##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CGEN.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CGEN_3.43.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CGEN.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘CGEN/DESCRIPTION’ ... OK
* this is package ‘CGEN’ version ‘3.43.0’
* 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 ‘CGEN’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
See ‘/home/biocbuild/bbs-3.21-bioc/meat/CGEN.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL-2 + file LICENSE
* 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 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 ... NOTE
checkRd: (-1) snp.effects.plot.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.effects.plot.Rd:38-40: Lost braces in \itemize; meant \describe ?
* 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 is not available
* checking usage of KIND in Fortran files ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
additive.test  36.609  0.208  36.823
snp.matched    14.530  0.002  14.534
getMatchedSets 12.067  0.089  12.156
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CGEN.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CGEN
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘CGEN’ ...
** this is package ‘CGEN’ version ‘3.43.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Additive.c -o Additive.o
Additive.c: In function ‘vecinit’:
Additive.c:103:13: warning: old-style function definition [-Wold-style-definition]
  103 | static void vecinit(vec, n, c)
      |             ^~~~~~~
Additive.c: In function ‘vecmove’:
Additive.c:115:13: warning: old-style function definition [-Wold-style-definition]
  115 | static void vecmove(invec, n, outvec)
      |             ^~~~~~~
Additive.c: In function ‘vecMultCon’:
Additive.c:130:13: warning: old-style function definition [-Wold-style-definition]
  130 | static void vecMultCon(invec, n, c, ret)
      |             ^~~~~~~~~~
Additive.c: In function ‘rMatMMultVec’:
Additive.c:144:13: warning: old-style function definition [-Wold-style-definition]
  144 | static void rMatMMultVec(mat, nrow, ncol, vec, ret)
      |             ^~~~~~~~~~~~
Additive.c: In function ‘mylog’:
Additive.c:172:15: warning: old-style function definition [-Wold-style-definition]
  172 | static double mylog(x)
      |               ^~~~~
Additive.c: In function ‘mylog2’:
Additive.c:187:15: warning: old-style function definition [-Wold-style-definition]
  187 | static double mylog2(x)
      |               ^~~~~~
Additive.c: In function ‘compute_g’:
Additive.c:203:13: warning: old-style function definition [-Wold-style-definition]
  203 | static void compute_g(method, theta, x1cols, x2cols, g11, g12, g21, g22)
      |             ^~~~~~~~~
Additive.c: In function ‘add1’:
Additive.c:242:15: warning: old-style function definition [-Wold-style-definition]
  242 | static double add1(theta, op)
      |               ^~~~
Additive.c: In function ‘getLL_mat’:
Additive.c:297:13: warning: old-style function definition [-Wold-style-definition]
  297 | static void getLL_mat(op)
      |             ^~~~~~~~~
Additive.c: In function ‘Pdg_xs’:
Additive.c:344:13: warning: old-style function definition [-Wold-style-definition]
  344 | static void Pdg_xs(eta, op)
      |             ^~~~~~
Additive.c: In function ‘add1_indep’:
Additive.c:416:15: warning: old-style function definition [-Wold-style-definition]
  416 | static double add1_indep(theta, op)
      |               ^~~~~~~~~~
Additive.c: In function ‘negloglike’:
Additive.c:463:15: warning: old-style function definition [-Wold-style-definition]
  463 | static double negloglike(theta, op)
      |               ^~~~~~~~~~
Additive.c: In function ‘gradient’:
Additive.c:484:13: warning: old-style function definition [-Wold-style-definition]
  484 | static void gradient(eta, op, ret)
      |             ^~~~~~~~
Additive.c: In function ‘getadd1’:
Additive.c:677:13: warning: old-style function definition [-Wold-style-definition]
  677 | static void getadd1(op, meth)
      |             ^~~~~~~
Additive.c: In function ‘additive1’:
Additive.c:730:6: warning: old-style function definition [-Wold-style-definition]
  730 | void additive1(theta0, nparms, x1cols, nx1, x2cols, nx2, datX, Xnrow, Xncol, covs, ncovs, y, method,\
      |      ^~~~~~~~~
Additive.c: In function ‘additive1_indep’:
Additive.c:784:6: warning: old-style function definition [-Wold-style-definition]
  784 | void additive1_indep(theta0, nparms, x1cols, nx1, x2cols, nx2, Xnrow, covCols, ncovs, method,\
      |      ^~~~~~~~~~~~~~~
Additive.c: In function ‘compute_g’:
