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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GlobalAncova.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GlobalAncova_4.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GlobalAncova.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 ‘GlobalAncova/DESCRIPTION’ ... OK
* this is package ‘GlobalAncova’ version ‘4.24.0’
* 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 ‘GlobalAncova’ can be installed ... WARNING
Found the following significant warnings:
  GlobalAncova.c:33:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:38:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:43:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:48:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:88:54: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:100:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:148:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:153:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:158:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:163:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:170:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:250:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:255:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:260:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:265:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  GlobalAncova.c:272:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/GlobalAncova.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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.nPerms: no visible global function definition for ‘terms’
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
.pAsymptotic: no visible global function definition for ‘qnorm’
.pAsymptotic: no visible global function definition for ‘pchisq’
.pGAapprox: no visible global function definition for ‘model.matrix’
GABroad: no visible global function definition for ‘is’
GABroad: no visible binding for global variable ‘collectionType’
GABroad: no visible binding for global variable ‘geneIds’
GABroad: no visible global function definition for ‘p.adjust’
GAGO: no visible binding for global variable ‘Ontology’
GAGO: no visible global function definition for ‘is’
GAGO: no visible global function definition for ‘p.adjust’
GAGO : <anonymous>: no visible global function definition for ‘is’
Gsquared: no visible global function definition for ‘glm’
Gsquared: no visible binding for global variable ‘multinomial’
Gsquared: no visible global function definition for ‘pchisq’
Gsquared: no visible global function definition for ‘qchisq’
Plot.all: no visible global function definition for ‘par’
Plot.all: no visible global function definition for ‘layout’
Plot.features: no visible global function definition for ‘barplot’
Plot.sequential: no visible global function definition for ‘par’
Plot.sequential: no visible global function definition for ‘barplot’
Plot.sequential: no visible global function definition for ‘legend’
Plot.sequential: no visible global function definition for ‘axis’
Tperm.catcat: no visible global function definition for ‘pchisq’
Tperm.catcat: no visible global function definition for ‘qchisq’
coldend: no visible global function definition for ‘is.leaf’
decomp.ssq: no visible global function definition for ‘model.matrix’
decomp.ssq: no visible global function definition for ‘as.formula’
decomp.ssq: no visible global function definition for ‘anova’
decomp.ssq: no visible global function definition for ‘lm’
decomp.ssq: no visible global function definition for ‘pf’
decomp.ssq.genewise: no visible global function definition for
  ‘model.matrix’
decomp.ssq.genewise: no visible global function definition for
  ‘as.formula’
decomp.ssq.genewise: no visible global function definition for ‘anova’
decomp.ssq.genewise: no visible global function definition for ‘lm’
decomp.ssq.genewise: no visible global function definition for ‘pf’
devtest: no visible global function definition for ‘formula’
devtest: no visible global function definition for ‘na.omit’
devtest: no visible global function definition for ‘pchisq’
devtest: no visible global function definition for ‘qchisq’
expr.test: no visible global function definition for ‘terms’
expr.test: no visible global function definition for ‘model.matrix’
gGAteststats: no visible global function definition for ‘terms’
gGAteststats: no visible global function definition for
  ‘complete.cases’
gGAteststats : <anonymous>: no visible global function definition for
  ‘na.omit’
gGAteststats: no visible global function definition for ‘model.matrix’
gGlobalAncova.hierarchical: no visible global function definition for
  ‘new’
getdev: no visible binding for global variable ‘nobs’
getdev: no visible global function definition for ‘glm.fit’
getdev: no visible global function definition for ‘binomial’
group2formula: no visible global function definition for ‘as.formula’
hiertest: no visible global function definition for ‘na.omit’
horizontal.bars: no visible global function definition for ‘plot.new’
horizontal.bars: no visible global function definition for ‘strwidth’
horizontal.bars: no visible global function definition for ‘par’
horizontal.bars: no visible global function definition for ‘rect’
horizontal.bars: no visible global function definition for ‘box’
horizontal.bars: no visible global function definition for ‘axis’
my.colors: no visible global function definition for ‘rainbow’
my.colors: no visible global function definition for ‘rgb’
pair.compare: no visible global function definition for ‘model.matrix’
plot.ssq.all: no visible global function definition for ‘par’
plot.ssq.all: no visible global function definition for ‘barplot’
plot.ssq.all: no visible global function definition for ‘axis’
plot.ssq.genewise2: no visible global function definition for ‘par’
plot.ssq.genewise2: no visible global function definition for ‘barplot’
plot.ssq.genewise2: no visible global function definition for ‘legend’
plot.ssq.genewise2: no visible global function definition for ‘axis’
plotallgenes: no visible global function definition for ‘par’
plotallgenes: no visible global function definition for ‘barplot’
plotallgenes: no visible global function definition for ‘lines’
plotgenes: no visible global function definition for ‘palette’
plotgenes: no visible global function definition for ‘rgb’
plotgenes: no visible global function definition for ‘lines’
plotgenes: no visible global function definition for ‘legend’
plotgenes2: no visible global function definition for ‘par’
