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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


INSTALL 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 INSTALL hapFabia
StartedAt: 2024-07-10 15:01:45 -0400 (Wed, 10 Jul 2024)
EndedAt: 2024-07-10 15:02:02 -0400 (Wed, 10 Jul 2024)
EllapsedTime: 16.4 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### 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)