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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:podkat.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings podkat_1.41.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/podkat.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘podkat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘podkat’ version ‘1.41.1’
* 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 ‘podkat’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   7.9Mb
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AssocTestResultRanges-class.Rd: GRanges-class
  GenotypeMatrix-class.Rd: dgCMatrix-class
  VariantInfo-class.Rd: GRanges-class
  assocTest-methods.Rd: GRanges-class, GRangesList-class
  computeKernel.Rd: Matrix-class
  filterResult-methods.Rd: GRanges-class, GRangesList-class
  genotypeMatrix-methods.Rd: dgCMatrix-class, GRanges-class
  hgA.Rd: GRanges-class
  partitionRegions-methods.Rd: GRanges-class, GRangesList-class
  plot-methods.Rd: GRanges-class
  readGenotypeMatrix-methods.Rd: TabixFile-class, GRanges-class
  readRegionsFromBedFile.Rd: GRanges-class, Seqinfo-class
  readSampleNamesFromVcfHeader.Rd: TabixFile-class, scanBcfHeader
  readVariantInfo-methods.Rd: TabixFile-class, GRanges-class
  sort-methods.Rd: GRanges-class
  split-methods.Rd: GRanges-class, GRangesList-class
  unmasked-datasets.Rd: GRangesList-class, GRanges-class
  unmaskedRegions.Rd: GRangesList-class, GRanges-class
  weights-methods.Rd: GRanges-class, GRangesList-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... INFO
GNU make is a SystemRequirements.
* 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-3.22-bioc/R/site-library/podkat/libs/podkat.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
unmaskedRegions   26.132  4.505  31.437
assocTest-methods  9.792  0.721  10.513
plot-methods       8.582  0.129   8.712
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/podkat.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL podkat
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘podkat’ ...
** this is package ‘podkat’ version ‘1.41.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c R_init_podkat.cpp -o R_init_podkat.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c bernoulliExact.cpp -o bernoulliExact.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c cumMax.cpp -o cumMax.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c doubleMale.cpp -o doubleMale.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c kernels.cpp -o kernels.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pValues.cpp -o pValues.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c partitionRegions.cpp -o partitionRegions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c qfc.cpp -o qfc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/include/R.h:73,
                 from readGenotypeMatrix.cpp:1:
/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include/Rcpp/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]’:
/home/biocbuild/bbs-3.22-bioc/R/include/R_ext/Error.h:85:17: warning: infinite recursion detected [-Winfinite-recursion]
   85 | #define warning Rf_warning
      |                 ^~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include/Rcpp/exceptions.h:190:17: note: in expansion of macro ‘warning’
  190 |     inline void warning(const char* fmt, Args&&... args ) {
      |                 ^~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include/RcppCommon.h:133,
                 from /home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include/Rcpp.h:27,
                 from readGenotypeMatrix.cpp:2:
/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include/Rcpp/exceptions.h:191:19: note: recursive call
  191 |         Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str());
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c readVariantInfo.cpp -o readVariantInfo.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/include/R.h:73,
                 from readVariantInfo.cpp:1:
/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include/Rcpp/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]’:
/home/biocbuild/bbs-3.22-bioc/R/include/R_ext/Error.h:85:17: warning: infinite recursion detected [-Winfinite-recursion]
   85 | #define warning Rf_warning
      |                 ^~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include/Rcpp/exceptions.h:190:17: note: in expansion of macro ‘warning’
  190 |     inline void warning(const char* fmt, Args&&... args ) {
      |                 ^~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include/RcppCommon.h:133,
                 from /home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include/Rcpp.h:27,
                 from readVariantInfo.cpp:2:
/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include/Rcpp/exceptions.h:191:19: note: recursive call
  191 |         Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str());
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o podkat.so R_init_podkat.o bernoulliExact.o checkAndFixGenotype.o cumMax.o doubleMale.o kernels.o pValues.o partitionRegions.o qfc.o readGenotypeMatrix.o readVariantInfo.o /home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-podkat/00new/podkat/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘p.adjust’ from package ‘stats’ in package ‘podkat’
** 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 (podkat)