Additive.c:235:25: warning: ‘t22’ may be used uninitialized [-Wmaybe-uninitialized]
  235 |       *g22 = logx - t12 - t22;
      |              ~~~~~~~~~~~^~~~~
Additive.c:207:25: note: ‘t22’ was declared here
  207 |   double t11, t12, t21, t22, x, et11, et12, et21, et22, logx;
      |                         ^~~
Additive.c:233:19: warning: ‘et22’ may be used uninitialized [-Wmaybe-uninitialized]
  233 |       x    = et12 + et22 - 1;
      |              ~~~~~^~~~~~
Additive.c:207:51: note: ‘et22’ was declared here
  207 |   double t11, t12, t21, t22, x, et11, et12, et21, et22, logx;
      |                                                   ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c CML.c -o CML.o
CML.c: In function ‘vecinit’:
CML.c:147:13: warning: old-style function definition [-Wold-style-definition]
  147 | static void vecinit(vec, n, c)
      |             ^~~~~~~
CML.c: In function ‘vecmove’:
CML.c:159:13: warning: old-style function definition [-Wold-style-definition]
  159 | static void vecmove(invec, n, outvec)
      |             ^~~~~~~
CML.c: In function ‘vecsum’:
CML.c:174:15: warning: old-style function definition [-Wold-style-definition]
  174 | static double vecsum(vec, n)
      |               ^~~~~~
CML.c: In function ‘vecMultCon’:
CML.c:191:13: warning: old-style function definition [-Wold-style-definition]
  191 | static void vecMultCon(invec, n, c, ret)
      |             ^~~~~~~~~~
CML.c: In function ‘rMatMMultVec’:
CML.c:205:13: warning: old-style function definition [-Wold-style-definition]
  205 | static void rMatMMultVec(mat, nrow, ncol, vec, ret)
      |             ^~~~~~~~~~~~
CML.c: In function ‘rmatrixMult’:
CML.c:229:13: warning: old-style function definition [-Wold-style-definition]
  229 | static void rmatrixMult(m1, m1_nr, m1_nc, m2, m2_nc, ret)
      |             ^~~~~~~~~~~
CML.c: In function ‘Pdg_xs’:
CML.c:249:13: warning: old-style function definition [-Wold-style-definition]
  249 | static void Pdg_xs(eta, op)
      |             ^~~~~~
CML.c: In function ‘Pd1_xs’:
CML.c:407:13: warning: old-style function definition [-Wold-style-definition]
  407 | static void Pd1_xs(op, ret, index)
      |             ^~~~~~
CML.c: In function ‘Edg_xs’:
CML.c:427:13: warning: old-style function definition [-Wold-style-definition]
  427 | static void Edg_xs(op, ret, ret2, index)
      |             ^~~~~~
CML.c: In function ‘Eg_xs’:
CML.c:461:13: warning: old-style function definition [-Wold-style-definition]
  461 | static void Eg_xs(op, ret, index)
      |             ^~~~~
CML.c: In function ‘getWtYmu’:
CML.c:482:13: warning: old-style function definition [-Wold-style-definition]
  482 | static void getWtYmu(eta, op, ret)
      |             ^~~~~~~~
CML.c: In function ‘fSNP’:
CML.c:565:15: warning: old-style function definition [-Wold-style-definition]
  565 | static double fSNP(SNP, gmodel)
      |               ^~~~
CML.c: In function ‘getLL_mat’:
CML.c:588:13: warning: old-style function definition [-Wold-style-definition]
  588 | static void getLL_mat(op)
      |             ^~~~~~~~~
CML.c: In function ‘negloglike’:
CML.c:638:15: warning: old-style function definition [-Wold-style-definition]
  638 | static double negloglike(eta, op)
      |               ^~~~~~~~~~
CML.c: In function ‘gradient’:
CML.c:666:13: warning: old-style function definition [-Wold-style-definition]
  666 | static void gradient(eta, op, ret)
      |             ^~~~~~~~
CML.c: In function ‘hessian’:
CML.c:697:13: warning: old-style function definition [-Wold-style-definition]
  697 | static void hessian(eta, op, ret)
      |             ^~~~~~~
CML.c: In function ‘chol’:
CML.c:895:13: warning: old-style function definition [-Wold-style-definition]
  895 | static void chol(mat, n, ret, retdiag)
      |             ^~~~
CML.c: In function ‘cholinv’:
CML.c:931:13: warning: old-style function definition [-Wold-style-definition]
  931 | static void cholinv(L, diag, n, ret)
      |             ^~~~~~~
CML.c: In function ‘rmatTranspose’:
CML.c:957:13: warning: old-style function definition [-Wold-style-definition]
  957 | static void rmatTranspose(mat, n, ret)
      |             ^~~~~~~~~~~~~
CML.c: In function ‘symrMatInv’:
CML.c:973:13: warning: old-style function definition [-Wold-style-definition]
  973 | static void symrMatInv(mat, n, ret)
      |             ^~~~~~~~~~
CML.c: In function ‘getCML’:
CML.c:995:13: warning: old-style function definition [-Wold-style-definition]
  995 | static void getCML(eta, op)
      |             ^~~~~~
CML.c: In function ‘getEB’:
CML.c:1044:13: warning: old-style function definition [-Wold-style-definition]
 1044 | static void getEB(op)
      |             ^~~~~
