Leonardo Collado-Torres
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/recount3 |
| Branch: RELEASE_3_12 |
| Last Commit: 66048cf |
| Last Changed Date: 2021-02-10 16:20:59 -0400 (Wed, 10 Feb 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:10 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the recount3 package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1490/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| recount3 1.0.7 (landing page) Leonardo Collado-Torres
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: recount3 |
| Version: 1.0.7 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:recount3.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings recount3_1.0.7.tar.gz |
| StartedAt: 2021-05-06 06:04:05 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:38:17 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 2052.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: recount3.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:recount3.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings recount3_1.0.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/recount3.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'recount3/DESCRIPTION' ... OK
* this is package 'recount3' version '1.0.7'
* 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 whether package 'recount3' can be installed ... OK
* 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 ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
expand_sra_attributes: no visible global function definition for
'colData<-'
Undefined global functions or variables:
colData<-
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'recount3-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_rse_manual
> ### Title: Internal function for creating a recount3
> ### RangedSummarizedExperiment object
> ### Aliases: create_rse_manual
>
> ### ** Examples
>
>
> ## Unlike create_rse(), here we create an RSE object by
> ## fully specifying all the arguments for locating this study
> rse_gene_SRP009615_manual <- create_rse_manual(
+ "SRP009615",
+ "data_sources/sra"
+ )
2021-05-06 06:14:20 downloading and reading the metadata.
2021-05-06 06:14:21 caching file sra.sra.SRP009615.MD.gz.
2021-05-06 06:14:21 caching file sra.recount_project.SRP009615.MD.gz.
2021-05-06 06:14:22 caching file sra.recount_qc.SRP009615.MD.gz.
2021-05-06 06:14:23 caching file sra.recount_seq_qc.SRP009615.MD.gz.
2021-05-06 06:14:23 caching file sra.recount_pred.SRP009615.MD.gz.
2021-05-06 06:14:24 downloading and reading the feature information.
2021-05-06 06:14:24 caching file human.gene_sums.G026.gtf.gz.
2021-05-06 06:14:26 downloading and reading the counts: 12 samples across 63856 features.
2021-05-06 06:14:27 caching file sra.gene_sums.SRP009615.G026.gz.
2021-05-06 06:14:28 construcing the RangedSummarizedExperiment (rse) object.
> rse_gene_SRP009615_manual
class: RangedSummarizedExperiment
dim: 63856 12
metadata(8): time_created recount3_version ... annotation recount3_url
assays(1): raw_counts
rownames(63856): ENSG00000278704.1 ENSG00000277400.1 ...
ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y
rowData names(10): source type ... havana_gene tag
colnames(12): SRR387777 SRR387778 ... SRR389077 SRR389078
colData names(175): rail_id external_id ...
recount_pred.curated.cell_line BigWigURL
>
> ## Check how much memory this RSE object uses
> pryr::object_size(rse_gene_SRP009615_manual)
20.2 MB
>
> ## Test with a collection that has a single sample
> ## NOTE: this requires loading the full data for this study when
> ## creating the RSE object
> rse_gene_ERP110066_collection_manual <- create_rse_manual(
+ "ERP110066",
+ "collections/geuvadis_smartseq",
+ recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3"
+ )
2021-05-06 06:14:28 downloading and reading the metadata.
2021-05-06 06:14:29 caching file geuvadis_smartseq.recount_project.gz.
adding rname 'http://snaptron.cs.jhu.edu/data/temp/recount3/human/collections/geuvadis_smartseq/metadata/geuvadis_smartseq.recount_project.gz'
2021-05-06 06:14:29 caching file sra.sra.ERP110066.MD.gz.
adding rname 'http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/metadata/66/ERP110066/sra.sra.ERP110066.MD.gz'
2021-05-06 06:14:30 caching file sra.recount_project.ERP110066.MD.gz.
adding rname 'http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/metadata/66/ERP110066/sra.recount_project.ERP110066.MD.gz'
2021-05-06 06:14:31 caching file sra.recount_qc.ERP110066.MD.gz.
adding rname 'http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/metadata/66/ERP110066/sra.recount_qc.ERP110066.MD.gz'
Warning: The 'url' <http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/metadata/66/ERP110066/sra.recount_seq_qc.ERP110066.MD.gz> does not exist or is not available.
