##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SUITOR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SUITOR_1.9.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/SUITOR.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SUITOR/DESCRIPTION' ... OK
* this is package 'SUITOR' version '1.9.0'
* 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 'SUITOR' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* 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 ... 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 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
suitorExtractWH 11.7   0.08   11.78
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/SUITOR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL SUITOR
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'SUITOR' ...
** this is package 'SUITOR' version '1.9.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SUITOR_init.c -o SUITOR_init.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c source.c -o source.o
source.c: In function 'dVec_alloc':
source.c:166:17: warning: old-style function definition [-Wold-style-definition]
  166 | static double * dVec_alloc(n, initFlag, initVal)
      |                 ^~~~~~~~~~
source.c: In function 'iVec_alloc':
source.c:185:14: warning: old-style function definition [-Wold-style-definition]
  185 | static int * iVec_alloc(n, initFlag, initVal)
      |              ^~~~~~~~~~
source.c: In function 'cVec_alloc':
source.c:203:15: warning: old-style function definition [-Wold-style-definition]
  203 | static char * cVec_alloc(n, initFlag, initVal)
      |               ^~~~~~~~~~
source.c: In function 'copy_dVec':
source.c:222:13: warning: old-style function definition [-Wold-style-definition]
  222 | static void copy_dVec(v, n, ret)
      |             ^~~~~~~~~
source.c: In function 'matrixMult':
source.c:233:13: warning: old-style function definition [-Wold-style-definition]
  233 | static void matrixMult(m1, m1_nr, m1_nc, m2, m2_nc, ret)
      |             ^~~~~~~~~~
source.c: In function 'which_max':
source.c:256:12: warning: old-style function definition [-Wold-style-definition]
  256 | static int which_max(v, n)
      |            ^~~~~~~~~
source.c: In function 'which_max_cols':
source.c:280:13: warning: old-style function definition [-Wold-style-definition]
  280 | static void which_max_cols(mat, nr, nc, ret)
      |             ^~~~~~~~~~~~~~
source.c: In function 'update_cons':
source.c:292:12: warning: old-style function definition [-Wold-style-definition]
  292 | static int update_cons(cons, cons_len, index, nc)
      |            ^~~~~~~~~~~
source.c: In function 'myStopFun':
source.c:323:12: warning: old-style function definition [-Wold-style-definition]
  323 | static int myStopFun(cons, cons_len, inc, hMat, hnr, hnc, maxIndex)
      |            ^~~~~~~~~
source.c: In function 'get_runif_vec':
source.c:348:13: warning: old-style function definition [-Wold-style-definition]
  348 | static void get_runif_vec(v, n, a, b)
      |             ^~~~~~~~~~~~~
source.c: In function 'get_idxMat0':
source.c:359:12: warning: old-style function definition [-Wold-style-definition]
  359 | static int get_idxMat0(idx, nr, nc, k, kfold)
      |            ^~~~~~~~~~~
source.c: In function 'loglike':
source.c:385:15: warning: old-style function definition [-Wold-style-definition]
  385 | static double loglike(input, log_input, input_k_hat, idxMat, delta_denom, len, which_idx)
      |               ^~~~~~~
source.c: In function 'replaceZeroVal_dVec':
source.c:416:13: warning: old-style function definition [-Wold-style-definition]
  416 | static void replaceZeroVal_dVec(v, n, minval)
      |             ^~~~~~~~~~~~~~~~~~~
source.c: In function 'get_delta_denom':
source.c:428:15: warning: old-style function definition [-Wold-style-definition]
  428 | static double get_delta_denom(v, n)
      |               ^~~~~~~~~~~~~~~
source.c: In function 'get_max':
source.c:444:15: warning: old-style function definition [-Wold-style-definition]
  444 | static double get_max(v, n)
      |               ^~~~~~~
source.c: In function 'my_update_H':
source.c:460:13: warning: old-style function definition [-Wold-style-definition]
  460 | static void my_update_H(pV, w, h, wnr, wnc, hnc)
      |             ^~~~~~~~~~~
source.c: In function 'my_update_W':
