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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VegaMC.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings VegaMC_3.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/VegaMC.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'VegaMC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VegaMC' version '3.32.0'
* 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 whether package 'VegaMC' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    example   4.9Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/VegaMC/libs/i386/VegaMC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/VegaMC/libs/x64/VegaMC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/VegaMC.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/VegaMC_3.32.0.tar.gz && rm -rf VegaMC.buildbin-libdir && mkdir VegaMC.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VegaMC.buildbin-libdir VegaMC_3.32.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL VegaMC_3.32.0.zip && rm VegaMC_3.32.0.tar.gz VegaMC_3.32.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 65 1614k   65 1058k    0     0  1014k      0  0:00:01  0:00:01 --:--:-- 1013k
100 1614k  100 1614k    0     0  1201k      0  0:00:01  0:00:01 --:--:-- 1201k

install for i386

* installing *source* package 'VegaMC' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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]
     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]
         temp_probe->chromosome = chr;
         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~
run_vegaMC.c:535:30: warning: 'position' may be used uninitialized in this function [-Wmaybe-uninitialized]
         temp_probe->position = position;
         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
run_vegaMC.c:564:14: warning: 'first_probe' may be used uninitialized in this function [-Wmaybe-uninitialized]
     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]
             seg_chromosomes[j] = (tmp->chromosome) + 1;
                                  ~~~~^~~~~~~~~~~~~
run_vegaMC.c:435:32: warning: 'prev_seg' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 prev_seg->next = tmp;
                 ~~~~~~~~~~~~~~~^~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sort_data.c -o sort_data.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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]
     node deleted;
          ^~~~~~~
vegaMC.c: In function 'init_trivial_segmentation':
vegaMC.c:592:15: warning: variable 'index' set but not used [-Wunused-but-set-variable]
     int i, j, index;
               ^~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o VegaMC.dll tmp.def run_vegaMC.o sort_data.o vegaMC.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/VegaMC.buildbin-libdir/00LOCK-VegaMC/00new/VegaMC/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'VegaMC'
    finding HTML links ... done
    VegaMC-package                          html  
    sortData                                html  
    vegaMC-methods                          html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/VegaMC.buildbin-libdir/00LOCK-VegaMC/00new/VegaMC/help/vegaMC.html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'VegaMC' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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]
     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]
         temp_probe->chromosome = chr;
         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~
run_vegaMC.c:535:30: warning: 'position' may be used uninitialized in this function [-Wmaybe-uninitialized]
         temp_probe->position = position;
         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
run_vegaMC.c:564:14: warning: 'first_probe' may be used uninitialized in this function [-Wmaybe-uninitialized]
     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]
             seg_chromosomes[j] = (tmp->chromosome) + 1;
                                  ~~~~^~~~~~~~~~~~~
run_vegaMC.c:435:32: warning: 'prev_seg' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 prev_seg->next = tmp;
                 ~~~~~~~~~~~~~~~^~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sort_data.c -o sort_data.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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]
     node deleted;
          ^~~~~~~
vegaMC.c: In function 'init_trivial_segmentation':
vegaMC.c:592:15: warning: variable 'index' set but not used [-Wunused-but-set-variable]
     int i, j, index;
               ^~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o VegaMC.dll tmp.def run_vegaMC.o sort_data.o vegaMC.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/VegaMC.buildbin-libdir/VegaMC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VegaMC' as VegaMC_3.32.0.zip
* DONE (VegaMC)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'VegaMC' successfully unpacked and MD5 sums checked