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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metahdep.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings metahdep_1.53.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/metahdep.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 'metahdep/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metahdep' version '1.53.0'
* 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 whether package 'metahdep' can be installed ... WARNING
Found the following significant warnings:
  D:/biocbuild/bbs-3.15-bioc/R/include/Rinternals.h:197:17: warning: passing argument 5 of 'metan_binary_search_unique' makes integer from pointer without a cast [-Wint-conversion]
See 'D:/biocbuild/bbs-3.15-bioc/meat/metahdep.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 ... NOTE
'library' or 'require' call to 'affyPLM' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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
LinMod.HBLM.fast.dep: no visible global function definition for 'pnorm'
LinMod.MetAn.dep.FEMA: no visible global function definition for
  'pchisq'
LinMod.MetAn.dep.FEMA: no visible global function definition for 'pt'
LinMod.MetAn.dep.REMA: no visible global function definition for
  'pchisq'
LinMod.MetAn.dep.REMA: no visible global function definition for 'pt'
LinMod.REMA.delta.split: no visible global function definition for 'pt'
LinMod.REMA.delta.split: no visible global function definition for
  'pchisq'
getPLM.es: no visible global function definition for 'fitPLM'
getPLM.es: no visible global function definition for 'coefs'
getPLM.es: no visible global function definition for 'varcov'
getPLM.es: no visible global function definition for 'new'
getPLM.es: no visible global function definition for 'annotation'
metahdep: no visible global function definition for 'flush.console'
metahdep.FEMA: no visible global function definition for 'pchisq'
metahdep.FEMA: no visible global function definition for 'pnorm'
metahdep.HBLM: no visible global function definition for 'new'
metahdep.REMA: no visible global function definition for 'new'
metahdep.format: no visible global function definition for 'sd'
metahdep.format: no visible global function definition for
  'flush.console'
metahdep.format: no visible global function definition for 'new'
new.LinMod.HBLM.fast.dep.delta.split: no visible global function
  definition for 'pnorm'
Undefined global functions or variables:
  annotation coefs fitPLM flush.console new pchisq pnorm pt sd varcov
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "pchisq", "pnorm", "pt", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: metahdep.other.Rd:40-42: Dropping empty section \usage
prepare_Rd: metahdep.other.Rd:43-45: Dropping empty section \arguments
prepare_Rd: metahdep.other.Rd:46-48: Dropping empty section \value
* 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/metahdep/libs/x64/metahdep.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 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, 5 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/metahdep.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL metahdep
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'metahdep' ...
** 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 metahdep.c -o metahdep.o
In file included from metahdep.c:3:
metahdep.c: In function 'get_row_indices2':
D:/biocbuild/bbs-3.15-bioc/R/include/Rinternals.h:197:17: warning: passing argument 5 of 'metan_binary_search_unique' makes integer from pointer without a cast [-Wint-conversion]
 #define CHAR(x) R_CHAR(x)
                 ^~~~~~~~~
metahdep.c:471:79: note: in expansion of macro 'CHAR'
     index = metan_binary_search_unique(name_list, sort_index, R_old_names, j, CHAR(STRING_ELT(R_old_chipsets, j)), i);
                                                                               ^~~~
metahdep.c:372:103: note: expected 'char' but argument is of type 'const char *'
 SEXP metan_binary_search_unique(SEXP name_list, SEXP sort_index, SEXP gene_name, int gene_index, char chipset_name, int study_num)
                                                                                                  ~~~~~^~~~~~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o metahdep.dll tmp.def metahdep.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-metahdep/00new/metahdep/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'metahdep'
    finding HTML links ... done
    ES.obj-class                            html  
    HGU.DifExp.list                         html  
    HGU.newnames                            html  
    HGU.prep.list                           html  
    getPLM.es                               html  
    gloss                                   html  
    metahdep.FEMA                           html  
    metahdep.HBLM                           html  
    metahdep.REMA                           html  
    metahdep                                html  
    metahdep.format                         html  
    metahdep.other                          html  
    metaprep-class                          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 (metahdep)
Making 'packages.html' ... done