| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:18 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1541/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| recount 1.18.1 (landing page) Leonardo Collado-Torres
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: recount |
| Version: 1.18.1 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:recount.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings recount_1.18.1.tar.gz |
| StartedAt: 2021-10-15 04:16:45 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 04:30:31 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 826.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: recount.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:recount.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings recount_1.18.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/recount.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'recount/DESCRIPTION' ... OK
* this is package 'recount' version '1.18.1'
* 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 'recount' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.3Mb
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
* 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 ... 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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'recount-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geo_characteristics
> ### Title: Build a data.frame from GEO's charactersitics for a given sample
> ### Aliases: geo_characteristics
>
> ### ** Examples
>
>
> ## Load required library
> library("SummarizedExperiment")
>
> ## Get the GEO accession ids
> # geoids <- sapply(colData(rse_gene_SRP009615)$run[1:2], find_geo)
> ## The previous example code works nearly all the time but it
> ## can occassionally fail depending on how rentrez is doing.
> ## This code makes sure that the example code runs.
> geoids <- tryCatch(
+ sapply(colData(rse_gene_SRP009615)$run[1:2], find_geo),
+ error = function(e) {
+ c(
+ "SRR387777" = "GSM836270",
+ "SRR387778" = "GSM836271"
+ )
+ }
+ )
>
> ## Get the data from GEO
> geodata <- do.call(rbind, sapply(geoids, geo_info))
File stored at:
C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpoTVHO0/GSM836270.soft
File stored at:
C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpoTVHO0/GSM836271.soft
Error in .aggregate_and_align_all_colnames(all_colnames, strict.colnames = strict.colnames) :
the DFrame objects to combine must have the same column names
Calls: do.call ... .combine_DFrame_rows -> .aggregate_and_align_all_colnames
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'recount-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geo_characteristics
> ### Title: Build a data.frame from GEO's charactersitics for a given sample
> ### Aliases: geo_characteristics
>
> ### ** Examples
>
>
> ## Load required library
> library("SummarizedExperiment")
>
> ## Get the GEO accession ids
> # geoids <- sapply(colData(rse_gene_SRP009615)$run[1:2], find_geo)
> ## The previous example code works nearly all the time but it
> ## can occassionally fail depending on how rentrez is doing.
> ## This code makes sure that the example code runs.
> geoids <- tryCatch(
+ sapply(colData(rse_gene_SRP009615)$run[1:2], find_geo),
+ error = function(e) {
+ c(
+ "SRR387777" = "GSM836270",
+ "SRR387778" = "GSM836271"
+ )
+ }
+ )
>
> ## Get the data from GEO
> geodata <- do.call(rbind, sapply(geoids, geo_info))
File stored at:
C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpiAKQp7/GSM836270.soft
File stored at:
C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpiAKQp7/GSM836271.soft
Error in .aggregate_and_align_all_colnames(all_colnames, strict.colnames = strict.colnames) :
the DFrame objects to combine must have the same column names
Calls: do.call ... .combine_DFrame_rows -> .aggregate_and_align_all_colnames
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R'
ERROR
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
error: cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
Backtrace:
x
1. \-recount::reproduce_ranges("both", db = "Gencode.v25") test-annotation.R:5:0
2. \-recount::download_retry(...)
-- Failure (test-misc.R:15:5): Geo info ----------------------------------------
info$geo_accession not equal to "GSM836270".
target is NULL, current is character
-- Failure (test-misc.R:18:5): Geo info ----------------------------------------
geo_characteristics(info) not equal to `chars`.
Length mismatch: comparison on first 1 components
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 47 ]
Error: Test failures
Execution halted
** running tests for arch 'x64' ...
Running 'test-all.R'
ERROR
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
error: cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
Backtrace:
x
1. \-recount::reproduce_ranges("both", db = "Gencode.v25") test-annotation.R:5:0
2. \-recount::download_retry(...)