2021-05-06 06:14:32 caching file sra.recount_pred.ERP110066.MD.gz.
adding rname 'http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/metadata/66/ERP110066/sra.recount_pred.ERP110066.MD.gz'
2021-05-06 06:14:33 caching file geuvadis_smartseq.custom.gz.
adding rname 'http://snaptron.cs.jhu.edu/data/temp/recount3/human/collections/geuvadis_smartseq/metadata/geuvadis_smartseq.custom.gz'
2021-05-06 06:14:34 downloading and reading the feature information.
2021-05-06 06:14:34 caching file human.gene_sums.G026.gtf.gz.
adding rname 'http://snaptron.cs.jhu.edu/data/temp/recount3/human/annotations/gene_sums/human.gene_sums.G026.gtf.gz'
2021-05-06 06:14:36 downloading and reading the counts: 1 sample across 63856 features.
2021-05-06 06:14:36 caching file sra.gene_sums.ERP110066.G026.gz.
adding rname 'http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/gene_sums/66/ERP110066/sra.gene_sums.ERP110066.G026.gz'
2021-05-06 06:14:41 construcing the RangedSummarizedExperiment (rse) object.
> rse_gene_ERP110066_collection_manual
class: RangedSummarizedExperiment
dim: 63856 1
metadata(8): time_created recount3_version ... annotation recount3_url
assays(1): raw_counts
rownames(63856): ENSG00000278704.1 ENSG00000277400.1 ...
ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y
rowData names(10): source type ... havana_gene tag
colnames(1): ERR2713106
colData names(162): rail_id external_id ... custom.sequencing_type
BigWigURL
>
> ## Check how much memory this RSE object uses
> pryr::object_size(rse_gene_ERP110066_collection_manual)
14.5 MB
>
> ## Mouse example
> rse_gene_DRP002367_manual <- create_rse_manual(
+ "DRP002367",
+ "data_sources/sra",
+ organism = "mouse"
+ )
2021-05-06 06:14:42 downloading and reading the metadata.
2021-05-06 06:14:43 caching file sra.sra.DRP002367.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/mouse/data_sources/sra/metadata/67/DRP002367/sra.sra.DRP002367.MD.gz'
Warning: download failed
web resource path: 'http://duffel.rail.bio/recount3/mouse/data_sources/sra/metadata/67/DRP002367/sra.sra.DRP002367.MD.gz'
local file path: 'C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpmKo39X/BiocFileCache/d343946385e_sra.sra.DRP002367.MD.gz'
reason: Gateway Timeout (HTTP 504).
Warning: bfcadd() failed; resource removed
rid: BFC42
fpath: 'http://duffel.rail.bio/recount3/mouse/data_sources/sra/metadata/67/DRP002367/sra.sra.DRP002367.MD.gz'
reason: download failed
Warning in value[[3L]](cond) :
trying to add rname 'http://duffel.rail.bio/recount3/mouse/data_sources/sra/metadata/67/DRP002367/sra.sra.DRP002367.MD.gz' produced error:
bfcadd() failed; see warnings()
Error in BiocFileCache::bfcrpath(bfc, url, exact = TRUE, verbose = verbose) :
not all 'rnames' found or unique.
Calls: create_rse_manual ... file_retrieve -> vapply -> FUN -> <Anonymous> -> <Anonymous>
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
create_rse 158.92 6.22 261.21
available_projects 36.11 0.71 41.92
create_rse_manual 23.55 1.73 41.37
compute_read_counts 22.13 1.23 40.01
available_samples 22.23 0.11 24.43
expand_sra_attributes 20.23 0.46 26.59
read_counts 12.44 1.23 16.54
read_metadata 12.22 0.35 21.58
transform_counts 6.36 0.33 11.72
is_paired_end 6.28 0.11 10.24
compute_scale_factors 5.89 0.19 10.17
file_retrieve 4.75 0.03 7.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
x
1. +-testthat::expect_equal(...) test-available_projects.R:2:4
2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
3. | \-rlang::eval_bare(expr, quo_get_env(quo))
4. \-recount3::available_projects("human")
5. \-recount3::available_samples(...)
6. \-recount3::file_retrieve(urls, bfc = bfc, verbose = verbose)
7. \-base::vapply(url, file_retrieve, character(1), bfc = bfc, verbose = verbose)
8. \-recount3:::FUN(X[[i]], ...)