source.c:539:13: warning: old-style function definition [-Wold-style-definition]
  539 | static void my_update_W(pV, w, h, wnr, wnc, hnc)
      |             ^~~~~~~~~~~
source.c: In function 'my_update_brunet':
source.c:611:13: warning: old-style function definition [-Wold-style-definition]
  611 | static void my_update_brunet(i, x, w, h, str)
      |             ^~~~~~~~~~~~~~~~
source.c: In function 'get_init_WH':
source.c:636:13: warning: old-style function definition [-Wold-style-definition]
  636 | static void get_init_WH(runifVec, w, h, wlen, hlen, maxval)
      |             ^~~~~~~~~~~
source.c: In function 'call_nmf':
source.c:655:13: warning: old-style function definition [-Wold-style-definition]
  655 | static void call_nmf(mat, str)
      |             ^~~~~~~~
source.c: In function 'update_x_k':
source.c:714:13: warning: old-style function definition [-Wold-style-definition]
  714 | static void update_x_k(x_k, x_k_hat, idxMat, n)
      |             ^~~~~~~~~~
source.c: In function 'get_median':
source.c:838:15: warning: old-style function definition [-Wold-style-definition]
  838 | static double get_median(v, n)
      |               ^~~~~~~~~~
source.c: In function 'get_init_x_k':
source.c:863:13: warning: old-style function definition [-Wold-style-definition]
  863 | static void get_init_x_k(x, x_k, idxMat, nr, nc, tmpvec, minvalue)
      |             ^~~~~~~~~~~~
source.c: In function 'get_colsums':
source.c:916:13: warning: old-style function definition [-Wold-style-definition]
  916 | static void get_colsums(x, nr, nc, ret)
      |             ^~~~~~~~~~~
source.c: In function 'transpose':
source.c:934:13: warning: old-style function definition [-Wold-style-definition]
  934 | static void transpose(v, nr, nc, ret)
      |             ^~~~~~~~~
source.c: In function 'ECM_update_h':
source.c:949:13: warning: old-style function definition [-Wold-style-definition]
  949 | static void ECM_update_h(h1, h0, w0, x_k, hnr, hnc, wnr, wnc, xnr, xnc, vM, vN, vN2)
      |             ^~~~~~~~~~~~
source.c: In function 'ECM_update_w':
source.c:983:13: warning: old-style function definition [-Wold-style-definition]
  983 | static void ECM_update_w(w1, h1, w0, x_k, hnr, hnc, wnr, wnc, xnr, xnc, vM, vN, vN2)
      |             ^~~~~~~~~~~~
source.c: In function 'ECM_alg':
source.c:1017:12: warning: old-style function definition [-Wold-style-definition]
 1017 | static int ECM_alg(str)
      |            ^~~~~~~
source.c: In function 'init_wh_rank':
source.c:1093:13: warning: old-style function definition [-Wold-style-definition]
 1093 | static void init_wh_rank(str, rank)
      |             ^~~~~~~~~~~~
source.c: In function 'suitor_main':
source.c:1119:13: warning: old-style function definition [-Wold-style-definition]
 1119 | static void suitor_main(str)
      |             ^~~~~~~~~~~
source.c: In function 'init_logx':
source.c:1203:13: warning: old-style function definition [-Wold-style-definition]
 1203 | static void init_logx(x, logx, n)
      |             ^~~~~~~~~
source.c: In function 'NMFSTR_init':
source.c:1221:13: warning: old-style function definition [-Wold-style-definition]
 1221 | static void NMFSTR_init(str, iargs, dargs, xmat)
      |             ^~~~~~~~~~~
source.c: In function 'NMFSTR_free':
source.c:1311:13: warning: old-style function definition [-Wold-style-definition]
 1311 | static void NMFSTR_free(str, EMflag)
      |             ^~~~~~~~~~~
source.c: In function 'C_call_nmf':
source.c:1339:6: warning: old-style function definition [-Wold-style-definition]
 1339 | void C_call_nmf(mat, iargs, dargs, retW, retH)
      |      ^~~~~~~~~~
source.c: In function 'C_call_suitor':
source.c:1361:6: warning: old-style function definition [-Wold-style-definition]
 1361 | void C_call_suitor(mat, iargs, dargs, rankVec, kVec, ret_train, ret_test, ret_convVec, ret_EM_niterVec)
      |      ^~~~~~~~~~~~~
gcc -shared -s -static-libgcc -o SUITOR.dll tmp.def SUITOR_init.o source.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-SUITOR/00new/SUITOR/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SUITOR)

R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> BiocGenerics:::testPackage("SUITOR")


RUNIT TEST PROTOCOL -- Wed Mar 19 06:42:42 2025 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SUITOR RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.39    0.29    1.67