Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:36 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the biovizBase package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biovizBase.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 193/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biovizBase 1.40.0 (landing page) Michael Lawrence
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: biovizBase |
Version: 1.40.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:biovizBase.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings biovizBase_1.40.0.tar.gz |
StartedAt: 2021-10-14 09:03:52 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:08:57 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 305.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: biovizBase.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:biovizBase.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings biovizBase_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/biovizBase.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘biovizBase/DESCRIPTION’ ... OK * this is package ‘biovizBase’ version ‘1.40.0’ * 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 ‘biovizBase’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 ... NOTE 'library' or 'require' calls in package code: 'BSgenome' 'rtracklayer' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE genSymbols: no visible binding for global variable 'start_location' genSymbols: no visible binding for global variable 'end_location' genSymbols: no visible binding for global variable 'Chromosome' genSymbols: no visible binding for global variable 'symbol' transformToLinkInCircle: no visible binding for global variable '.circle.x' transformToLinkInCircle: no visible binding for global variable '.circle.y' transformToLinkInCircle : <anonymous>: no visible binding for global variable 'from.x' transformToLinkInCircle : <anonymous>: no visible binding for global variable 'from.y' transformToLinkInCircle : <anonymous>: no visible binding for global variable 'to.x' transformToLinkInCircle : <anonymous>: no visible binding for global variable 'to.y' mold,ExpressionSet: no visible global function definition for 'exprs' mold,ExpressionSet: no visible global function definition for 'pData' mold,RleList: no visible binding for global variable 'xRleList' mold,eSet: no visible global function definition for 'phenoData' mold,eSet: no visible global function definition for 'melt' mold,eSet: no visible global function definition for 'varLabels' Undefined global functions or variables: .circle.x .circle.y Chromosome end_location exprs from.x from.y melt pData phenoData start_location symbol to.x to.y varLabels xRleList * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... WARNING Found the following significant warnings: Warning: 'GenenameFilter' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed crunch-method 16.97 0.516 17.533 * 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, 4 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/biovizBase.Rcheck/00check.log’ for details.
biovizBase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL biovizBase ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘biovizBase’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_biovizBase.c -o R_init_biovizBase.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bin_offsets.c -o bin_offsets.o bin_offsets.c: In function ‘scan_bam_bin_offsets’: bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness [-Wpointer-sign] 57 | if (strncmp(b, "BAI\1", 4)) | ^ | | | Rbyte * {aka unsigned char *} In file included from /home/biocbuild/bbs-3.13-bioc/R/include/R_ext/RS.h:34, from /home/biocbuild/bbs-3.13-bioc/R/include/Rdefines.h:39, from bin_offsets.h:1, from bin_offsets.c:3: /usr/include/string.h:140:33: note: expected ‘const char *’ but argument is of type ‘Rbyte *’ {aka ‘unsigned char *’} 140 | extern int strncmp (const char *__s1, const char *__s2, size_t __n) | ~~~~~~~~~~~~^~~~ gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-biovizBase/00new/biovizBase/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** 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 (biovizBase)
biovizBase.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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("biovizBase") Loading required package: ensembldb Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: AnnotationFilter Attaching package: 'ensembldb' The following object is masked from 'package:stats': filter Fetching data...OK Parsing exons...OK Defining introns...OK Defining UTRs...OK Defining CDS...OK aggregating... Done Fetching data...OK Parsing exons...OK Defining introns...OK Defining UTRs...OK Defining CDS...OK aggregating... Done Fetching data...Fetching data...OK Parsing exons...OK Defining introns...OK Defining UTRs...OK Defining CDS...OK aggregating... Done Fetching data...OK Parsing exons...OK Defining introns...OK Defining UTRs...OK Defining CDS...OK aggregating... Done Fetching data...OK Parsing exons...OK Defining introns...OK Defining UTRs...OK Defining CDS...OK aggregating... Done Fetching data...OK Parsing exons...OK Defining introns...OK Defining UTRs...OK Defining CDS...OK aggregating... Done RUNIT TEST PROTOCOL -- Thu Oct 14 09:08:54 2021 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : biovizBase RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 Warning message: 'GenenameFilter' is deprecated. Use 'GeneNameFilter' instead. See help("Deprecated") > > proc.time() user system elapsed 21.304 1.251 22.587
biovizBase.Rcheck/biovizBase-Ex.timings
name | user | system | elapsed | |
CRC | 0.002 | 0.000 | 0.002 | |
GCcontent | 0.465 | 0.017 | 0.481 | |
addStepping-method | 0.793 | 0.080 | 0.873 | |
aes-utils | 0.001 | 0.000 | 0.001 | |
colorBlindSafePal | 0 | 0 | 0 | |
containLetters | 0 | 0 | 0 | |
crc1.GeRL | 0.087 | 0.002 | 0.089 | |
crunch-method | 16.970 | 0.516 | 17.533 | |
darned_hg19_subset500 | 0.025 | 0.004 | 0.029 | |
flatGrl | 0.330 | 0.004 | 0.334 | |
genesymbol | 0.054 | 0.000 | 0.054 | |
getBioColor | 0.001 | 0.000 | 0.001 | |
getFormalNames | 0.001 | 0.000 | 0.001 | |
getGaps | 1.34 | 0.00 | 1.34 | |
getIdeoGR | 0.282 | 0.008 | 0.290 | |
getIdeogram | 0 | 0 | 0 | |
hg19Ideogram | 0.021 | 0.000 | 0.021 | |
hg19IdeogramCyto | 0.023 | 0.000 | 0.023 | |
ideo | 0.229 | 0.004 | 0.233 | |
ideoCyto | 0.077 | 0.011 | 0.088 | |
isIdeogram | 0.006 | 0.000 | 0.006 | |
isMatchedWithModel | 0.346 | 0.012 | 0.360 | |
isSimpleIdeogram | 0.026 | 0.000 | 0.025 | |
maxGap-method | 0.419 | 0.004 | 0.422 | |
pileupAsGRanges | 0.000 | 0.000 | 0.001 | |
pileupGRangesAsVariantTable | 0 | 0 | 0 | |
plotColorLegend | 0.002 | 0.000 | 0.002 | |
scale | 0.353 | 0.008 | 0.361 | |
showColor | 0.000 | 0.000 | 0.001 | |
shrinkageFun-method | 0.240 | 0.008 | 0.249 | |
splitByFacets-method | 0.486 | 0.012 | 0.497 | |
strip_formula_dots | 0.001 | 0.000 | 0.001 | |
subsetArgsByFormals | 0.000 | 0.000 | 0.001 | |
transform | 1.671 | 0.288 | 1.959 | |
transformGRangesForEvenSpace | 0.263 | 0.004 | 0.267 | |