| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 909/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hapFabia 1.42.0 (landing page) Andreas Mitterecker
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK |  | |||||||
|
To the developers/maintainers of the hapFabia 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: hapFabia |
| Version: 1.42.0 |
| 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_1.42.0.tar.gz |
| StartedAt: 2023-10-18 00:14:53 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 00:16:52 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 119.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: hapFabia.Rcheck |
| Warnings: 1 |
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### Running command:
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### /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_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/hapFabia.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hapFabia/DESCRIPTION’ ... OK
* this is package ‘hapFabia’ version ‘1.42.0’
* 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
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
The beginning
* 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 startup messages can be suppressed ... 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 ... WARNING
checkRd: (5) IBDsegment-class.Rd:439: \item in \value must have non-empty label
checkRd: (5) IBDsegment-class.Rd:205-209: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:211-215: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:219-223: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:227-231: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:235-239: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:243-247: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:251-255: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:259-263: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:267-271: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:275-279: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:283-287: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:291-295: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:299-303: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:307-311: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:315-319: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:323-327: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:331-335: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:339-343: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:347-351: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:355-359: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:363-367: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:371-375: \item in \describe must have non-empty label
checkRd: (5) IBDsegment-class.Rd:379-383: \item in \describe must have non-empty label
checkRd: (5) IBDsegmentList-class.Rd:171: \item in \value must have non-empty label
checkRd: (5) IBDsegmentList-class.Rd:92-96: \item in \describe must have non-empty label
checkRd: (5) IBDsegmentList-class.Rd:98-102: \item in \describe must have non-empty label
checkRd: (5) IBDsegmentList-class.Rd:104-108: \item in \describe must have non-empty label
checkRd: (5) IBDsegmentList-class.Rd:111-116: \item in \describe must have non-empty label
checkRd: (5) IBDsegmentList-class.Rd:118-123: \item in \describe must have non-empty label
checkRd: (5) toolsFactorizationClass.Rd:83: \item in \value must have non-empty label
checkRd: (5) toolsFactorizationClass.Rd:84: \item in \value must have non-empty label
checkRd: (5) toolsFactorizationClass.Rd:85: \item in \value must have non-empty label
* 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 5.419 0.84 11.384
* 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: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/Resources/library’ * installing *source* package ‘hapFabia’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c interfaceR.c -o interfaceR.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c split_sparse_matrixB.c -o split_sparse_matrixB.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vcftoFABIAB.c -o vcftoFABIAB.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation clang -arch arm64 -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -falign-functions=64 -Wall -g -O2 clang -arch arm64 -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -falign-functions=64 -Wall -g -O2 clang -arch arm64 ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix mv ./commandLine/split_sparse_matrix ../inst/commandLine/ clang -arch arm64 -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -falign-functions=64 -Wall -g -O2 clang -arch arm64 -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -falign-functions=64 -Wall -g -O2 clang -arch arm64 ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA mv ./commandLine/vcftoFABIA ../inst/commandLine/ installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/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 | 0.362 | 0.137 | 0.910 | |
| IBDsegmentList-class | 0.011 | 0.002 | 0.023 | |
| IBDsegmentList2excel | 0.008 | 0.002 | 0.022 | |
| analyzeIBDsegments | 0.000 | 0.001 | 0.002 | |
| compareIBDsegmentLists | 0.021 | 0.002 | 0.041 | |
| extractIBDsegments | 0.049 | 0.003 | 0.084 | |
| findDenseRegions | 0.004 | 0.002 | 0.006 | |
| hapFabia | 2.098 | 0.338 | 4.079 | |
| hapFabiaVersion | 0.001 | 0.000 | 0.001 | |
| identifyDuplicates | 0.001 | 0.001 | 0.004 | |
| iterateIntervals | 5.419 | 0.840 | 11.384 | |
| makePipelineFile | 0.003 | 0.004 | 0.014 | |
| matrixPlot | 0.004 | 0.002 | 0.012 | |
| mergeIBDsegmentLists | 0.013 | 0.002 | 0.028 | |
| plotIBDsegment | 0.303 | 0.117 | 0.779 | |
| setAnnotation | 0.054 | 0.008 | 0.110 | |
| setStatistics | 0.038 | 0.003 | 0.072 | |
| sim | 0.001 | 0.000 | 0.001 | |
| simulateIBDsegments | 0.000 | 0.000 | 0.004 | |
| simulateIBDsegmentsFabia | 1.136 | 0.153 | 2.319 | |
| split_sparse_matrix | 0.001 | 0.001 | 0.003 | |
| toolsFactorizationClass | 0.763 | 0.031 | 1.395 | |
| vcftoFABIA | 0.001 | 0.001 | 0.003 | |