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 814/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
genomation 1.38.0 (landing page) Altuna Akalin
| 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 genomation package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genomation.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: genomation |
Version: 1.38.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomation_1.38.0.tar.gz |
StartedAt: 2024-12-20 03:51:05 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:01:20 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 615.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: genomation.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomation_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/genomation.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 ‘genomation/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘genomation’ version ‘1.38.0’ * package encoding: latin1 * 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 ‘genomation’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ See ‘/Users/biocbuild/bbs-3.20-bioc/meat/genomation.Rcheck/00install.out’ for details. * 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 ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: in ScoreMatrixBin() function. Cannot process chunk/lines: NEW FUNCTIONS AND FEATURES Cannot process chunk/lines: The character vectors will label the x-axis of heatmaps. Examples: xcoords=c("-2kb","0","2kb") Cannot process chunk/lines: Implemented by Bozena Mika-Gospodorz. Cannot process chunk/lines: Implemented by Bozena Mika-Gospodorz. Cannot process chunk/lines: Implemented by Bozena Mika-Gospodorz. Cannot process chunk/lines: Implemented by Bozena Mika-Gospodorz. * 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 ... NOTE Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE ScoreMatrixBin,RleList-GRangesList: no visible binding for global variable ‘id’ ScoreMatrixBin,RleList-GRangesList: no visible global function definition for ‘:=’ Undefined global functions or variables: := id * checking Rd files ... NOTE checkRd: (-1) plotMeta.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotMeta.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotMeta.Rd:59-60: Lost braces in \itemize; meant \describe ? * 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 compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed enrichmentMatrix-ScoreMatrixList-method 7.852 2.749 11.422 enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method 7.435 2.133 9.314 enrichmentMatrix-ScoreMatrix-method 6.107 1.046 7.483 ScoreMatrixBin-methods 4.782 0.226 5.238 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘genomation_unit_tests.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/genomation.Rcheck/00check.log’ for details.
genomation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL genomation ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘genomation’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c binSum.cpp -o binSum.o 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 genomation.so RcppExports.o binSum.o -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-genomation/00new/genomation/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ ** 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 ‘genomation’ ** 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 ‘genomation’ ** testing if installed package keeps a record of temporary installation path * DONE (genomation)
genomation.Rcheck/tests/genomation_unit_tests.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. > (require("genomation") & require("GenomicRanges") & require("GenomicAlignments") & require("rtracklayer") & require("readr") & require("Biostrings")) || stop("unable to load genomation package") Loading required package: genomation Loading required package: grid Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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, aperm, 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicAlignments Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars 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")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:grid': pattern The following object is masked from 'package:base': strsplit Loading required package: Rsamtools Loading required package: rtracklayer Loading required package: readr [1] TRUE Warning message: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' > genomation:::.test() Normalizing to rpm ... Normalizing to rpm ... Normalizing to rpm ... testing:min testing:max testing:median Normalizing to rpm ... Normalizing to rpm ... Normalizing to rpm ... Normalizing to rpm ... Normalizing to rpm ... Normalizing to rpm ... Normalizing to rpm ... Rows: 2 Columns: 9 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "\t" chr (3): X1, X4, X6 dbl (5): X2, X3, X5, X7, X8 num (1): X9 ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 2 Columns: 9 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "\t" chr (3): X1, X4, X6 dbl (5): X2, X3, X5, X7, X8 num (1): X9 ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. RUNIT TEST PROTOCOL -- Fri Dec 20 04:01:03 2024 *********************************************** Number of test functions: 24 Number of errors: 0 Number of failures: 0 1 Test Suite : genomation RUnit Tests - 24 test functions, 0 errors, 0 failures Number of test functions: 24 Number of errors: 0 Number of failures: 0 There were 50 or more warnings (use warnings() to see the first 50) > > proc.time() user system elapsed 59.911 2.586 63.995
genomation.Rcheck/genomation-Ex.timings
name | user | system | elapsed | |
AnnotationByGeneParts-methods | 1.792 | 0.203 | 2.015 | |
ScoreMatrix-methods | 3.678 | 0.157 | 3.950 | |
ScoreMatrixBin-methods | 4.782 | 0.226 | 5.238 | |
ScoreMatrixList-methods | 1.375 | 0.171 | 1.628 | |
annotateWithFeature-methods | 0.099 | 0.006 | 0.112 | |
annotateWithFeatureFlank-methods | 0.809 | 0.008 | 0.867 | |
annotateWithFeatures-methods | 1.387 | 0.048 | 1.532 | |
annotateWithGeneParts-methods | 0.952 | 0.025 | 1.010 | |
binMatrix-methods | 0.380 | 0.013 | 0.410 | |
convertBed2Exons-methods | 0.103 | 0.003 | 0.112 | |
convertBed2Introns-methods | 0.100 | 0.003 | 0.107 | |
enrichmentMatrix-ScoreMatrix-method | 6.107 | 1.046 | 7.483 | |
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method | 7.435 | 2.133 | 9.314 | |
enrichmentMatrix-ScoreMatrixList-method | 7.852 | 2.749 | 11.422 | |
findFeatureComb-methods | 1.177 | 0.726 | 0.989 | |
getFeatsWithTargetsStats-methods | 0.899 | 0.164 | 1.100 | |
getFlanks-methods | 0.453 | 0.053 | 0.534 | |
getRandomEnrichment-methods | 0.007 | 0.005 | 0.012 | |
getTargetAnnotationStats-methods | 0.809 | 0.070 | 0.888 | |
gffToGRanges | 0.165 | 0.012 | 0.178 | |
heatMatrix | 0.467 | 0.059 | 0.542 | |
heatMeta | 0.777 | 0.080 | 0.867 | |
heatTargetAnnotation-methods | 1.459 | 0.069 | 1.417 | |
intersectScoreMatrixList-methods | 0.597 | 0.019 | 0.569 | |
multiHeatMatrix | 0.758 | 0.056 | 0.819 | |
orderBy-methods | 2.409 | 0.417 | 2.865 | |
patternMatrix-methods | 0.281 | 0.016 | 0.298 | |
plotMeta | 0.758 | 0.044 | 0.816 | |
plotTargetAnnotation-methods | 0.779 | 0.024 | 0.840 | |
readBed | 0.286 | 0.034 | 0.327 | |
readBroadPeak | 0.065 | 0.013 | 0.077 | |
readFeatureFlank-methods | 0.468 | 0.037 | 0.535 | |
readGeneric | 0.068 | 0.017 | 0.087 | |
readNarrowPeak | 0.066 | 0.017 | 0.084 | |
readTranscriptFeatures-methods | 0.395 | 0.022 | 0.432 | |
scaleScoreMatrix-methods | 0.368 | 0.014 | 0.417 | |
scaleScoreMatrixList | 1.444 | 0.150 | 1.715 | |