Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:21:37 -0400 (Wed, 19 Oct 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
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 |
To the developers/maintainers of the h5vc package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/h5vc.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 874/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
h5vc 2.30.0 (landing page) Paul Theodor Pyl
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
Package: h5vc |
Version: 2.30.0 |
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:h5vc.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings h5vc_2.30.0.tar.gz |
StartedAt: 2022-10-19 00:55:16 -0400 (Wed, 19 Oct 2022) |
EndedAt: 2022-10-19 01:00:14 -0400 (Wed, 19 Oct 2022) |
EllapsedTime: 298.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: h5vc.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:h5vc.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings h5vc_2.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/h5vc.Rcheck' * using R version 4.2.1 (2022-06-23 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'h5vc/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'h5vc' version '2.30.0' * 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 'h5vc' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'h5vc' See 'F:/biocbuild/bbs-3.15-bioc/meat/h5vc.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 7.8Mb sub-directories of 1Mb or more: libs 7.4Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Versioned 'LinkingTo' value for 'Rhtslib' is only usable in R >= 3.0.2 * 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 ... NOTE .h5dapplyIRanges: no visible binding for global variable 'Sample' binnedAFs : <anonymous>: no visible global function definition for 'hist' callVariantsPaired : <anonymous> : <anonymous>: no visible global function definition for 'binom.test' callVariantsPairedFisher : <anonymous> : <anonymous> : <anonymous>: no visible global function definition for 'fisher.test' callVariantsPairedFisher : <anonymous> : <anonymous>: no visible binding for global variable 'pValue' callVariantsPairedFisher : <anonymous> : <anonymous>: no visible binding for global variable 'BlockID' callVariantsSingle : <anonymous> : <anonymous>: no visible binding for global variable 'Support' callVariantsSingle : <anonymous> : <anonymous>: no visible binding for global variable 'AF' callVariantsSingle : <anonymous> : <anonymous>: no visible binding for global variable 'SupFwd' callVariantsSingle : <anonymous> : <anonymous>: no visible binding for global variable 'SupRev' callVariantsSingle : <anonymous> : <anonymous> : binom.test.safe: no visible global function definition for 'binom.test' callVariantsSingle : <anonymous> : <anonymous> : <anonymous>: no visible global function definition for 'fisher.test' callVariantsSingle : <anonymous> : <anonymous>: no visible binding for global variable 'BlockID' mergeTallyFiles : <anonymous>: no visible binding for global variable 'group' mergeTallyFiles: no visible binding for global variable 'SourceFile' mismatchPlot: no visible binding for global variable 'Sample' plotMutationSpectrum: no visible binding for global variable 'altAllele' plotMutationSpectrum: no visible binding for global variable 'tmp' rerunBatchTallies: no visible binding for global variable 'regID' resizeCohort: no visible binding for global variable 'newSamples' tallyRangesBatch : <anonymous>: no visible binding for global variable 'bamFiles' tallyRangesBatch: no visible binding for global variable 'verbose' Undefined global functions or variables: AF BlockID Sample SourceFile SupFwd SupRev Support altAllele bamFiles binom.test fisher.test group hist newSamples pValue regID tmp verbose Consider adding importFrom("graphics", "hist") importFrom("stats", "binom.test", "fisher.test") to your NAMESPACE file. * 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-3.15-bioc/R/library/h5vc/libs/x64/h5vc.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) Found 'putchar', possibly from 'putchar' (C) Found 'puts', possibly from 'printf' (C), 'puts' (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. 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed applyTallies 21.27 0.59 41.92 callVariantsFisher 6.87 0.05 6.92 writeToTallyFile 5.92 0.16 6.14 tallyRanges 3.70 0.33 13.72 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.R' OK * 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: 1 WARNING, 5 NOTEs See 'F:/biocbuild/bbs-3.15-bioc/meat/h5vc.Rcheck/00check.log' for details.
h5vc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL h5vc ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'h5vc' ... ** using staged installation ** libs gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam.c -o bam.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam.c -o sam.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tallyBAM.cpp -o tallyBAM.o tallyBAM.cpp: In function 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)': tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable] 47 | int len = nttable->end - nttable->beg; | ^~~ tallyBAM.cpp: In function 'int pileup_func(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)': tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable] 96 | int len = nttable->end - nttable->beg; | ^~~ tallyBAM.cpp: In function 'int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)': tallyBAM.cpp:140:6: warning: unused variable 'c' [-Wunused-variable] 140 | int c = 0; | ^ tallyBAM.cpp: At global scope: tallyBAM.cpp:43:12: warning: 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)' defined but not used [-Wunused-function] 43 | static int pileup_func_old(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data) | ^~~~~~~~~~~~~~~ g++ -std=gnu++11 -shared -s -static-libgcc -o h5vc.dll tmp.def bam.o bam_plbuf.o sam.o tallyBAM.o F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -lsbml-static -lwinmm -lwldap32 -lgdi32 -lbz2 -lcurl -lrtmp -lssl -lssh2 -lidn2 -lunistring -lcharset -lintl -liconv -lgcrypt -lcrypto -lgpg-error -lws2_32 -llzma -lz -lzstd -lmincore -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-h5vc/00new/h5vc/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'h5vc' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'h5vc' ** testing if installed package can be loaded from final location Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'h5vc' ** testing if installed package keeps a record of temporary installation path * DONE (h5vc)
h5vc.Rcheck/tests/runTests.Rout
R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("h5vc") RUNIT TEST PROTOCOL -- Wed Oct 19 01:00:03 2022 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : h5vc RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 Warning message: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'h5vc' > > proc.time() user system elapsed 5.32 0.53 5.78
h5vc.Rcheck/h5vc-Ex.timings
name | user | system | elapsed | |
applyTallies | 21.27 | 0.59 | 41.92 | |
batchTallies | 0 | 0 | 0 | |
binGenome | 0.25 | 0.06 | 0.35 | |
binnedAFs | 2.71 | 0.22 | 3.43 | |
callVariants | 0.66 | 0.02 | 0.97 | |
callVariantsFisher | 6.87 | 0.05 | 6.92 | |
callVariantsSingle | 1.00 | 0.01 | 1.02 | |
coverage | 3.11 | 0.44 | 3.70 | |
geom_h5vc | 0.61 | 0.03 | 0.64 | |
getSampleData | 0.06 | 0.02 | 0.53 | |
h5dapply | 1.08 | 0.06 | 1.14 | |
h5readBlock | 0.24 | 0.02 | 0.25 | |
helpers | 0.18 | 0.03 | 0.22 | |
mergeTallies | 0.86 | 0.14 | 1.00 | |
mergeTallyFiles | 0 | 0 | 0 | |
mismatchPlot | 4.29 | 0.13 | 4.45 | |
mutationSpectrum | 3.15 | 0.47 | 3.63 | |
plotMutationSpectrum | 4.12 | 0.54 | 4.67 | |
prepareForHDF5 | 0.67 | 0.05 | 0.72 | |
prepareTallyFile | 0.08 | 0.03 | 0.25 | |
tallyBAM | 0.03 | 0.00 | 0.03 | |
tallyRanges | 3.70 | 0.33 | 13.72 | |
writeReference | 0.23 | 0.01 | 0.26 | |
writeToTallyFile | 5.92 | 0.16 | 6.14 | |