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This page was generated on 2022-04-13 12:05:27 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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CHECK results for hapFabia on nebbiolo2


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 851/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hapFabia 1.36.0  (landing page)
Andreas Mitterecker
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/hapFabia
git_branch: RELEASE_3_14
git_last_commit: b5514bc
git_last_commit_date: 2021-10-26 12:04:29 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: hapFabia
Version: 1.36.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:hapFabia.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings hapFabia_1.36.0.tar.gz
StartedAt: 2022-04-12 07:45:24 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 07:46:30 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 66.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: hapFabia.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:hapFabia.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings hapFabia_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/hapFabia.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.36.0’
* 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 ... 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-3.14-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 5.059  0.068   5.543
* 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-3.14-bioc/meat/hapFabia.Rcheck/00check.log’
for details.



Installation output

hapFabia.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL hapFabia
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘hapFabia’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c interfaceR.c -o interfaceR.o
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/R/lib -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/biocbuild/bbs-3.14-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-3.14-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)

Tests output


Example timings

hapFabia.Rcheck/hapFabia-Ex.timings

nameusersystemelapsed
IBDsegment-class0.2550.0160.272
IBDsegmentList-class0.0110.0000.010
IBDsegmentList2excel0.0080.0000.008
analyzeIBDsegments0.0010.0000.001
compareIBDsegmentLists0.0150.0030.019
extractIBDsegments0.0340.0000.035
findDenseRegions0.0020.0000.003
hapFabia2.0770.0362.115
hapFabiaVersion0.0010.0000.001
identifyDuplicates0.0010.0000.001
iterateIntervals5.0590.0685.543
makePipelineFile0.0020.0000.002
matrixPlot0.0010.0030.004
mergeIBDsegmentLists0.0100.0000.011
plotIBDsegment0.1920.0160.208
setAnnotation0.0520.0000.052
setStatistics0.0540.0000.053
sim000
simulateIBDsegments0.0010.0000.000
simulateIBDsegmentsFabia0.8430.0040.847
split_sparse_matrix0.0000.0000.001
toolsFactorizationClass0.6700.0000.671
vcftoFABIA0.0000.0000.001