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This page was generated on 2021-10-15 15:05:42 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the hapFabia package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 838/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hapFabia 1.34.0 (landing page) Andreas Mitterecker
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.34.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:hapFabia.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings hapFabia_1.34.0.tar.gz |
| StartedAt: 2021-10-14 10:08:36 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 10:09:53 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 76.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: hapFabia.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:hapFabia.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings hapFabia_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/hapFabia.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hapFabia/DESCRIPTION’ ... OK
* this is package ‘hapFabia’ version ‘1.34.0’
* 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 ... WARNING
Found the following significant warnings:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
See ‘/home/biocbuild/bbs-3.13-bioc/meat/hapFabia.Rcheck/00install.out’ for details.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
iterateIntervals 5.153 0.512 5.744
* 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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.13-bioc/meat/hapFabia.Rcheck/00check.log’
for details.
hapFabia.Rcheck/00install.out
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###
### Running command:
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### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL hapFabia
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘hapFabia’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c interfaceR.c -o interfaceR.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c split_sparse_matrixB.c -o split_sparse_matrixB.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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) {
| ^~~~~
In file included from /usr/include/string.h:495,
from vcftoFABIAB.c:3:
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:394:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:382:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:372:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:362:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:352:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:342:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:332:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
gcc -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -g -O2 -Wall
gcc -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -g -O2 -Wall
gcc ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix
mv ./commandLine/split_sparse_matrix ../inst/commandLine/
gcc -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -g -O2 -Wall
gcc -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -g -O2 -Wall
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) {
| ^~~~~
In file included from /usr/include/string.h:495,
from vcftoFABIAB.c:3:
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:394:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:382:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:372:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:362:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:352:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:342:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:332:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine/
installing to /home/biocbuild/bbs-3.13-bioc/R/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 | 0.351 | 0.019 | 0.371 | |
| IBDsegmentList-class | 0.02 | 0.00 | 0.02 | |
| IBDsegmentList2excel | 0.015 | 0.000 | 0.014 | |
| analyzeIBDsegments | 0.000 | 0.004 | 0.004 | |
| compareIBDsegmentLists | 0.055 | 0.000 | 0.055 | |
| extractIBDsegments | 0.082 | 0.000 | 0.082 | |
| findDenseRegions | 0.002 | 0.004 | 0.007 | |
| hapFabia | 2.947 | 0.076 | 3.119 | |
| hapFabiaVersion | 0.000 | 0.002 | 0.001 | |
| identifyDuplicates | 0.000 | 0.003 | 0.003 | |
| iterateIntervals | 5.153 | 0.512 | 5.744 | |
| makePipelineFile | 0.003 | 0.003 | 0.006 | |
| matrixPlot | 0.001 | 0.004 | 0.005 | |
| mergeIBDsegmentLists | 0.014 | 0.000 | 0.014 | |
| plotIBDsegment | 0.244 | 0.004 | 0.248 | |
| setAnnotation | 0.052 | 0.000 | 0.052 | |
| setStatistics | 0.036 | 0.004 | 0.040 | |
| sim | 0.001 | 0.000 | 0.001 | |
| simulateIBDsegments | 0.001 | 0.000 | 0.001 | |
| simulateIBDsegmentsFabia | 0.898 | 0.016 | 0.914 | |
| split_sparse_matrix | 0.002 | 0.000 | 0.002 | |
| toolsFactorizationClass | 0.768 | 0.048 | 0.816 | |
| vcftoFABIA | 0.002 | 0.000 | 0.003 | |