plotgenes2: no visible global function definition for ‘barplot’
plotgenes2: no visible global function definition for ‘axis’
plotgenes2: no visible global function definition for ‘lines’
plotgenes2: no visible global function definition for ‘rect’
plotsubjects: no visible global function definition for ‘palette’
plotsubjects: no visible global function definition for ‘rgb’
plotsubjects: no visible global function definition for ‘legend’
reduSQ: no visible global function definition for ‘model.matrix’
GlobalAncova.closed,matrix-list-formula-missing-ANY-missing-missing-character:
  no visible global function definition for ‘model.matrix’
GlobalAncova,matrix-formula-missing-ANY-missing-missing-character: no
  visible global function definition for ‘model.matrix’
Plot.genes,matrix-formula-missing-ANY-missing-missing-character: no
  visible global function definition for ‘model.matrix’
Plot.subjects,matrix-formula-missing-ANY-missing-missing-character: no
  visible global function definition for ‘model.matrix’
pGAapprox,matrix-formula-missing-ANY-missing-missing-character: no
  visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  Ontology addVigs2WinMenu anova as.formula axis barplot binomial box
  collectionType complete.cases formula geneIds glm glm.fit is is.leaf
  layout legend lines lm model.matrix multinomial na.omit new nobs
  p.adjust palette par pchisq pf plot.new qchisq qnorm rainbow rect rgb
  strwidth terms
Consider adding
  importFrom("grDevices", "palette", "rainbow", "rgb")
  importFrom("graphics", "axis", "barplot", "box", "layout", "legend",
             "lines", "par", "plot.new", "rect", "strwidth")
  importFrom("methods", "is", "new")
  importFrom("stats", "anova", "as.formula", "binomial",
             "complete.cases", "formula", "glm", "glm.fit", "is.leaf",
             "lm", "model.matrix", "na.omit", "nobs", "p.adjust",
             "pchisq", "pf", "qchisq", "qnorm", "terms")
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 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
File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/GlobalAncova/libs/GlobalAncova.so’:
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘srand’, possibly from ‘srand’ (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 nor [v]sprintf. 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/GlobalAncova.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GlobalAncova
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘GlobalAncova’ ...
** 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 GlobalAncova.c -o GlobalAncova.o
GlobalAncova.c: In function ‘row_orth2d’:
GlobalAncova.c:33:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
   33 |    { error("Warning in row_orth2d: Memory block of %d bytes unavailable",
      |                                                    ~^
      |                                                     |
      |                                                     int
      |                                                    %ld
   34 |       (*sD)*(*sD)*sizeof(double));
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~                     
      |                  |
      |                  long unsigned int
GlobalAncova.c:38:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
   38 |    { error("Warning in row_orth2d: Memory block of %d bytes unavailable",
      |                                                    ~^
      |                                                     |
      |                                                     int
      |                                                    %ld
   39 |       (*sD)*(*sD)*sizeof(double) );
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~                     
      |                  |
      |                  long unsigned int
GlobalAncova.c:43:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
   43 |    { error("Warning in row_orth2d: Memory block of %d bytes unavailable",
      |                                                    ~^
      |                                                     |
      |                                                     int
      |                                                    %ld
   44 |       (*zD)*(*sD)*sizeof(double)  );
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~                     
      |                  |
      |                  long unsigned int
GlobalAncova.c:48:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
   48 |    { error("Warning in row_orth2d: Memory block of %d bytes unavailable",
      |                                                    ~^
      |                                                     |
      |                                                     int
      |                                                    %ld
   49 |       (*zD)*(*zD)*sizeof(double) );
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~                     
      |                  |
      |                  long unsigned int
GlobalAncova.c: In function ‘genewiseGA’:
GlobalAncova.c:88:54: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
   88 |     { error("Warning in genewiseGA: Memory block of %d bytes unavailable",
      |                                                     ~^
      |                                                      |
      |                                                      int
      |                                                     %ld
   89 |       (*zxx)*(*zD_full) * sizeof(double) );
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~              
      |                         |
      |                         long unsigned int
GlobalAncova.c:100:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  100 |       { error("Warning in genewiseGA: Memory block of %d bytes unavailable",
      |                                                       ~^
      |                                                        |
      |                                                        int
      |                                                       %ld
  101 |         (*zxx)*(*zD_red) * sizeof(double) );
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~               
      |                          |
      |                          long unsigned int
GlobalAncova.c: In function ‘permut_withFperm’:
GlobalAncova.c:148:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  148 |   { error("Warning in permut: Memory block of %d bytes unavailable",
      |                                               ~^
