Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:08 -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 hapFabia package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/hapFabia.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 851/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
hapFabia 1.36.0 (landing page) Andreas Mitterecker
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: hapFabia |
Version: 1.36.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hapFabia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hapFabia_1.36.0.tar.gz |
StartedAt: 2022-04-12 14:11:01 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 14:12:26 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 85.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: hapFabia.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hapFabia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hapFabia_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/hapFabia.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hapFabia/DESCRIPTION’ ... OK * this is package ‘hapFabia’ version ‘1.36.0’ * 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 ‘hapFabia’ can be installed ... OK * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘hapFabia/R/zzz.R’: .onLoad calls: packageStartupMessage("+--------------------------+ # # ## ##### \n", "|#.....#...#.......#.#....#| # # # # # # \n", "|#.....#...#.......#.#....#| ###### # # # # \n", "|#.....#...#...............| # # ###### ##### \n", "|#.....#...#.......#.#....#| # # # # # \n", "|#.....#...#...............| # # # # # \n", "|#.....#...#.......#.#....#| ####### \n", "|..................#.#....#| # ## ##### # ## \n", "|#.....#...#.......#.#....#| # # # # # # # # \n", "|..................#.#....#| ##### # # ##### # # # \n", "|#.....#...#.......#.#....#| # ###### # # # ###### \n", "|#.....#...#.......#.#....#| # # # # # # # # \n", "+--------------------------+ # # # ##### # # # \n") packageStartupMessage("Citation: S. Hochreiter,", "\n", "HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data,", "\n", "Nucleic Acids Research, 2013, doi: 10.1093/nar/gkt1013.", "\n", "BibTex: enter 'toBibtex(citation(\"hapFabia\"))'", "\n\n", "Homepage: http://www.bioinf.jku.at/software/hapFabia/index.html", "\n\n", "hapFabia Package Version ", version, "\n") See section ‘Good practice’ in '?.onAttach'. * 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 shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * 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 iterateIntervals 7.429 1.02 8.542 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/hapFabia.Rcheck/00check.log’ for details.
hapFabia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL hapFabia ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘hapFabia’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c interfaceR.c -o interfaceR.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c split_sparse_matrixB.c -o split_sparse_matrixB.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c vcftoFABIAB.c -o vcftoFABIAB.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation clang -mmacosx-version-min=10.13 -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -Wall -g -O2 clang -mmacosx-version-min=10.13 -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -Wall -g -O2 clang -mmacosx-version-min=10.13 ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix mv ./commandLine/split_sparse_matrix ../inst/commandLine/ clang -mmacosx-version-min=10.13 -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -Wall -g -O2 clang -mmacosx-version-min=10.13 -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -Wall -g -O2 clang -mmacosx-version-min=10.13 ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA mv ./commandLine/vcftoFABIA ../inst/commandLine/ installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-hapFabia/00new/hapFabia/libs ** 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 ** 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 (hapFabia)
hapFabia.Rcheck/hapFabia-Ex.timings
name | user | system | elapsed | |
IBDsegment-class | 0.506 | 0.129 | 0.637 | |
IBDsegmentList-class | 0.020 | 0.004 | 0.024 | |
IBDsegmentList2excel | 0.013 | 0.003 | 0.016 | |
analyzeIBDsegments | 0.001 | 0.003 | 0.004 | |
compareIBDsegmentLists | 0.030 | 0.004 | 0.034 | |
extractIBDsegments | 0.074 | 0.003 | 0.078 | |
findDenseRegions | 0.005 | 0.003 | 0.008 | |
hapFabia | 2.945 | 0.368 | 3.357 | |
hapFabiaVersion | 0.000 | 0.000 | 0.001 | |
identifyDuplicates | 0.001 | 0.002 | 0.004 | |
iterateIntervals | 7.429 | 1.020 | 8.542 | |
makePipelineFile | 0.004 | 0.006 | 0.009 | |
matrixPlot | 0.006 | 0.002 | 0.008 | |
mergeIBDsegmentLists | 0.021 | 0.003 | 0.024 | |
plotIBDsegment | 0.417 | 0.103 | 0.520 | |
setAnnotation | 0.090 | 0.009 | 0.100 | |
setStatistics | 0.067 | 0.003 | 0.070 | |
sim | 0.000 | 0.000 | 0.001 | |
simulateIBDsegments | 0.000 | 0.000 | 0.001 | |
simulateIBDsegmentsFabia | 1.299 | 0.196 | 1.496 | |
split_sparse_matrix | 0.000 | 0.002 | 0.003 | |
toolsFactorizationClass | 0.911 | 0.034 | 0.947 | |
vcftoFABIA | 0.001 | 0.003 | 0.003 | |