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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fmrs.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings fmrs_1.5.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/fmrs.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fmrs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fmrs' version '1.5.0'
* package encoding: UTF-8
* 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 'fmrs' 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/fmrs/libs/x64/fmrs.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/fmrs.Rcheck/00check.log'
for details.

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###
### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL fmrs
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'fmrs' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c fmrs.c -o fmrs.o
fmrs.c: In function 'minimum':
fmrs.c:138:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
   for(i = 0; i < ncov1; i++)
   ^~~
fmrs.c:142:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
     return(min1);
     ^~~~~~
fmrs.c: In function 'maximum':
fmrs.c:152:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
   for(i = 0; i < ncov1; i++)
   ^~~
fmrs.c:156:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
     return(max1);
     ^~~~~~
fmrs.c: In function 'FMR_Norm_Surv_EM_MLE':
fmrs.c:457:11: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
           for(j = 0; j < (ONCOV[k1] + 1); j++)
           ^~~
fmrs.c:463:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
             for (i = 0; i < (ONCOV[k1] + 1); i++) {
             ^~~
fmrs.c:285:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
     double multX[nsize][NCOV][NCOMP];
            ^~~~~
fmrs.c: In function 'FMR_Norm_Surv_EM_VarSel':
fmrs.c:883:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
         for(j = 0; j < NCOV; j++)
         ^~~
fmrs.c:887:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
           for(i = 0; i < ONCOV[k1]; i++){
           ^~~
fmrs.c:915:13: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
             for(j = 0; j < (ONCOV[k1] + 1); j++)
             ^~~
fmrs.c:921:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
               for (i = 0; i < (ONCOV[k1] + 1); i++) {
               ^~~
fmrs.c:687:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
     double multX[nsize][NCOV][NCOMP];
            ^~~~~
fmrs.c: In function 'FMR_Norm_Surv_CwTuneParSel':
fmrs.c:1403:11: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
           for(j = 0; j < (ONCOV[k1] + 1); j++)
           ^~~
fmrs.c:1409:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
             for (i = 0; i < (ONCOV[k1] + 1); i++) {
             ^~~
fmrs.c:1218:12: warning: variable 'new_pi0' set but not used [-Wunused-but-set-variable]
     double new_pi0[NCOMP];
            ^~~~~~~
fmrs.c:1211:12: warning: variable 'new_sigma0' set but not used [-Wunused-but-set-variable]
     double new_sigma0[NCOMP];
            ^~~~~~~~~~
fmrs.c:1196:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
     double multX[nsize][NCOV][NCOMP];
            ^~~~~
fmrs.c: In function 'FMR_Weibl_Surv_EM_MLE':
fmrs.c:1752:13: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
             for(j = 0; j < (ONCOV[k1] + 1); j++)
             ^~~
fmrs.c:1758:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
               for (i = 0; i < (ONCOV[k1] + 1); i++) {
               ^~~
fmrs.c:1547:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
     double multX[nsize][NCOV][NCOMP];
            ^~~~~
fmrs.c: In function 'FMR_Weibl_Surv_EM_VarSel':
fmrs.c:2205:11: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
           for(j = 0; j < (NCOV + 1); j++)
           ^~~
fmrs.c:2212:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
             for(i = 0; i < (NCOV + 1); i++){
             ^~~
fmrs.c:2251:15: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
               for(j = 0; j < (NCOV + 2); j++)
               ^~~
fmrs.c:2257:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
                 for (i = 0; i < (NCOV + 2); i++) {
                 ^~~
fmrs.c:2271:19: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
                   for(j = 0; j < (NCOV + 1); j++)
                   ^~~
fmrs.c:2277:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
                     sumi5[k1] = 0.0;
                     ^~~~~
fmrs.c: In function 'FMR_Weibl_Surv_CwTuneParSel':
fmrs.c:2745:11: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
           for(j = 0; j < NCOV; j++)
           ^~~
fmrs.c:2750:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
             for(i = 0; i < ONCOV[k1]; i++){
             ^~~
fmrs.c:2553:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
     double multX[nsize][NCOV][k1];
            ^~~~~
fmrs.c: In function 'FMR_Norm_Surv_EM_VarSel':
fmrs.c:748:12: warning: 'sat_den' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double sat_den;
            ^~~~~~~
fmrs.c: In function 'FMR_Weibl_Surv_EM_VarSel':
fmrs.c:2072:12: warning: 'sat_den' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double sat_den;
            ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c fmrs_init.c -o fmrs_init.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o fmrs.dll tmp.def fmrs.o fmrs_init.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-fmrs/00new/fmrs/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'fmrs'
    finding HTML links ... done
    BIC-methods                             html  
    coefficients-methods                    html  
    dispersion-methods                      html  
    fitted-methods                          html  
    fmrs-package                            html  
    fmrs.gendata-methods                    html  
    fmrs.mle-methods                        html  
    fmrs.tunsel-methods                     html  
    fmrs.varsel-methods                     html  
    fmrsfit-class                           html  
    fmrstunpar-class                        html  
    logLik-methods                          html  
    mixProp-methods                         html  
    ncomp-methods                           html  
    ncov-methods                            html  
    nobs-methods                            html  
    residuals-methods                       html  
    summary-methods                         html  
    weights-methods                         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
* DONE (fmrs)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'RLMM' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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.

> library(testthat)
> library(fmrs)
BugReports: https://github.com/shokoohi/fmrs/issues
> 
> test_check("fmrs")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   1.59    0.18    1.76