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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GraphAlignment.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GraphAlignment_1.70.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GraphAlignment.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 ‘GraphAlignment/DESCRIPTION’ ... OK
* this is package ‘GraphAlignment’ version ‘1.70.0’
* 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 ‘GraphAlignment’ can be installed ... WARNING
Found the following significant warnings:
  lap.c:348:9: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  lap.c:358:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  lap.c:371:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  lap.c:384:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  lap.c:394:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GraphAlignment.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* 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 ‘GraphAlignment/R/GraphAlignment.R’:
  .Last.lib calls:
    library.dynam.unload("GraphAlignment", libpath)

Package detach functions should not call ‘library.dynam.unload’.
See section ‘Good practice’ in '?.Last.lib'.

AlignNetworks: no visible global function definition for ‘rnorm’
GenerateExample: no visible global function definition for ‘runif’
GenerateExample: no visible global function definition for ‘rnorm’
GenerateExample: no visible global function definition for ‘pnorm’
InitialAlignment: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  pnorm rnorm runif
Consider adding
  importFrom("stats", "pnorm", "rnorm", "runif")
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 ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/GraphAlignment/libs/GraphAlignment.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (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 nor [v]sprintf. 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GraphAlignment.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GraphAlignment
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘GraphAlignment’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c GA_alloc.c -o GA_alloc.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c GA_matrix.c -o GA_matrix.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c GA_matrix_R.c -o GA_matrix_R.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c GA_message.c -o GA_message.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c GA_vector.c -o GA_vector.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c GA_vector_R.c -o GA_vector_R.o
GA_vector_R.c: In function ‘GA_clamp_mode_from_R’:
GA_vector_R.c:139:9: warning: unused variable ‘size’ [-Wunused-variable]
  139 |     int size = LENGTH(robj);
      |         ^~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c GraphAlignment.c -o GraphAlignment.o
GraphAlignment.c: In function ‘GA_encode_directed_graph’:
GraphAlignment.c:138:20: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
  138 |                 if (matrix->elts[i][j] == 1)
      |                    ^
GraphAlignment.c:159:20: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
  159 |                 if (matrix->elts[i][j] == 1)
      |                    ^
GraphAlignment.c: In function ‘GA_directed_mode_from_R’:
GraphAlignment.c:264:9: warning: unused variable ‘size’ [-Wunused-variable]
  264 |     int size = LENGTH(robj);
      |         ^~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c lap.c -o lap.o
lap.c: In function ‘LAP_checklap’:
lap.c:348:9: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  348 |         scanf("%c", &wait);
      |         ^~~~~~~~~~~~~~~~~~
lap.c:358:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  358 |       scanf("%c", &wait);
      |       ^~~~~~~~~~~~~~~~~~
lap.c:371:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  371 |       scanf("%c", &wait);
      |       ^~~~~~~~~~~~~~~~~~
lap.c:384:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  384 |       scanf("%c", &wait);
      |       ^~~~~~~~~~~~~~~~~~
lap.c:394:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  394 |       scanf("%c", &wait);
      |       ^~~~~~~~~~~~~~~~~~
lap.c: In function ‘LAP_lap’:
lap.c:260:11: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized]
  260 |         h = assigncost[i][j1] - v[j1] - min;
      |         ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lap.c:65:8: note: ‘min’ was declared here
   65 |   cost min, h, umin, usubmin, v2, *d;
      |        ^~~
lap.c:293:19: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized]
  293 |     for (k = 0; k <= last; k++)
      |                 ~~^~~~~~~
lap.c:64:30: note: ‘last’ was declared here
   64 |   col  j, j1, j2, endofpath, last, low, up, *collist, *matches;
      |                              ^~~~
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o GraphAlignment.so GA_alloc.o GA_matrix.o GA_matrix_R.o GA_message.o GA_vector.o GA_vector_R.o GraphAlignment.o lap.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-GraphAlignment/00new/GraphAlignment/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 (GraphAlignment)