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 11:36:13 -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 909/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
hapFabia 1.42.0 (landing page) Andreas Mitterecker
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the hapFabia package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hapFabia.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: hapFabia |
Version: 1.42.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hapFabia.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings hapFabia_1.42.0.tar.gz |
StartedAt: 2023-10-16 02:57:13 -0400 (Mon, 16 Oct 2023) |
EndedAt: 2023-10-16 02:58:22 -0400 (Mon, 16 Oct 2023) |
EllapsedTime: 68.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: hapFabia.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hapFabia.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings hapFabia_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/hapFabia.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 '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 whether package 'hapFabia' can be installed ... WARNING Found the following significant warnings: vcftoFABIAB.c:394:19: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] vcftoFABIAB.c:382:19: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation] vcftoFABIAB.c:372:19: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] vcftoFABIAB.c:362:19: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] vcftoFABIAB.c:352:19: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] vcftoFABIAB.c:342:19: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] vcftoFABIAB.c:332:19: warning: 'strncat' output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation] See 'F:/biocbuild/bbs-3.17-bioc/meat/hapFabia.Rcheck/00install.out' for details. * 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 ... 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 for x64 is not available File 'F:/biocbuild/bbs-3.17-bioc/R/library/hapFabia/libs/x64/hapFabia.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 iterateIntervals 4.16 0.96 5.45 * 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 WARNINGs, 3 NOTEs See 'F:/biocbuild/bbs-3.17-bioc/meat/hapFabia.Rcheck/00check.log' for details.
hapFabia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL hapFabia ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'hapFabia' ... ** 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 interfaceR.c -o interfaceR.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 split_sparse_matrixB.c -o split_sparse_matrixB.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 vcftoFABIAB.c -o vcftoFABIAB.o vcftoFABIAB.c: In function 'getdelimS': vcftoFABIAB.c:50:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 50 | if (ch == EOF) | ^~ vcftoFABIAB.c:54:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 54 | while (idx > *linebufsz - 2) { | ^~~~~ vcftoFABIAB.c: In function 'vcftoFABIAB': vcftoFABIAB.c:394:19: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] 394 | strncat(format[j],Iformat,19); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:382:19: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation] 382 | strncat(info[j],Iinfo,190); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:372:19: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] 372 | strncat(filter[j],Ifilter,19); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:362:19: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] 362 | strncat(qual[j],Iqual,19); | ^~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:352:19: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] 352 | strncat(minor[j],Iminor,190); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:342:19: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] 342 | strncat(major[j],Imajor,190); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:332:19: warning: 'strncat' output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation] 332 | strncat(snpName[j],IsnpName,49); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:250:21: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 250 | snpName[0] = calloc((long) 50*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from vcftoFABIAB.c:2: c:\rtools43\x86_64-w64-mingw32.static.posix\include\stdlib.h:535:17: note: in a call to allocation function 'calloc' declared here 535 | void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); | ^~~~~~ vcftoFABIAB.c:258:20: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 258 | filter[0] = calloc((long) 20*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c:\rtools43\x86_64-w64-mingw32.static.posix\include\stdlib.h:535:17: note: in a call to allocation function 'calloc' declared here 535 | void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); | ^~~~~~ vcftoFABIAB.c:266:18: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | qual[0] = calloc((long) 20*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c:\rtools43\x86_64-w64-mingw32.static.posix\include\stdlib.h:535:17: note: in a call to allocation function 'calloc' declared here 535 | void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); | ^~~~~~ vcftoFABIAB.c:281:20: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 281 | format[0] = calloc((long) 20*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c:\rtools43\x86_64-w64-mingw32.static.posix\include\stdlib.h:535:17: note: in a call to allocation function 'calloc' declared here 535 | void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); | ^~~~~~ gcc -shared -s -static-libgcc -o hapFabia.dll tmp.def interfaceR.o split_sparse_matrixB.o vcftoFABIAB.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-hapFabia/00new/hapFabia/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 (hapFabia)
hapFabia.Rcheck/hapFabia-Ex.timings
name | user | system | elapsed | |
IBDsegment-class | 0.37 | 0.13 | 0.59 | |
IBDsegmentList-class | 0.02 | 0.00 | 0.01 | |
IBDsegmentList2excel | 0.00 | 0.00 | 0.02 | |
analyzeIBDsegments | 0 | 0 | 0 | |
compareIBDsegmentLists | 0.02 | 0.00 | 0.01 | |
extractIBDsegments | 0.03 | 0.00 | 0.03 | |
findDenseRegions | 0.00 | 0.01 | 0.02 | |
hapFabia | 1.65 | 0.53 | 2.36 | |
hapFabiaVersion | 0 | 0 | 0 | |
identifyDuplicates | 0 | 0 | 0 | |
iterateIntervals | 4.16 | 0.96 | 5.45 | |
makePipelineFile | 0.02 | 0.01 | 0.03 | |
matrixPlot | 0 | 0 | 0 | |
mergeIBDsegmentLists | 0.01 | 0.00 | 0.02 | |
plotIBDsegment | 0.36 | 0.13 | 0.51 | |
setAnnotation | 0.05 | 0.00 | 0.08 | |
setStatistics | 0.11 | 0.00 | 0.11 | |
sim | 0.00 | 0.01 | 0.02 | |
simulateIBDsegments | 0 | 0 | 0 | |
simulateIBDsegmentsFabia | 0.75 | 0.16 | 0.95 | |
split_sparse_matrix | 0.00 | 0.01 | 0.02 | |
toolsFactorizationClass | 0.56 | 0.07 | 0.64 | |
vcftoFABIA | 0 | 0 | 0 | |