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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gaga.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gaga_2.52.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gaga.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘gaga/DESCRIPTION’ ... OK
* this is package ‘gaga’ version ‘2.52.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘gaga’ can be installed ... WARNING
Found the following significant warnings:
  cstat.c:667:20: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘v + (sizetype)((long unsigned int)nl * 4)’ must not be NULL [-Waddress]
  cstat.c:673:20: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘v + (sizetype)((long unsigned int)nl * 8)’ must not be NULL [-Waddress]
  cstat.c:679:20: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘v + (sizetype)((long unsigned int)nl * 4)’ must not be NULL [-Waddress]
  cstat.c:687:47: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘*(m + (sizetype)((long unsigned int)i * 8)) + (sizetype)((long unsigned int)ncl * 8)’ must not be NULL [-Waddress]
  cstat.c:689:21: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘m + (sizetype)((long unsigned int)nrl * 8)’ must not be NULL [-Waddress]
  cstat.c:697:47: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘*(m + (sizetype)((long unsigned int)i * 8)) + (sizetype)((long unsigned int)ncl * 4)’ must not be NULL [-Waddress]
  cstat.c:699:21: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘m + (sizetype)((long unsigned int)nrl * 8)’ must not be NULL [-Waddress]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/gaga.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 ... 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 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 ... NOTE
adjustfitNN: no visible global function definition for ‘predict’
checkfit.gagafit: no visible global function definition for ‘is’
checkfit.gagafit: no visible global function definition for ‘density’
checkfit.gagafit: no visible global function definition for ‘lines’
checkfit.gagafit: no visible global function definition for ‘legend’
checkfit.gagafit: no visible global function definition for ‘quantile’
checkfit.gagafit: no visible global function definition for ‘points’
classpred.gagafit: no visible global function definition for ‘is’
findgenes.gagafit: no visible global function definition for ‘is’
findgenes.gagafit: no visible global function definition for ‘kmeans’
fitGG: no visible global function definition for ‘is’
fitGG: no visible global function definition for ‘quantile’
fitGG: no visible global function definition for ‘var’
fitGG: no visible global function definition for ‘kmeans’
fitNN: no visible global function definition for ‘is’
fitNNSingleHyp: no visible global function definition for ‘is’
forwsimDiffExpr.gagafit: no visible global function definition for ‘is’
forwsimDiffExpr.nnfit: no visible global function definition for ‘is’
forwsimDiffExpr.nnfit: no visible global function definition for
  ‘quantile’
makeEBarraysSingleHyp: no visible global function definition for ‘new’
parest.gagafit: no visible global function definition for ‘is’
parest.gagafit: no visible binding for global variable ‘quantile’
parest.gagafit: no visible global function definition for ‘quantile’
plotForwSim: no visible global function definition for ‘lines’
posmeansGG.gagafit: no visible global function definition for ‘is’
powclasspred.gagafit: no visible global function definition for ‘is’
powfindgenes.gagafit: no visible global function definition for ‘is’
powfindgenes.nnfit: no visible global function definition for ‘is’
powfindgenes.nnfit: no visible global function definition for ‘sd’
powsimprior.nnfit: no visible global function definition for ‘sd’
ppGG: no visible global function definition for ‘is’
sigmaPriorEst: no visible global function definition for ‘is’
sigmaPriorEst: no visible binding for global variable ‘var’
sigmaPriorEst: no visible global function definition for ‘var’
simGG: no visible global function definition for ‘rgamma’
simGG: no visible global function definition for ‘new’
simNN: no visible global function definition for ‘runif’
simNN: no visible global function definition for ‘rnorm’
simNN: no visible global function definition for ‘rgamma’
simNN: no visible global function definition for ‘new’
simnewsamples.gagafit: no visible global function definition for ‘is’
simnewsamples.gagafit: no visible global function definition for ‘new’
simnewsamples.nnfit: no visible global function definition for ‘is’
simnewsamples.nnfit: no visible global function definition for ‘runif’
simnewsamples.nnfit: no visible global function definition for ‘rgamma’
simnewsamples.nnfit: no visible global function definition for ‘rnorm’
simnewsamples.nnfit: no visible global function definition for
  ‘model.matrix’
simnewsamples.nnfit: no visible global function definition for ‘new’
Undefined global functions or variables:
  density is kmeans legend lines model.matrix new points predict
  quantile rgamma rnorm runif sd var
Consider adding
  importFrom("graphics", "legend", "lines", "points")
  importFrom("methods", "is", "new")
  importFrom("stats", "density", "kmeans", "model.matrix", "predict",
             "quantile", "rgamma", "rnorm", "runif", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/gaga.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 gaga
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘gaga’ ...
** 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 cseqdesma.c -o cseqdesma.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cstat.c -o cstat.o
cstat.c: In function ‘free_vector’:
cstat.c:667:20: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘v + (sizetype)((long unsigned int)nl * 4)’ must not be NULL [-Waddress]
  667 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                    ^~
cstat.c: In function ‘free_dvector’:
cstat.c:673:20: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘v + (sizetype)((long unsigned int)nl * 8)’ must not be NULL [-Waddress]
  673 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                    ^~
cstat.c: In function ‘free_ivector’:
cstat.c:679:20: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘v + (sizetype)((long unsigned int)nl * 4)’ must not be NULL [-Waddress]
  679 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                    ^~
cstat.c: In function ‘free_dmatrix’:
cstat.c:687:47: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘*(m + (sizetype)((long unsigned int)i * 8)) + (sizetype)((long unsigned int)ncl * 8)’ must not be NULL [-Waddress]
  687 |         for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL )
      |                                               ^~
cstat.c:689:21: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘m + (sizetype)((long unsigned int)nrl * 8)’ must not be NULL [-Waddress]
  689 |         if( (m+nrl) != NULL ) free((char  *) (m+nrl));
      |                     ^~
cstat.c: In function ‘free_imatrix’:
cstat.c:697:47: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘*(m + (sizetype)((long unsigned int)i * 8)) + (sizetype)((long unsigned int)ncl * 4)’ must not be NULL [-Waddress]
  697 |         for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL )
      |                                               ^~
cstat.c:699:21: warning: the comparison will always evaluate as ‘true’ for the pointer operand in ‘m + (sizetype)((long unsigned int)nrl * 8)’ must not be NULL [-Waddress]
  699 |         if( (m+nrl) != NULL ) free((char  *) (m+nrl));
      |                     ^~
cstat.c: At top level:
cstat.c:22:19: warning: ‘css_c_sccs_id’ defined but not used [-Wunused-const-variable=]
   22 | static const char css_c_sccs_id[] = "@(#)$Workfile: rand.c$ $Revision: 5$";
      |                   ^~~~~~~~~~~~~
cstat.c:21:19: warning: ‘vector_c_sccs_id’ defined but not used [-Wunused-const-variable=]
   21 | static const char vector_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~~~
cstat.c:20:19: warning: ‘nrutil_c_sccs_id’ defined but not used [-Wunused-const-variable=]
   20 | static const char nrutil_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~~~
cstat.c:19:19: warning: ‘mess_c_sccs_id’ defined but not used [-Wunused-const-variable=]
   19 | static const char mess_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~
cstat.c:18:19: warning: ‘interface_c_sccs_id’ defined but not used [-Wunused-const-variable=]
   18 | static const char interface_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o gaga.so cseqdesma.o cstat.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-gaga/00new/gaga/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 (gaga)