Ulrich Bodenhofer
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/podkat |
| git_branch: RELEASE_3_17 |
| git_last_commit: 68a149b |
| git_last_commit_date: 2023-04-25 10:38:38 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:28 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1539/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| podkat 1.32.0 (landing page) Ulrich Bodenhofer
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.32.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:podkat.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings podkat_1.32.0.tar.gz |
| StartedAt: 2023-10-16 05:22:42 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 05:31:32 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 530.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: podkat.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:podkat.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings podkat_1.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/podkat.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'podkat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'podkat' version '1.32.0'
* 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 'podkat' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
installed size is 10.9Mb
sub-directories of 1Mb or more:
R 1.1Mb
libs 9.5Mb
* 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 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 ... 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 ... 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/podkat/libs/x64/podkat.dll':
Found '_assert', possibly from 'assert' (C)
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (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 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 sizes of PDF files under 'inst/doc' ... NOTE
'qpdf' made some significant size reductions:
compacted 'podkat.pdf' from 893Kb to 778Kb
consider running tools::compactPDF() on these files
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
unmaskedRegions 161.59 2.14 177.33
assocTest-methods 10.26 0.47 10.75
plot-methods 9.57 0.51 10.10
* 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: 4 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc/meat/podkat.Rcheck/00check.log'
for details.
podkat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL podkat ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'podkat' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"C:/rtools43/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bernoulliExact.cpp -o bernoulliExact.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cumMax.cpp -o cumMax.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleMale.cpp -o doubleMale.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kernels.cpp -o kernels.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pValues.cpp -o pValues.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c partitionRegions.cpp -o partitionRegions.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c qfc.cpp -o qfc.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readVariantInfo.cpp -o readVariantInfo.o 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 F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-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)
podkat.Rcheck/podkat-Ex.timings
| name | user | system | elapsed | |
| AssocTestResult-class | 1.22 | 0.05 | 1.28 | |
| AssocTestResultRanges-class | 1.32 | 0.11 | 1.44 | |
| GenotypeMatrix-class | 3.97 | 0.17 | 4.14 | |
| NullModel-class | 1.69 | 0.02 | 1.72 | |
| VariantInfo-class | 0.24 | 0.00 | 0.25 | |
| assocTest-methods | 10.26 | 0.47 | 10.75 | |
| computeKernel | 0 | 0 | 0 | |
| filterResult-methods | 1.17 | 0.03 | 1.20 | |
| genotypeMatrix-methods | 0.68 | 0.04 | 0.72 | |
| hgA | 0.01 | 0.00 | 0.01 | |
| nullModel-methods | 0.76 | 0.08 | 0.84 | |
| p.adjust-methods | 0.92 | 0.00 | 0.93 | |
| partitionRegions-methods | 0.68 | 0.02 | 0.68 | |
| plot-methods | 9.57 | 0.51 | 10.10 | |
| podkat-package | 1.00 | 0.00 | 1.02 | |
| print-methods | 0.98 | 0.02 | 1.00 | |
| qqplot-methods | 1.60 | 0.00 | 1.59 | |
| readGenotypeMatrix-methods | 0.22 | 0.02 | 0.24 | |
| readRegionsFromBedFile | 0.04 | 0.00 | 0.04 | |
| readSampleNamesFromVcfHeader | 0.04 | 0.00 | 0.03 | |
| readVariantInfo-methods | 0.32 | 0.01 | 0.35 | |
| sort-methods | 0.96 | 0.02 | 0.97 | |
| split-methods | 2.32 | 0.09 | 2.42 | |
| unmasked-datasets | 0.41 | 0.00 | 0.40 | |
| unmaskedRegions | 161.59 | 2.14 | 177.33 | |
| weightFuncs | 0.00 | 0.02 | 0.02 | |
| weights-methods | 1.21 | 0.03 | 1.23 | |