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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:SICtools.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings SICtools_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/SICtools.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 ‘SICtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SICtools’ version ‘1.24.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Rsamtools', 'doParallel', 'Biostrings', 'stringr', 'matrixStats',
  'plyr', 'GenomicRanges', 'IRanges'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SICtools’ can be installed ... WARNING
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  bam_index.c:335:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  bam_index.c:342:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  bam_index.c:355:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  bam_index.c:358:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  bam_index.c:362:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  bam_index.c:366:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  bam_index.c:376:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  bam_index.c:380:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  razf.c:221:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  razf.c:234:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  razf.c:201:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  razf.c:804:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  razf.c:805:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  razf.c:808:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  razf.c:810:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  razf.c:258:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  razf.c:96:12: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  razf.c:99:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  razf.c:106:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  razf.c:107:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare]
  md5.c:155:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess]
  Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’
See ‘/home/biocbuild/bbs-3.14-bioc/meat/SICtools.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
.indelDiffFunc: no visible global function definition for ‘fisher.test’
.indelDiffFunc: no visible global function definition for ‘dist’
indelDiff: no visible global function definition for ‘read.delim’
snpDiff : calcInfoRange : <anonymous>: no visible global function
  definition for ‘fisher.test’
snpDiff : calcInfoRange : <anonymous>: no visible global function
  definition for ‘dist’
Undefined global functions or variables:
  dist fisher.test read.delim
Consider adding
  importFrom("stats", "dist", "fisher.test")
  importFrom("utils", "read.delim")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... 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 include directives in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'applyPileups' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/SICtools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL SICtools
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘SICtools’ ...
** using staged installation
** libs
** arch - 
Makefile:24: warning: overriding recipe for target '.c.o'
/home/biocbuild/bbs-3.14-bioc/R/etc/Makeconf:168: warning: ignoring old recipe for target '.c.o'
make[1]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/SICtools/src'
make[2]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/SICtools/src'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
bgzf.c: In function ‘worker_aux’:
bgzf.c:392:9: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
  392 |  int i, tmp, stop = 0;
      |         ^~~
bgzf.c: In function ‘bgzf_close’:
bgzf.c:572:11: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
  572 |  int ret, count, block_length;
      |           ^~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
In file included from /usr/include/string.h:495,
                 from bam.h:47,
                 from bam.c:5:
In function ‘strncpy’,
    inlined from ‘bam_header_write’ at bam.c:128:2:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
bam_index.c: In function ‘bam_index_load_core’:
bam_index.c:335:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  335 |  fread(magic, 1, 4, fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~
bam_index.c:342:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  342 |  fread(&idx->n, 4, 1, fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~
bam_index.c:355:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  355 |   fread(&size, 4, 1, fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~
bam_index.c:358:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  358 |    fread(&key, 4, 1, fp);
      |    ^~~~~~~~~~~~~~~~~~~~~
bam_index.c:362:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  362 |    fread(&p->n, 4, 1, fp);
      |    ^~~~~~~~~~~~~~~~~~~~~~
bam_index.c:366:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  366 |    fread(p->list, 16, p->n, fp);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam_index.c:376:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  376 |   fread(&index2->n, 4, 1, fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~
bam_index.c:380:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  380 |   fread(index2->offset, index2->n, 8, fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
bam_pileup.c: In function ‘resolve_cigar2’:
bam_pileup.c:75:9: warning: variable ‘is_head’ set but not used [-Wunused-but-set-variable]
   75 |  int k, is_head = 0;
      |         ^~~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
