Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:20:45 -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 recount package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/recount.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 1609/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
recount 1.22.0 (landing page) Leonardo Collado-Torres
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: recount |
Version: 1.22.0 |
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:recount.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings recount_1.22.0.tar.gz |
StartedAt: 2022-10-18 21:24:25 -0400 (Tue, 18 Oct 2022) |
EndedAt: 2022-10-18 21:32:28 -0400 (Tue, 18 Oct 2022) |
EllapsedTime: 483.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: recount.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:recount.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings recount_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/recount.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘recount/DESCRIPTION’ ... OK * this is package ‘recount’ version ‘1.22.0’ * package encoding: UTF-8 * 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 ‘recount’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: data 5.9Mb * 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 ... NOTE Note: found 347 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed coverage_matrix 4.629 0.698 7.493 geo_characteristics 0.479 0.038 5.721 snaptron_query 0.324 0.016 12.649 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.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: 2 NOTEs See ‘/home/biocbuild/bbs-3.15-bioc/meat/recount.Rcheck/00check.log’ for details.
recount.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL recount ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘recount’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (recount)
recount.Rcheck/tests/test-all.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid" Copyright (C) 2022 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. > ## Disable the tests if the system variable 'R_DISABLE_TESTS' is set to TRUE > > flag <- as.logical(Sys.getenv("R_DISABLE_TESTS")) > if (is.na(flag) | flag == FALSE) { + library("testthat") + test_check("recount") + } Loading required package: recount 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: 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, 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: 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: 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 Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata' Content type 'application/octet-stream' length 3130229 bytes (3.0 MB) ================================================== downloaded 3.0 MB trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/rse_gene.Rdata' Content type 'application/octet-stream' length 1753074 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/rse_exon.Rdata' Content type 'application/octet-stream' length 3973986 bytes (3.8 MB) ================================================== downloaded 3.8 MB trying URL 'http://duffel.rail.bio/recount/SRP002001/rse_jx.Rdata' Content type 'application/octet-stream' length 1257137 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/rse_tx.RData' Content type 'application/octet-stream' length 14016087 bytes (13.4 MB) ================================================== downloaded 13.4 MB trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/counts_gene.tsv.gz' Content type 'application/x-gzip' length 258000 bytes (251 KB) ================================================== downloaded 251 KB trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/counts_exon.tsv.gz' Content type 'application/x-gzip' length 435233 bytes (425 KB) ================================================== downloaded 425 KB trying URL 'http://duffel.rail.bio/recount/SRP002001/counts_jx.tsv.gz' Content type 'application/x-gzip' length 8833 bytes ================================================== downloaded 8833 bytes trying URL 'http://duffel.rail.bio/recount/SRP002001/SRP002001.tsv' Content type 'text/tab-separated-values' length 629 bytes ================================================== downloaded 629 bytes trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/files_info.tsv' Content type 'text/tab-separated-values' length 705 bytes ================================================== downloaded 705 bytes trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/SRR036661.bw' Content type 'text/plain; charset=UTF-8' length 19539759 bytes (18.6 MB) ================================================== downloaded 