CML.c: In function ‘check_init’:
CML.c:1256:13: warning: old-style function definition [-Wold-style-definition]
 1256 | static void check_init(eta, op)
      |             ^~~~~~~~~~
CML.c: In function ‘CML_EB’:
CML.c:1318:6: warning: old-style function definition [-Wold-style-definition]
 1318 | void CML_EB(eta0, nparms, nbeta, D, snp, nrow, xMain, nx, xInt, nv, xStrata, nstrata, gmodel, genoBinary,\
      |      ^~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ccl.c -o ccl.o
gfortran  -fpic  -g -O2  -Wall -Werror=format-security -c csclust.f -o csclust.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
f951: Warning: Nonconforming tab character in column 1 of line 46 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 83 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 203 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 205 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 207 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 270 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 271 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 275 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 276 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 277 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 278 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 282 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 283 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 286 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 287 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 288 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 289 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 290 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 291 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 292 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 293 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 294 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 295 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 296 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 306 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 307 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 309 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 310 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 311 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 312 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 313 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 314 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 315 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 316 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 317 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 319 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 320 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 321 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 329 [-Wtabs]
csclust.f:72:72:

   72 |  10      FLAG(I)=.TRUE.
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
csclust.f:222:3:

  222 | 650   RETURN
      |   1
Warning: Label 650 at (1) defined but not used [-Wunused-label]
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c fsclust.c -o fsclust.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c hcl.c -o hcl.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c pmatch.c -o pmatch.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c score.c -o score.o
score.c: In function ‘infoSmallStandard’:
score.c:14:6: warning: old-style function definition [-Wold-style-definition]
   14 | void infoSmallStandard(xmat, pnr, pnc, pphat, infoSum)
      |      ^~~~~~~~~~~~~~~~~
score.c: In function ‘getCOV0’:
score.c:48:6: warning: old-style function definition [-Wold-style-definition]
   48 | void getCOV0(pncinf, phatprod, pn, pinfoprods, retcov)
      |      ^~~~~~~
score.c: In function ‘getCOV1’:
score.c:80:6: warning: old-style function definition [-Wold-style-definition]
   80 | void getCOV1(pnc, pn, weights, twopmu, pinfob1, pinfoh, pinfohnc, retcov)
      |      ^~~~~~~
score.c: In function ‘getScore’:
score.c:133:6: warning: old-style function definition [-Wold-style-definition]
  133 | void getScore(y, score, pnr, pnc, avgscore0, avgscore1, retcov)
      |      ^~~~~~~~
score.c: In function ‘getScoreEB’:
score.c:174:6: warning: old-style function definition [-Wold-style-definition]
  174 | void getScoreEB(y, score1, score2, pnr, pnc1, pnc2, avgscore1_0, avgscore1_1,
      |      ^~~~~~~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-CGEN/00new/CGEN/libs
** 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
** 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 (CGEN)