9. +-BiocFileCache::bfcrpath(bfc, url, exact = TRUE, verbose = verbose)
10. \-BiocFileCache::bfcrpath(bfc, url, exact = TRUE, verbose = verbose)
[ FAIL 1 | WARN 3 | SKIP 0 | PASS 55 ]
Error: Test failures
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
2. +-recount3::read_counts(...)
3. | \-utils::read.delim(counts_file, skip = 2, nrows = 1, check.names = FALSE)
4. | \-utils::read.table(...)
5. +-recount3::file_retrieve(...)
6. \-recount3::locate_url(...)
7. +-base::match.arg(project_home)
8. | \-base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
9. | \-base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
10. \-recount3::project_homes(organism = organism, recount3_url = recount3_url)
11. \-base::readLines(homes_url)
12. \-base::file(con, "r")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 55 ]
Error: Test failures
Execution halted
* 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: 3 ERRORs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/recount3.Rcheck/00check.log'
for details.
recount3.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/recount3_1.0.7.tar.gz && rm -rf recount3.buildbin-libdir && mkdir recount3.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=recount3.buildbin-libdir recount3_1.0.7.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL recount3_1.0.7.zip && rm recount3_1.0.7.tar.gz recount3_1.0.7.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 117k 100 117k 0 0 6514k 0 --:--:-- --:--:-- --:--:-- 6940k
install for i386
* installing *source* package 'recount3' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'recount3'
finding HTML links ... done
annotation_ext html
annotation_options html
available_projects html
available_samples html
compute_read_counts html
compute_scale_factors html
create_rse html
create_rse_manual html
expand_sra_attributes html
file_retrieve html
is_paired_end html
locate_url html
locate_url_ann html
project_homes html
read_counts html
read_metadata html
recount3-package html
recount3_cache html
recount3_cache_files html
recount3_cache_rm html
transform_counts html
*** 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
install for x64
* installing *source* package 'recount3' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'recount3' as recount3_1.0.7.zip
* DONE (recount3)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'recount3' successfully unpacked and MD5 sums checked
|
recount3.Rcheck/tests_i386/testthat.Rout.fail
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
> library(testthat)
> library(recount3)
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
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: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
>
> test_check("recount3")
== Failed tests ================================================================
-- Error (test-available_projects.R:2:5): number of available projects by organism works --
Error: not all 'rnames' found or unique.
Backtrace:
x
1. +-testthat::expect_equal(...) test-available_projects.R:2:4
2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
3. | \-rlang::eval_bare(expr, quo_get_env(quo))
4. \-recount3::available_projects("human")
5. \-recount3::available_samples(...)
6. \-recount3::file_retrieve(urls, bfc = bfc, verbose = verbose)
7. \-base::vapply(url, file_retrieve, character(1), bfc = bfc, verbose = verbose)
8. \-recount3:::FUN(X[[i]], ...)
9. +-BiocFileCache::bfcrpath(bfc, url, exact = TRUE, verbose = verbose)
10. \-BiocFileCache::bfcrpath(bfc, url, exact = TRUE, verbose = verbose)
[ FAIL 1 | WARN 3 | SKIP 0 | PASS 55 ]
Error: Test failures
Execution halted
|
recount3.Rcheck/tests_x64/testthat.Rout.fail
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> library(testthat)
> library(recount3)
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
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: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
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The following object is masked from 'package:MatrixGenerics':
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The following objects are masked from 'package:matrixStats':
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>
> test_check("recount3")
== Failed tests ================================================================
-- Error (test-create_rse_manual.R:27:5): Creating an RSE works (ercc) ---------
Error: cannot open the connection
Backtrace:
x
1. \-recount3::create_rse_manual(...) test-create_rse_manual.R:27:4
2. +-recount3::read_counts(...)
3. | \-utils::read.delim(counts_file, skip = 2, nrows = 1, check.names = FALSE)
4. | \-utils::read.table(...)
5. +-recount3::file_retrieve(...)
6. \-recount3::locate_url(...)
7. +-base::match.arg(project_home)
8. | \-base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
9. | \-base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
10. \-recount3::project_homes(organism = organism, recount3_url = recount3_url)
11. \-base::readLines(homes_url)
12. \-base::file(con, "r")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 55 ]
Error: Test failures
Execution halted
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recount3.Rcheck/examples_i386/recount3-Ex.timings
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recount3.Rcheck/examples_x64/recount3-Ex.timings
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