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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:VegaMC.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings VegaMC_3.34.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/VegaMC.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VegaMC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VegaMC’ version ‘3.34.0’
* 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 ‘VegaMC’ can be installed ... OK
* 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 ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getGenes: no visible global function definition for ‘write.table’
qvalue: no visible global function definition for ‘smooth.spline’
qvalue: no visible global function definition for ‘predict’
vegaMC,character: no visible global function definition for
  ‘read.table’
vegaMC,character: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  predict read.table smooth.spline write.table
Consider adding
  importFrom("stats", "predict", "smooth.spline")
  importFrom("utils", "read.table", "write.table")
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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.15-bioc/R/library/VegaMC/libs/VegaMC.so’:
  Found ‘rand’, possibly from ‘rand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/VegaMC.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL VegaMC
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘VegaMC’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c run_vegaMC.c -o run_vegaMC.o
run_vegaMC.c: In function ‘read_params’:
run_vegaMC.c:618:18: warning: unused variable ‘brkt’ [-Wunused-variable]
  618 |     char *elem, *brkt;
      |                  ^~~~
run_vegaMC.c: In function ‘load_data’:
run_vegaMC.c:534:32: warning: ‘chr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  534 |         temp_probe->chromosome = chr;
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~
run_vegaMC.c:535:30: warning: ‘position’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  535 |         temp_probe->position = position;
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
run_vegaMC.c:564:14: warning: ‘first_probe’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  564 |     prev_chr = temp_probe->chromosome;
      |     ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
run_vegaMC.c: In function ‘call_VegaMC’:
run_vegaMC.c:466:38: warning: ‘first_seg’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  466 |             seg_chromosomes[j] = (tmp->chromosome) + 1;
      |                                  ~~~~^~~~~~~~~~~~~
run_vegaMC.c:435:32: warning: ‘prev_seg’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  435 |                 prev_seg->next = tmp;
      |                 ~~~~~~~~~~~~~~~^~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c sort_data.c -o sort_data.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c vegaMC.c -o vegaMC.o
vegaMC.c: In function ‘heap_delete’:
vegaMC.c:235:10: warning: variable ‘deleted’ set but not used [-Wunused-but-set-variable]
  235 |     node deleted;
      |          ^~~~~~~
vegaMC.c: In function ‘init_trivial_segmentation’:
vegaMC.c:592:15: warning: variable ‘index’ set but not used [-Wunused-but-set-variable]
  592 |     int i, j, index;
      |               ^~~~~
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o VegaMC.so run_vegaMC.o sort_data.o vegaMC.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-VegaMC/00new/VegaMC/libs
** R
** 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 (VegaMC)