Ulrich Bodenhofer
| Snapshot Date: 2024-07-21 14:00 -0400 (Sun, 21 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/podkat |
| git_branch: RELEASE_3_19 |
| git_last_commit: 5627ec7 |
| git_last_commit_date: 2024-04-30 10:42:40 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-24 09:05 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
| 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 1589/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| podkat 1.36.0 (landing page) Ulrich Bodenhofer
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: podkat |
| Version: 1.36.0 |
| Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL podkat |
| StartedAt: 2024-07-21 16:40:24 -0400 (Sun, 21 Jul 2024) |
| EndedAt: 2024-07-21 16:42:19 -0400 (Sun, 21 Jul 2024) |
| EllapsedTime: 114.5 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL podkat
###
##############################################################################
##############################################################################
* installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'podkat' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_podkat.cpp -o R_init_podkat.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bernoulliExact.cpp -o bernoulliExact.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cumMax.cpp -o cumMax.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleMale.cpp -o doubleMale.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kernels.cpp -o kernels.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pValues.cpp -o pValues.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c partitionRegions.cpp -o partitionRegions.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c qfc.cpp -o qfc.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o
In file included from E:/biocbuild/bbs-3.19-bioc/R/include/R.h:73,
from readGenotypeMatrix.cpp:1:
E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h: In function 'void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]':
E:/biocbuild/bbs-3.19-bioc/R/include/R_ext/Error.h:69:17: warning: infinite recursion detected [-Winfinite-recursion]
69 | #define warning Rf_warning
| ^~~~~~~~~~
E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:46:13: note: in expansion of macro 'warning'
46 | inline void warning(const char* fmt, Args&&... args ) {
| ^~~~~~~
In file included from E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/exceptions.h:180,
from E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/RcppCommon.h:130,
from E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp.h:27,
from readGenotypeMatrix.cpp:2:
E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:47:15: note: recursive call
47 | Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str());
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readVariantInfo.cpp -o readVariantInfo.o
In file included from E:/biocbuild/bbs-3.19-bioc/R/include/R.h:73,
from readVariantInfo.cpp:1:
E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h: In function 'void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]':
E:/biocbuild/bbs-3.19-bioc/R/include/R_ext/Error.h:69:17: warning: infinite recursion detected [-Winfinite-recursion]
69 | #define warning Rf_warning
| ^~~~~~~~~~
E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:46:13: note: in expansion of macro 'warning'
46 | inline void warning(const char* fmt, Args&&... args ) {
| ^~~~~~~
In file included from E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/exceptions.h:180,
from E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/RcppCommon.h:130,
from E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp.h:27,
from readVariantInfo.cpp:2:
E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:47:15: note: recursive call
47 | Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str());
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o podkat.dll tmp.def R_init_podkat.o bernoulliExact.o checkAndFixGenotype.o cumMax.o doubleMale.o kernels.o pValues.o partitionRegions.o qfc.o readGenotypeMatrix.o readVariantInfo.o E:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-podkat/00new/podkat/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (podkat)