-1) quantileNormalize.Rd:12: Lost braces; missing escapes or markup? 12 | \item{channelInclude}{This field allows user to set channel with weights which have to be in {0,1}. | ^ checkRd: (-1) singleArrayNormalize.Rd:13: Lost braces; missing escapes or markup? 13 | \item{channelInclude}{This field allows user to set channel with weights which have to be in {0,1}. | ^ checkRd: (-1) varianceBeadStabilise.Rd:11: Lost braces; missing escapes or markup? 11 | \item{channelInclude}{This field allows user to set channel with weights which have to be in {0,1}. | ^ checkRd: (-1) varianceBeadStabiliseSingleArray.Rd:11: Lost braces; missing escapes or markup? 11 | \item{channelInclude}{This field allows user to set channel with weights which have to be in {0,1}. | ^ checkRd: (-1) xieBacgroundCorrect.Rd:16: Lost braces; missing escapes or markup? 16 | \item{channelInclude}{This field allows user to set channel with weights which have to be from {0,1}. | ^ checkRd: (-1) xieBacgroundCorrectSingleArray.Rd:18: Lost braces; missing escapes or markup? 18 | \item{channelInclude}{This field allows user to set channel with weights which have to be from {0,1}. | ^ * 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 ... NOTE Rd files without \description: ‘interpolateSortedVectorRcpp_.Rd’ Argument items with no description in Rd file 'interpolateSortedVectorRcpp_.Rd': ‘vector’ ‘newSize’ Argument items with no description in Rd file 'nonParametricEstimator.Rd': ‘toCorrectAll’ ‘toCorrectNeg’ Argument items with no description in Rd file 'numberOfDistributionElements.Rd': ‘channelInclude’ Argument items with no description in Rd file 'performXieCorrection.Rd': ‘value’ ‘alpha’ ‘mu’ ‘sigma’ Argument items with no description in Rd file 'singleNumberOfDistributionElements.Rd': ‘channelInclude’ Argument items with no description in Rd file 'updateMeanDistribution.Rd': ‘meanDistribution’ * 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/blima.Rcheck/00check.log’ for details.
blima.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL blima ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘blima’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c interpolateSortedVector.cpp -o interpolateSortedVector.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o blima.so RcppExports.o interpolateSortedVector.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-blima/00new/blima/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (blima)
blima.Rcheck/blima-Ex.timings
name | user | system | elapsed | |
bacgroundCorrect | 0.011 | 0.000 | 0.011 | |
backgroundChannelSubtract | 0.009 | 0.001 | 0.010 | |
chipArrayStatistics | 0.005 | 0.002 | 0.008 | |
createSummarizedMatrix | 0.438 | 0.026 | 0.467 | |
doProbeTTests | 0.086 | 0.006 | 0.092 | |
doTTests | 0.087 | 0.005 | 0.091 | |
log2TransformPositive | 0.089 | 0.002 | 0.091 | |
nonPositiveCorrect | 0.006 | 0.001 | 0.006 | |
plotBackgroundImageAfterCorrection | 0.006 | 0.000 | 0.006 | |
plotBackgroundImageBeforeCorrection | 0.005 | 0.001 | 0.006 | |
quantileNormalize | 0.007 | 0.000 | 0.007 | |
selectedChannelTransform | 0.006 | 0.000 | 0.006 | |
varianceBeadStabilise | 0.006 | 0.000 | 0.006 | |
writeBackgroundImages | 0.005 | 0.001 | 0.006 | |
xieBacgroundCorrect | 0.006 | 0.000 | 0.006 | |