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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:hapFabia.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings hapFabia_1.48.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/hapFabia.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘hapFabia/DESCRIPTION’ ... OK
* this is package ‘hapFabia’ version ‘1.48.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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:
  vcftoFABIAB.c:394:19: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
  vcftoFABIAB.c:382:19: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
  vcftoFABIAB.c:372:19: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
  vcftoFABIAB.c:362:19: warning: ‘__builtin_strncat’ output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
  vcftoFABIAB.c:352:19: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
  vcftoFABIAB.c:342:19: warning: ‘__builtin_strncat’ output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
  vcftoFABIAB.c:332:19: warning: ‘__builtin_strncat’ output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/hapFabia.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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-3.20-bioc/meat/hapFabia.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL hapFabia
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘hapFabia’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c interfaceR.c -o interfaceR.o
gcc -I"/home/biocbuild/bbs-3.20-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-3.20-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) {
      |          ^~~~~
vcftoFABIAB.c: In function ‘vcftoFABIAB’:
vcftoFABIAB.c:394:19: warning: ‘__builtin_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: ‘__builtin_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: ‘__builtin_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: ‘__builtin_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: ‘__builtin_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: ‘__builtin_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: ‘__builtin_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 [9223372036854775808, 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:
/usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
vcftoFABIAB.c:258:20: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  258 |       filter[0] =  calloc((long) 20*snps, sizeof(char));
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
vcftoFABIAB.c:266:18: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  266 |       qual[0] =  calloc((long) 20*snps, sizeof(char));
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
vcftoFABIAB.c:281:20: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  281 |       format[0] =  calloc((long) 20*snps, sizeof(char));
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/biocbuild/bbs-3.20-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) {
      |          ^~~~~
vcftoFABIAB.c: In function ‘vcftoFABIAB’:
vcftoFABIAB.c:394:19: warning: ‘__builtin_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: ‘__builtin_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: ‘__builtin_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: ‘__builtin_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: ‘__builtin_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: ‘__builtin_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: ‘__builtin_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 [9223372036854775808, 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:
/usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
vcftoFABIAB.c:258:20: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  258 |       filter[0] =  calloc((long) 20*snps, sizeof(char));
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
vcftoFABIAB.c:266:18: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  266 |       qual[0] =  calloc((long) 20*snps, sizeof(char));
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
vcftoFABIAB.c:281:20: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  281 |       format[0] =  calloc((long) 20*snps, sizeof(char));
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
gcc ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine/
installing to /home/biocbuild/bbs-3.20-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)