Ulrich Bodenhofer
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/podkat |
| git_branch: devel |
| git_last_commit: af07a5d |
| git_last_commit_date: 2025-09-19 07:35:34 -0400 (Fri, 19 Sep 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:07 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1621/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| podkat 1.41.1 (landing page) Ulrich Bodenhofer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: podkat |
| Version: 1.41.1 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL podkat |
| StartedAt: 2025-10-23 20:50:02 -0000 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 20:51:46 -0000 (Thu, 23 Oct 2025) |
| EllapsedTime: 104.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL podkat
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘podkat’ ...
** this is package ‘podkat’ version ‘1.41.1’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bernoulliExact.cpp -o bernoulliExact.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c cumMax.cpp -o cumMax.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c doubleMale.cpp -o doubleMale.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c kernels.cpp -o kernels.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c pValues.cpp -o pValues.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c partitionRegions.cpp -o partitionRegions.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c qfc.cpp -o qfc.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/include/R.h:73,
from readGenotypeMatrix.cpp:1:
/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include/Rcpp/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]’:
/home/biocbuild/R/R-4.5.0/include/R_ext/Error.h:85:17: warning: infinite recursion detected [-Winfinite-recursion]
85 | #define warning Rf_warning
| ^~~~~~~~~~
/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/site-library/Rcpp/include/RcppCommon.h:133,
from /home/biocbuild/R/R-4.5.0/site-library/Rcpp/include/Rcpp.h:27,
from readGenotypeMatrix.cpp:2:
/home/biocbuild/R/R-4.5.0/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());
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/include/R.h:73,
from readVariantInfo.cpp:1:
/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include/Rcpp/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]’:
/home/biocbuild/R/R-4.5.0/include/R_ext/Error.h:85:17: warning: infinite recursion detected [-Winfinite-recursion]
85 | #define warning Rf_warning
| ^~~~~~~~~~
/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/site-library/Rcpp/include/RcppCommon.h:133,
from /home/biocbuild/R/R-4.5.0/site-library/Rcpp/include/Rcpp.h:27,
from readVariantInfo.cpp:2:
/home/biocbuild/R/R-4.5.0/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());
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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)