Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 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 932/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
h5vc 2.40.0 (landing page) Paul Theodor Pyl
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the h5vc package: - 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 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: h5vc |
Version: 2.40.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:h5vc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings h5vc_2.40.0.tar.gz |
StartedAt: 2024-12-20 04:28:44 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:34:54 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 369.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: h5vc.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:h5vc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings h5vc_2.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/h5vc.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘h5vc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘h5vc’ version ‘2.40.0’ * 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 for sufficient/correct file permissions ... 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/h5vc.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * 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 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 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 ... NOTE checkRd: (-1) prepareTallyFile.Rd:30: Lost braces 30 | \code{resizeCohort}{Resizes the datasets to a new number of samples, this is limited by the value of \code{maxsamples} that was provided in the initial call to \code{prepareTallyFile}} | ^ * 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 is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/h5vc/libs/h5vc.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (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 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 21.509 2.156 22.759 callVariantsFisher 21.009 0.284 21.727 writeToTallyFile 11.911 3.168 14.706 tallyRanges 8.084 2.558 9.944 mismatchPlot 9.303 0.153 9.480 binnedAFs 7.239 0.812 8.242 plotMutationSpectrum 5.124 1.075 6.249 coverage 5.581 0.370 6.035 mutationSpectrum 4.159 1.428 5.678 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/h5vc.Rcheck/00check.log’ for details.
h5vc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL h5vc ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘h5vc’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tallyBAM.cpp -o tallyBAM.o tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable] int len = nttable->end - nttable->beg; ^ tallyBAM.cpp:60:18: warning: variable 'c' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] }else if(p->indel > 0){ ^~~~~~~~~~~~ tallyBAM.cpp:64:16: note: uninitialized use occurs here str += c; ^ tallyBAM.cpp:60:15: note: remove the 'if' if its condition is always true }else if(p->indel > 0){ ^~~~~~~~~~~~~~~~ tallyBAM.cpp:55:15: note: initialize the variable 'c' to silence this warning char c; ^ = '\0' tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable] int len = nttable->end - nttable->beg; ^ tallyBAM.cpp:140:6: warning: unused variable 'c' [-Wunused-variable] int c = 0; ^ tallyBAM.cpp:43:12: warning: unused function 'pileup_func_old' [-Wunused-function] static int pileup_func_old(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data) ^ 5 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o h5vc.so bam_plbuf.o tallyBAM.o /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-h5vc/00new/h5vc/libs ** 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’ ** checking absolute paths in shared objects and dynamic libraries ** 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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 -- Fri Dec 20 04:34:37 2024 *********************************************** 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 10.258 0.599 11.338
h5vc.Rcheck/h5vc-Ex.timings
name | user | system | elapsed | |
applyTallies | 21.509 | 2.156 | 22.759 | |
batchTallies | 0.000 | 0.000 | 0.001 | |
binGenome | 0.466 | 0.071 | 0.540 | |
binnedAFs | 7.239 | 0.812 | 8.242 | |
callVariants | 0.923 | 0.112 | 1.141 | |
callVariantsFisher | 21.009 | 0.284 | 21.727 | |
callVariantsSingle | 1.781 | 0.138 | 1.961 | |
coverage | 5.581 | 0.370 | 6.035 | |
geom_h5vc | 1.421 | 0.062 | 1.493 | |
getSampleData | 0.085 | 0.204 | 0.307 | |
h5dapply | 1.640 | 0.086 | 1.738 | |
h5readBlock | 0.355 | 0.021 | 0.381 | |
helpers | 0.222 | 0.016 | 0.238 | |
mergeTallies | 1.656 | 0.077 | 1.753 | |
mergeTallyFiles | 0.000 | 0.000 | 0.001 | |
mismatchPlot | 9.303 | 0.153 | 9.480 | |
mutationSpectrum | 4.159 | 1.428 | 5.678 | |
plotMutationSpectrum | 5.124 | 1.075 | 6.249 | |
prepareForHDF5 | 1.629 | 0.079 | 1.715 | |
prepareTallyFile | 0.179 | 0.013 | 0.193 | |
tallyBAM | 0.069 | 0.008 | 0.077 | |
tallyRanges | 8.084 | 2.558 | 9.944 | |
writeReference | 0.523 | 0.106 | 0.632 | |
writeToTallyFile | 11.911 | 3.168 | 14.706 | |