      |                                                |
      |                                                int
      |                                               %ld
  149 |      (*zrr) * sizeof(double) );
      |      ~~~~~~~~~~~~~~~~~~~~~~~                    
      |             |
      |             long unsigned int
GlobalAncova.c:153:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  153 |   { error("Warning in permut: Memory block of %d bytes unavailable",
      |                                               ~^
      |                                                |
      |                                                int
      |                                               %ld
  154 |     (*zrr) * sizeof(double));
      |     ~~~~~~~~~~~~~~~~~~~~~~~                     
      |            |
      |            long unsigned int
GlobalAncova.c:158:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  158 |   { error("Warning in permut: Memory block of %d bytes unavailable",
      |                                               ~^
      |                                                |
      |                                                int
      |                                               %ld
  159 |     (*n_test_genes) * sizeof(double));
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~            
      |                     |
      |                     long unsigned int
GlobalAncova.c:163:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  163 |   { error("Warning in permut: Memory block of %d bytes unavailable",
      |                                               ~^
      |                                                |
      |                                                int
      |                                               %ld
  164 |     (*sD_full)*(*sD_full) * sizeof(double));
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~      
      |                           |
      |                           long unsigned int
GlobalAncova.c:170:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  170 |     { error("Warning in permut: Memory block of %d bytes unavailable",
      |                                                 ~^
      |                                                  |
      |                                                  int
      |                                                 %ld
  171 |       (*N_Subjects) * sizeof(int));
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~                 
      |                     |
      |                     long unsigned int
GlobalAncova.c: In function ‘permut’:
GlobalAncova.c:250:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  250 |   { error("Warning in permut: Memory block of %d bytes unavailable",
      |                                               ~^
      |                                                |
      |                                                int
      |                                               %ld
  251 |      (*zrr) * sizeof(double) );
      |      ~~~~~~~~~~~~~~~~~~~~~~~                    
      |             |
      |             long unsigned int
GlobalAncova.c:255:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  255 |   { error("Warning in permut: Memory block of %d bytes unavailable",
      |                                               ~^
      |                                                |
      |                                                int
      |                                               %ld
  256 |     (*zrr) * sizeof(double));
      |     ~~~~~~~~~~~~~~~~~~~~~~~                     
      |            |
      |            long unsigned int
GlobalAncova.c:260:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  260 |   { error("Warning in permut: Memory block of %d bytes unavailable",
      |                                               ~^
      |                                                |
      |                                                int
      |                                               %ld
  261 |     (*n_test_genes) * sizeof(double));
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~            
      |                     |
      |                     long unsigned int
GlobalAncova.c:265:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  265 |   { error("Warning in permut: Memory block of %d bytes unavailable",
      |                                               ~^
      |                                                |
      |                                                int
      |                                               %ld
  266 |     (*sD_full)*(*sD_full) * sizeof(double));
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~      
      |                           |
      |                           long unsigned int
GlobalAncova.c:272:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  272 |     { error("Warning in permut: Memory block of %d bytes unavailable",
      |                                                 ~^
      |                                                  |
      |                                                  int
      |                                                 %ld
  273 |       (*N_Subjects) * sizeof(int));
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~                 
      |                     |
      |                     long unsigned int
GlobalAncova.c: In function ‘permut_withFperm’:
GlobalAncova.c:177:8: warning: ‘ord_perm’ may be used uninitialized [-Wmaybe-uninitialized]
  177 |        sample ( ord_perm , N_Subjects )   ;
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GlobalAncova.c:166:8: note: ‘ord_perm’ was declared here
  166 |   int *ord_perm ;
      |        ^~~~~~~~
GlobalAncova.c: In function ‘permut’:
GlobalAncova.c:280:8: warning: ‘ord_perm’ may be used uninitialized [-Wmaybe-uninitialized]
  280 |        sample ( ord_perm , N_Subjects )   ;
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GlobalAncova.c:268:8: note: ‘ord_perm’ was declared here
  268 |   int *ord_perm ;
      |        ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c ludcmp.c -o ludcmp.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix.c -o matrix.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o GlobalAncova.so GlobalAncova.o ludcmp.o matrix.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-GlobalAncova/00new/GlobalAncova/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 (GlobalAncova)