Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2025-08-04 12:05 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1587/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
podkat 1.41.1  (landing page)
Ulrich Bodenhofer
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/podkat
git_branch: devel
git_last_commit: 27b54a9
git_last_commit_date: 2025-07-24 19:31:29 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for podkat on nebbiolo2

To the developers/maintainers of the podkat package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/podkat.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: podkat
Version: 1.41.1
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
StartedAt: 2025-08-04 01:32:56 -0400 (Mon, 04 Aug 2025)
EndedAt: 2025-08-04 01:39:41 -0400 (Mon, 04 Aug 2025)
EllapsedTime: 404.4 seconds
RetCode: 0
Status:   OK  
CheckDir: podkat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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 24.04.2 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   26.677  4.519  31.723
assocTest-methods 11.718  0.501  12.220
plot-methods       8.491  0.449   8.941
split-methods      5.492  0.083   5.574
* 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.


Installation output

podkat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL podkat
###
##############################################################################
##############################################################################


* 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)

Tests output


Example timings

podkat.Rcheck/podkat-Ex.timings

nameusersystemelapsed
AssocTestResult-class0.4680.0560.525
AssocTestResultRanges-class1.400.071.47
GenotypeMatrix-class3.4820.0403.522
NullModel-class1.7000.0201.721
VariantInfo-class0.2390.0000.240
assocTest-methods11.718 0.50112.220
computeKernel0.0020.0000.003
filterResult-methods1.2670.0021.269
genotypeMatrix-methods0.6780.0030.682
hgA0.0210.0010.022
nullModel-methods0.6230.0010.625
p.adjust-methods0.9650.0140.980
partitionRegions-methods0.7230.0040.728
plot-methods8.4910.4498.941
podkat-package0.9650.0030.968
print-methods0.9640.0040.968
qqplot-methods1.5870.0021.589
readGenotypeMatrix-methods0.2150.0000.216
readRegionsFromBedFile0.1240.0020.127
readSampleNamesFromVcfHeader0.0350.0000.034
readVariantInfo-methods0.2520.0000.251
sort-methods0.9040.0000.903
split-methods5.4920.0835.574
unmasked-datasets0.3850.0010.386
unmaskedRegions26.677 4.51931.723
weightFuncs0.0060.0000.006
weights-methods1.1420.0281.170