razf.c: In function ‘razf_flush’:
razf.c:221:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  221 |   write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:234:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  234 |    write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c: In function ‘_razf_write’:
razf.c:201:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  201 |   write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c: In function ‘razf_close’:
razf.c:804:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  804 |    write(rz->x.fpw, &rz->in, sizeof(int64_t));
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:805:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  805 |    write(rz->x.fpw, &rz->out, sizeof(int64_t));
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:808:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  808 |    write(rz->x.fpw, &v64, sizeof(int64_t));
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:810:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  810 |    write(rz->x.fpw, &v64, sizeof(int64_t));
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c: In function ‘razf_end_flush’:
razf.c:258:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  258 |    write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c: In function ‘save_zindex’:
razf.c:96:12: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   96 |  if(is_be) write(fd, &rz->index->size, sizeof(int));
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:99:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   99 |   write(fd, &v32, sizeof(uint32_t));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:106:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  106 |  write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:107:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  107 |  write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
faidx.c: In function ‘fai_load’:
faidx.c:277:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
  277 |     else
      |     ^~~~
faidx.c:280:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
  280 |  if (fp == 0) {
      |  ^~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
In file included from knetfile.c:46:
knetfile.c: In function ‘kftp_send_cmd’:
knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
    9 | #define netwrite(fd, ptr, len) write(fd, ptr, len)
      |                                ^~~~~~~~~~~~~~~~~~~
knetfile.c:236:2: note: in expansion of macro ‘netwrite’
  236 |  netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
      |  ^~~~~~~~
knetfile.c: In function ‘khttp_connect_file’:
knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
    9 | #define netwrite(fd, ptr, len) write(fd, ptr, len)
      |                                ^~~~~~~~~~~~~~~~~~~
knetfile.c:415:2: note: in expansion of macro ‘netwrite’
  415 |  netwrite(fp->fd, buf, l);
      |  ^~~~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
bam_reheader.c: In function ‘bam_reheader’:
bam_reheader.c:12:16: warning: variable ‘old’ set but not used [-Wunused-but-set-variable]
   12 |  bam_header_t *old;
      |                ^~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
kprobaln.c: In function ‘kpa_glocal’:
kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
   78 |  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
      |                     ^~~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/SICtools/src'
make[2]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/SICtools/src/bcftools'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
bcf.c: In function ‘bcf_fmt_core’:
bcf.c:233:9: warning: variable ‘iPL’ set but not used [-Wunused-but-set-variable]
  233 |     int iPL = -1;
      |         ^~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
bcfutils.c: In function ‘bcf_fit_alt’:
bcfutils.c:119:9: warning: variable ‘ipl’ set but not used [-Wunused-but-set-variable]
  119 |     int ipl=-1, igt=-1;
      |         ^~~
bcfutils.c: In function ‘bcf_fix_gt’:
bcfutils.c:254:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
  254 |     else
      |     ^~~~
bcfutils.c:256:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
  256 |  b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
      |  ^
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function ‘bcf_em1’:
em.c:174:12: warning: variable ‘n2’ set but not used [-Wunused-but-set-variable]
  174 |  int i, n, n2;
      |            ^~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/SICtools/src/bcftools'
make[2]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/SICtools/src/misc'
make[2]: Nothing to be done for 'lib'.
make[2]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/SICtools/src/misc'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
bam_plcmd.c: In function ‘mpileup’:
bam_plcmd.c:333:28: warning: variable ‘ref16’ set but not used [-Wunused-but-set-variable]
  333 |    int total_depth, _ref0, ref16;
      |                            ^~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
bam2bcf.c: In function ‘bcf_call2bcf’:
bam2bcf.c:428:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  428 |     if (bc->read_pos_bias != -1 )
      |     ^~
bam2bcf.c:430:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  430 |  kputc('\0', &s);
      |  ^~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
bam2bcf_indel.c: In function ‘bcf_call_add_rg’:
bam2bcf_indel.c:32:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   32 |    for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
      |    ^~~
bam2bcf_indel.c:32:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   32 |    for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
