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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:metaArray.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings metaArray_1.66.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/metaArray.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaArray/DESCRIPTION’ ... OK
* this is package ‘metaArray’ version ‘1.66.0’
* 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 ‘metaArray’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'MergeMaid' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.11-bioc/meat/metaArray.Rcheck/00install.out’ for details.
* 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 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 ... NOTE
poe.mcmc: no visible binding for global variable ‘R0’
Undefined global functions or variables:
  R0
* checking Rd files ... NOTE
prepare_Rd: em.draw.Rd:28-30: Dropping empty section \examples
prepare_Rd: find.init.Rd:20-21: Dropping empty section \examples
prepare_Rd: fit.em.Rd:31-33: Dropping empty section \examples
prepare_Rd: poe.em.Rd:22: Dropping empty section \examples
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.11-bioc/R/library/metaArray/libs/metaArray.so’:
  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 ... 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 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/metaArray.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL metaArray
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘metaArray’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c contr.c -o contr.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c dproc.c -o dproc.o
dproc.c: In function ‘malloc_CH’:
dproc.c:111:21: warning: variable ‘num’ set but not used [-Wunused-but-set-variable]
   int i, j, nr, nc, num;
                     ^~~
dproc.c: In function ‘free_CH’:
dproc.c:192:16: warning: unused variable ‘nc’ [-Wunused-variable]
   int num, nr, nc;
                ^~
dproc.c:192:12: warning: variable ‘nr’ set but not used [-Wunused-but-set-variable]
   int num, nr, nc;
            ^~
dproc.c:192:7: warning: variable ‘num’ set but not used [-Wunused-but-set-variable]
   int num, nr, nc;
       ^~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c dproc2.c -o dproc2.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c intcor.c -o intcor.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c lowess.c -o lowess.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c mmath.c -o mmath.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c perm.c -o perm.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c poe.c -o poe.o
poe.c: In function ‘poe_one_iter’:
poe.c:131:53: warning: variable ‘shift’ set but not used [-Wunused-but-set-variable]
   double kappa_b, kappa_a, kappa_new, aaa, res_max, shift;
                                                     ^~~~~
poe.c:120:20: warning: variable ‘accept’ set but not used [-Wunused-but-set-variable]
   int nr,nc,tt,gg, accept;
                    ^~~~~~
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o metaArray.so contr.o dproc.o dproc2.o intcor.o lowess.o mmath.o perm.o poe.o -lm -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-metaArray/00new/metaArray/libs
** R
** data
** byte-compile and prepare package for lazy loading
Warning: Package 'MergeMaid' is deprecated and will be removed from Bioconductor
  version 3.12
** 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 (metaArray)