-- Failure (test-misc.R:15:5): Geo info ----------------------------------------
info$geo_accession not equal to "GSM836270".
target is NULL, current is character
-- Failure (test-misc.R:18:5): Geo info ----------------------------------------
geo_characteristics(info) not equal to `chars`.
Length mismatch: comparison on first 1 components
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 47 ]
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: 4 ERRORs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/recount.Rcheck/00check.log'
for details.
recount.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/recount_1.18.1.tar.gz && rm -rf recount.buildbin-libdir && mkdir recount.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=recount.buildbin-libdir recount_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL recount_1.18.1.zip && rm recount_1.18.1.tar.gz recount_1.18.1.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
19 5805k 19 1129k 0 0 2244k 0 0:00:02 --:--:-- 0:00:02 2245k
99 5805k 99 5749k 0 0 3845k 0 0:00:01 0:00:01 --:--:-- 3845k
100 5805k 100 5805k 0 0 3854k 0 0:00:01 0:00:01 --:--:-- 3855k
install for i386
* 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
converting help for package 'recount'
finding HTML links ... done
abstract_search html
add_metadata html
add_predictions html
all_metadata html
browse_study html
coverage_matrix html
download_retry html
download_study html
expressed_regions html
find_geo html
geo_characteristics html
geo_info html
getRPKM html
getTPM html
read_counts html
recount-package html
recount_abstract html
recount_exons html
recount_genes html
recount_url html
reproduce_ranges html
rse_gene_SRP009615 html
scale_counts html
snaptron_query 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 'recount' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'recount' as recount_1.18.1.zip
* DONE (recount)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'recount' successfully unpacked and MD5 sums checked
|
recount.Rcheck/tests_i386/test-all.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
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.
> ## 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
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 objects are masked from 'package:base':
I, expand.grid, unname
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
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
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 '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'
== Failed tests ================================================================
-- Error (test-annotation.R:5:1): (code run outside of `test_that()`) ----------
Error in `download_retry(url = paste0("ftp://ftp.ebi.ac.uk/pub/databases/gencode/",
"Gencode_human/release_25/gencode.v25.annotation.gff3.gz"),
destfile = temp_gencode)`: 'download_retry()' failed:
URL: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz
error: cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
Backtrace:
x
1. \-recount::reproduce_ranges("both", db = "Gencode.v25") test-annotation.R:5:0
2. \-recount::download_retry(...)
-- Failure (test-misc.R:15:5): Geo info ----------------------------------------
info$geo_accession not equal to "GSM836270".
target is NULL, current is character
-- Failure (test-misc.R:18:5): Geo info ----------------------------------------
geo_characteristics(info) not equal to `chars`.
Length mismatch: comparison on first 1 components
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 47 ]
Error: Test failures
Execution halted
|
recount.Rcheck/tests_x64/test-all.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
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.
> ## 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
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 objects are masked from 'package:base':
I, expand.grid, unname
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
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
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 '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'
== Failed tests ================================================================
-- Error (test-annotation.R:5:1): (code run outside of `test_that()`) ----------
Error in `download_retry(url = paste0("ftp://ftp.ebi.ac.uk/pub/databases/gencode/",
"Gencode_human/release_25/gencode.v25.annotation.gff3.gz"),
destfile = temp_gencode)`: 'download_retry()' failed:
URL: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz
error: cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
Backtrace:
x
1. \-recount::reproduce_ranges("both", db = "Gencode.v25") test-annotation.R:5:0
2. \-recount::download_retry(...)
-- Failure (test-misc.R:15:5): Geo info ----------------------------------------
info$geo_accession not equal to "GSM836270".
target is NULL, current is character
-- Failure (test-misc.R:18:5): Geo info ----------------------------------------
geo_characteristics(info) not equal to `chars`.
Length mismatch: comparison on first 1 components
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 47 ]
Error: Test failures
Execution halted
|
|
recount.Rcheck/examples_i386/recount-Ex.timings
|
recount.Rcheck/examples_x64/recount-Ex.timings
|