      |                                                      ^~
bam2bcf_indel.c:33:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   33 |    for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
      |    ^~~
bam2bcf_indel.c:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   33 |    for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
      |                                                      ^~
bam2bcf_indel.c: In function ‘bcf_call_gap_prep’:
bam2bcf_indel.c:121:28: warning: variable ‘query’ set but not used [-Wunused-but-set-variable]
  121 |  char *inscns = 0, *ref2, *query, **ref_sample;
      |                            ^~~~~
bam2bcf_indel.c:121:21: warning: variable ‘ref2’ set but not used [-Wunused-but-set-variable]
  121 |  char *inscns = 0, *ref2, *query, **ref_sample;
      |                     ^~~~
bam2bcf_indel.c:120:16: warning: variable ‘ref_type’ set but not used [-Wunused-but-set-variable]
  120 |  int N, l_run, ref_type;
      |                ^~~~~~~~
bam2bcf_indel.c:119:82: warning: variable ‘score2’ set but not used [-Wunused-but-set-variable]
  119 |  int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
      |                                                                                  ^~~~~~
bam2bcf_indel.c:119:73: warning: variable ‘score1’ set but not used [-Wunused-but-set-variable]
  119 |  int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
      |                                                                         ^~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
errmod.c: In function ‘errmod_cal’:
errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare]
   79 |  if (m > m) return -1;
      |        ^
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function ‘main_cut_target’:
cut_target.c:137:36: warning: variable ‘lastpos’ set but not used [-Wunused-but-set-variable]
  137 |  int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l;
      |                                    ^~~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
gcc -g -Wall -O2 -o samtools2SIC bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o  libbam.a -Lbcftools -lbcf  -lcurses  -lm -lz -lpthread
make[1]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/SICtools/src'
make[1]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/SICtools/src/bcftools'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
call1.c: In function ‘write_header’:
call1.c:303:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  303 |     if (!strstr(str.s, "##FORMAT=<ID=GL,"))
      |     ^~
call1.c:305:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  305 |  if (!strstr(str.s, "##FORMAT=<ID=DP,"))
      |  ^~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L.  -lbcf -lm -lz -lpthread
make[1]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/SICtools/src/bcftools'
make[1]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/SICtools/src/misc'
gcc -c -g -Wall -O2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
md5.c: In function ‘MD5Final’:
md5.c:155:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess]
  155 |     memset(ctx, 0, sizeof(ctx));        /* In case it's sensitive */
      |                          ^
gcc -g -Wall -O2 -o md5sum-lite md5sum-lite.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
md5.c: In function ‘MD5Final’:
md5.c:155:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess]
  155 |     memset(ctx, 0, sizeof(ctx));        /* In case it's sensitive */
      |                          ^
gcc -g -Wall -O2 -c -I.. -o md5fa.o md5fa.c
gcc -g -Wall -O2 -o md5fa md5.o md5fa.o -lz
gcc -g -Wall -O2 -o maq2sam-short maq2sam.c -lz
gcc -g -Wall -O2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -g -Wall -O2 -c -I.. -o ace2sam.o ace2sam.c
ace2sam.c: In function ‘main’:
ace2sam.c:162:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  162 |    if (write_cns) puts(t[4].s); t[4].l = 0;
      |    ^~
ace2sam.c:162:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  162 |    if (write_cns) puts(t[4].s); t[4].l = 0;
      |                                 ^
gcc -g -Wall -O2 -o ace2sam ace2sam.o -lz
gcc -g -Wall -O2 -c -I.. -o wgsim.o wgsim.c
gcc -g -Wall -O2 -o wgsim wgsim.o -lm -lz
gcc -g -Wall -O2 -c -I.. -o bamcheck.o bamcheck.c
gcc -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
make[1]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/SICtools/src/misc'
installing via 'install.libs.R' to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-SICtools/00new/SICtools
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’
** testing if installed package keeps a record of temporary installation path
* DONE (SICtools)

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ## runTests
> 
> BiocGenerics:::testPackage("SICtools")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'plyr'

The following object is masked from 'package:matrixStats':

    count

The following object is masked from 'package:XVector':

    compact

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

[1] "chr07"  "828636" "G"     
[1] "chr07"  "828714" "C"     
[1] "chr04 1 1531933"
[1] "chr04 962501 1026983"


RUNIT TEST PROTOCOL -- Tue Apr 12 09:23:38 2022 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SICtools RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: replacing previous import 'plyr::count' by 'matrixStats::count' when loading 'SICtools' 
2: 'applyPileups' is deprecated.
Use 'pileup' instead.
See help("Deprecated") 
3: 'applyPileups' is deprecated.
Use 'pileup' instead.
See help("Deprecated") 
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  5.375   0.406   5.680