| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-01-29 12:20:35 -0500 (Mon, 29 Jan 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.5 Ventura | arm64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4239 |
| 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 1675/2234 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| recount 1.29.0 (landing page) Leonardo Collado-Torres
| kjohnson3 | macOS 13.5 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the recount package: - 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: recount |
| Version: 1.29.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recount.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recount_1.29.0.tar.gz |
| StartedAt: 2024-01-27 06:25:28 -0500 (Sat, 27 Jan 2024) |
| EndedAt: 2024-01-27 07:01:14 -0500 (Sat, 27 Jan 2024) |
| EllapsedTime: 2146.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: recount.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recount.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recount_1.29.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/recount.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: aarch64-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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recount/DESCRIPTION’ ... OK
* this is package ‘recount’ version ‘1.29.0’
* 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 6.1Mb
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 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))
+ }
2024-01-27 06:37:50.673147 loadCoverage: loading BigWig file http://duffel.rail.bio/recount/DRP002835/bw/mean_DRP002835.bw
2024-01-27 06:37:54.688841 loadCoverage: applying the cutoff to the merged data
2024-01-27 06:37:54.71273 filterData: originally there were 57227415 rows, now there are 57227415 rows. Meaning that 0 percent was filtered.
2024-01-27 06:37:54.714941 findRegions: identifying potential segments
2024-01-27 06:37:54.717403 findRegions: segmenting information
2024-01-27 06:37:54.717667 .getSegmentsRle: segmenting with cutoff(s) 5
2024-01-27 06:37:54.72948 findRegions: identifying candidate regions
2024-01-27 06:42:54.343437 findRegions: identifying region clusters
Warning in file(file, "rt") :
URL 'https://raw.githubusercontent.com/nellore/runs/master/gtex/hg38.sizes': status was 'Couldn't resolve host name'
Error in file(file, "rt") :
cannot open the connection to 'https://raw.githubusercontent.com/nellore/runs/master/gtex/hg38.sizes'
Calls: coverage_matrix -> read.table -> file
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’
ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
mode = "wb", ...)`: 'download_retry()' failed:
URL: http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw
error: cannot open URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-data.R:133:13
2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─recount::expressed_regions("SRP002001", "chrY", cutoff = 5, outdir = tmpdir)
5. └─recount::download_study(...)
6. └─recount::download_retry(...)
[ FAIL 1 | WARN 8 | SKIP 0 | PASS 48 ]
Error: Test failures
Execution halted
* 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: 2 ERRORs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/recount.Rcheck/00check.log’
for details.
recount.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL recount ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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.fail
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.
> ## 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':
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, 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':
expand.grid, I, 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'
trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/counts_exon.tsv.gz'
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 32.3 MB
trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
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 1 | WARN 8 | SKIP 0 | PASS 48 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-data.R:133:13'): Expressed regions ─────────────────────────────
Error in `download_retry(url = url, destfile = file.path(outdir, filename),
mode = "wb", ...)`: 'download_retry()' failed:
URL: http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw
error: cannot open URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-data.R:133:13
2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─recount::expressed_regions("SRP002001", "chrY", cutoff = 5, outdir = tmpdir)
5. └─recount::download_study(...)
6. └─recount::download_retry(...)
[ FAIL 1 | WARN 8 | SKIP 0 | PASS 48 ]
Error: Test failures
Execution halted
recount.Rcheck/recount-Ex.timings
| name | user | system | elapsed | |
| abstract_search | 0.071 | 0.001 | 0.073 | |
| add_metadata | 0.393 | 0.022 | 1.810 | |
| add_predictions | 0.119 | 0.015 | 1.349 | |
| all_metadata | 0.745 | 0.015 | 1.685 | |
| browse_study | 0.049 | 0.000 | 0.050 | |