| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:09 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 1700/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| recount 1.28.0 (landing page) Leonardo Collado-Torres
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the recount package: - 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 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: recount |
| Version: 1.28.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:recount.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings recount_1.28.0.tar.gz |
| StartedAt: 2023-11-02 13:33:10 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 13:53:01 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 1191.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: recount.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:recount.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings recount_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/recount.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recount/DESCRIPTION’ ... OK
* this is package ‘recount’ version ‘1.28.0’
* 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 5.8Mb
* 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 loading without being on the library search path ... 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 ... ERROR
Running examples in ‘recount-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coverage_matrix
> ### Title: Given a set of regions for a chromosome, compute the coverage
> ### matrix for a given SRA study.
> ### Aliases: coverage_matrix
>
> ### ** Examples
>
>
> if (.Platform$OS.type != "windows") {
+ ## Reading BigWig files is not supported by rtracklayer on Windows
+ ## Define expressed regions for study DRP002835, chrY
+ regions <- expressed_regions("DRP002835", "chrY",
+ cutoff = 5L,
+ maxClusterGap = 3000L
+ )
+
+ ## Now calculate the coverage matrix for this study
+ rse <- coverage_matrix("DRP002835", "chrY", regions)
+
+ ## One row per region
+ identical(length(regions), nrow(rse))
+ }
2023-11-02 13:40:22.689352 loadCoverage: loading BigWig file http://duffel.rail.bio/recount/DRP002835/bw/mean_DRP002835.bw
2023-11-02 13:40:44.079882 loadCoverage: applying the cutoff to the merged data
2023-11-02 13:40:44.141025 filterData: originally there were 57227415 rows, now there are 57227415 rows. Meaning that 0 percent was filtered.
2023-11-02 13:40:44.147825 findRegions: identifying potential segments
2023-11-02 13:40:44.158638 findRegions: segmenting information
2023-11-02 13:40:44.159325 .getSegmentsRle: segmenting with cutoff(s) 5
2023-11-02 13:40:44.212412 findRegions: identifying candidate regions
2023-11-02 13:40:45.942684 findRegions: identifying region clusters
2023-11-02 13:40:48.751001 railMatrix: processing regions 1 to 372
2023-11-02 13:40:48.773856 railMatrix: processing file http://duffel.rail.bio/recount/DRP002835/bw/DRR028129.bw
Error in makeRestartList(...) : object 'specs' not found
Calls: coverage_matrix ... <Anonymous> -> <Anonymous> -> .rng_reset_generator -> RNGkind
*** caught bus error ***
address 0xffffffffffff, cause 'invalid alignment'
Error in ..getNamespace(c("BiocParallel", "1.36.0"), "<unknown>") :
R_Reprotect: only 108 protected items, can't reprotect index 104
Calls: coverage_matrix ... .manager_recv -> .manager_recv -> .recv_any -> .recv_any -> $<-
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Error in .manager_cleanup(manager) : bad value
Calls: coverage_matrix ... bploop -> bploop.lapply -> .bploop_impl -> .RNGstream<-
Warning: stack imbalance in '$', 64 then 62
Error in bpstop(BPPARAM) :
R_Reprotect: only 50 protected items, can't reprotect index 62
Calls: coverage_matrix ... bplapply -> bplapply -> .bpinit -> bpstop -> <Anonymous>
Warning: stack imbalance in 'if', 62 then 65
*** caught segfault ***
address (nil), cause 'memory not mapped'
* 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: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/recount.Rcheck/00check.log’
for details.
recount.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL recount ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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, 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, setdiff, sort, 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: 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 'binary/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 'binary/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 'binary/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 'binary/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 'binary/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 'text/tab-separated-values' length 258000 bytes (251 KB)
==================================================
downloaded 251 KB
trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/counts_exon.tsv.gz'
Content type 'text/tab-separated-values' length 435233 bytes (425 KB)
==================================================
downloaded 425 KB
trying URL 'http://duffel.rail.bio/recount/SRP002001/counts_jx.tsv.gz'
Content type 'text/tab-separated-values' 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 'binary/octet-stream' length 19539759 bytes (18.6 MB)
==================================================
downloaded 18.6 MB
trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Content type 'binary/octet-stream' length 50936703 bytes (48.6 MB)
==================================================
downloaded 48.6 MB
trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Content type 'binary/octet-stream' length 50936703 bytes (48.6 MB)
==================================================
downloaded 48.6 MB
trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/SRR036661.bw'
Content type 'binary/octet-stream' 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 'binary/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 2 | SKIP 0 | PASS 49 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 49 ]
>
> proc.time()
user system elapsed
59.350 14.477 710.253
recount.Rcheck/recount-Ex.timings
| name | user | system | elapsed | |
| abstract_search | 1.273 | 0.048 | 1.324 | |
| add_metadata | 0.938 | 0.024 | 3.443 | |
| add_predictions | 0.351 | 0.009 | 4.028 | |
| all_metadata | 0.618 | 0.020 | 2.628 | |
| browse_study | 0.087 | 0.000 | 0.086 | |