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This page was generated on 2024-07-12 17:38 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 942/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hapFabia 1.46.0  (landing page)
Andreas Mitterecker
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/hapFabia
git_branch: RELEASE_3_19
git_last_commit: 4378320
git_last_commit_date: 2024-04-30 10:28:48 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for hapFabia on nebbiolo1

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.

raw results


Summary

Package: hapFabia
Version: 1.46.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:hapFabia.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings hapFabia_1.46.0.tar.gz
StartedAt: 2024-07-10 23:48:06 -0400 (Wed, 10 Jul 2024)
EndedAt: 2024-07-10 23:49:03 -0400 (Wed, 10 Jul 2024)
EllapsedTime: 57.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: hapFabia.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:hapFabia.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings hapFabia_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/hapFabia.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘hapFabia/DESCRIPTION’ ... OK
* this is package ‘hapFabia’ version ‘1.46.0’
* 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:138:10: 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:138:10: 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:138:10: 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:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
See ‘/home/biocbuild/bbs-3.19-bioc/meat/hapFabia.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 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 whether 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: (-1) IBDsegment-class.Rd:408-409: Lost braces
   408 | \item{plot}{\code{signature(x = "IBDsegment", y = "missing")}}{ Plot
       |                                                               ^
checkRd: (-1) IBDsegment-class.Rd:411-413: Lost braces
   411 | \item{plotLarger}{\code{signature(x="IBDsegment", filename="character",fact="numeric",addSamp="ANY")}}{ Plot
       |                                                                                                       ^
checkRd: (-1) IBDsegment-class.Rd:416-417: Lost braces
   416 | \item{summary}{\code{signature(object = "IBDsegment")}}{ Summary of
       |                                                        ^
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: (-1) IBDsegmentList-class.Rd:145-146: Lost braces
   145 | \item{plot}{\code{signature(x = "IBDsegmentList", y = "missing")}}{
       |                                                                   ^
checkRd: (-1) IBDsegmentList-class.Rd:149-151: Lost braces
   149 | \item{summary}{\code{signature(object = "IBDsegmentList")}}{ Summary
       |                                                            ^
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 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: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/hapFabia.Rcheck/00check.log’
for details.


Installation output

hapFabia.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL hapFabia
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘hapFabia’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c interfaceR.c -o interfaceR.o
gcc -I"/home/biocbuild/bbs-3.19-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-3.19-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:535,
                 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:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
    inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:382:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
    inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:372:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
    inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:362:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
    inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:352:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
    inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:342:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
    inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:332:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/biocbuild/bbs-3.19-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:535,
                 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:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
    inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:382:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
    inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:372:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
    inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:362:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
    inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:352:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
    inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:342:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
    inlined from ‘vcftoFABIAB’ at vcftoFABIAB.c:332:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin_strncat’ output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
  138 |   return __builtin___strncat_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
gcc ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine/
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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)

Tests output


Example timings

hapFabia.Rcheck/hapFabia-Ex.timings

nameusersystemelapsed
IBDsegment-class0.2800.0260.306
IBDsegmentList-class0.0070.0040.011
IBDsegmentList2excel0.0080.0000.008
analyzeIBDsegments0.0020.0000.002
compareIBDsegmentLists0.0160.0000.015
extractIBDsegments0.0340.0000.034
findDenseRegions0.0000.0030.003
hapFabia1.3930.0321.425
hapFabiaVersion0.0010.0000.001
identifyDuplicates0.0000.0010.002
iterateIntervals3.6430.0903.734
makePipelineFile0.0000.0050.006
matrixPlot0.0020.0020.004
mergeIBDsegmentLists0.0120.0010.011
plotIBDsegment0.2240.0080.231
setAnnotation0.0460.0000.046
setStatistics0.0330.0000.033
sim0.0000.0000.001
simulateIBDsegments0.0000.0000.001
simulateIBDsegmentsFabia0.4810.0000.481
split_sparse_matrix0.0020.0000.001
toolsFactorizationClass0.7700.0040.774
vcftoFABIA0.0000.0010.001