18.6 MB trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw' Content type 'text/plain; charset=UTF-8' length 50936703 bytes (48.6 MB) ================================================== downloaded 48.6 MB trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw' Content type 'text/plain; charset=UTF-8' length 50936703 bytes (48.6 MB) ================================================== downloaded 48.6 MB trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/SRR036661.bw' Content type 'text/plain; charset=UTF-8' length 19539759 bytes (18.6 MB) ================================================== downloaded 18.6 MB trying URL 'http://duffel.rail.bio/recount/SRP002001/SRP002001.tsv' Content type 'text/tab-separated-values' length 629 bytes ================================================== downloaded 629 bytes trying URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true' Content type 'application/octet-stream' length 2531337 bytes (2.4 MB) ================================================== downloaded 2.4 MB trying URL 'http://duffel.rail.bio/recount/SRP036843/SRP036843.tsv' Content type 'text/tab-separated-values' length 1278 bytes ================================================== downloaded 1278 bytes trying URL 'http://duffel.rail.bio/recount/SRP029334/SRP029334.tsv' Content type 'text/tab-separated-values' length 50296 bytes (49 KB) ================================================== downloaded 49 KB trying URL 'http://duffel.rail.bio/recount/SRP050563/SRP050563.tsv' Content type 'text/tab-separated-values' length 1296 bytes ================================================== downloaded 1296 bytes trying URL 'http://duffel.rail.bio/recount/SRP055438/SRP055438.tsv' Content type 'text/tab-separated-values' length 13953 bytes (13 KB) ================================================== downloaded 13 KB trying URL 'http://duffel.rail.bio/recount/SRP055749/SRP055749.tsv' Content type 'text/tab-separated-values' length 4823 bytes ================================================== downloaded 4823 bytes trying URL 'http://duffel.rail.bio/recount/SRP058120/SRP058120.tsv' Content type 'text/tab-separated-values' length 9768 bytes ================================================== downloaded 9768 bytes trying URL 'http://duffel.rail.bio/recount/SRP005342/SRP005342.tsv' Content type 'text/tab-separated-values' length 3628 bytes ================================================== downloaded 3628 bytes trying URL 'http://duffel.rail.bio/recount/SRP007508/SRP007508.tsv' Content type 'text/tab-separated-values' length 1801 bytes ================================================== downloaded 1801 bytes trying URL 'http://duffel.rail.bio/recount/SRP015668/SRP015668.tsv' Content type 'text/tab-separated-values' length 11186 bytes (10 KB) ================================================== downloaded 10 KB trying URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_tcga.Rdata?raw=true' Content type 'application/octet-stream' length 16334695 bytes (15.6 MB) ================================================== downloaded 15.6 MB trying URL 'https://github.com/leekgroup/recount-website/blob/master/predictions/PredictedPhenotypes_v0.0.06.rda?raw=true' Content type 'application/octet-stream' length 548129 bytes (535 KB) ================================================== downloaded 535 KB Loading objects: PredictedPhenotypes trying URL 'http://duffel.rail.bio/recount/v2/DRP000499/rse_gene.Rdata' Content type 'application/octet-stream' length 4636353 bytes (4.4 MB) ================================================== downloaded 4.4 MB trying URL 'http://duffel.rail.bio/recount/v2/DRP000366/files_info.tsv_fake' [ FAIL 0 | WARN 1 | SKIP 0 | PASS 58 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 58 ] > > proc.time() user system elapsed 51.661 12.634 146.078
recount.Rcheck/recount-Ex.timings
name | user | system | elapsed | |
abstract_search | 0.145 | 0.000 | 0.145 | |
add_metadata | 1.852 | 0.249 | 3.332 | |
add_predictions | 0.448 | 0.041 | 2.251 | |
all_metadata | 0.690 | 0.040 | 1.625 | |
browse_study | 0.075 | 0.007 | 0.083 | |
coverage_matrix | 4.629 | 0.698 | 7.493 | |
download_retry | 0.016 | 0.004 | 0.287 | |
download_study | 0.002 | 0.003 | 0.005 | |
expressed_regions | 2.409 | 0.472 | 3.512 | |
find_geo | 0.091 | 0.020 | 2.509 | |
geo_characteristics | 0.479 | 0.038 | 5.721 | |
geo_info | 0.097 | 0.007 | 0.104 | |
getRPKM | 0.433 | 0.100 | 0.534 | |
getTPM | 0.053 | 0.008 | 0.060 | |
read_counts | 0.613 | 0.089 | 1.424 | |
reproduce_ranges | 0 | 0 | 0 | |
scale_counts | 0.130 | 0.016 | 0.146 | |
snaptron_query | 0.324 | 0.016 | 12.649 | |