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CHECK report for recount on malbec2

This page was generated on 2019-10-16 12:09:24 -0400 (Wed, 16 Oct 2019).

Package 1345/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
recount 1.10.13
Leonardo Collado-Torres
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/recount
Branch: RELEASE_3_9
Last Commit: b248c65
Last Changed Date: 2019-09-03 11:55:25 -0400 (Tue, 03 Sep 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: recount
Version: 1.10.13
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:recount.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings recount_1.10.13.tar.gz
StartedAt: 2019-10-16 04:24:18 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:37:57 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 819.6 seconds
RetCode: 0
Status:  OK 
CheckDir: recount.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:recount.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings recount_1.10.13.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/recount.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recount/DESCRIPTION’ ... OK
* this is package ‘recount’ version ‘1.10.13’
* 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 12.0Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
coverage_matrix     4.100  0.119   9.339
geo_characteristics 1.015  0.040   6.371
snaptron_query      0.286  0.011  12.696
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/recount.Rcheck/00check.log’
for details.

Installation output

recount.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL recount
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘recount’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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)

Tests output

recount.Rcheck/tests/test-all.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ## Disable the tests if the system variable 'R_DISABLE_TESTS' is set to TRUE
> 
> flag <- as.logical(Sys.getenv('R_DISABLE_TESTS'))
> if(is.na(flag) | flag == FALSE) {
+     library('testthat')
+     test_check('recount')
+ }
Loading required package: recount
Loading required package: SummarizedExperiment
Loading required package: 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, 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
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

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'
Content type 'unknown' length 46738343 bytes (44.6 MB)
==================================================
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Content type 'application/octet-stream' length 3130229 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/rse_gene.Rdata'
Content type 'application/octet-stream' length 1753074 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/rse_exon.Rdata'
Content type 'application/octet-stream' length 3973986 bytes (3.8 MB)
==================================================
downloaded 3.8 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/rse_jx.Rdata'
Content type 'application/octet-stream' length 1257137 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/rse_tx.RData'
Content type 'application/octet-stream' length 14016087 bytes (13.4 MB)
==================================================
downloaded 13.4 MB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/counts_gene.tsv.gz'
Content type 'application/x-gzip' length 258000 bytes (251 KB)
==================================================
downloaded 251 KB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/counts_exon.tsv.gz'
Content type 'application/x-gzip' length 435233 bytes (425 KB)
==================================================
downloaded 425 KB

trying URL 'http://duffel.rail.bio/recount/SRP002001/counts_jx.tsv.gz'
Content type 'application/x-gzip' length 8833 bytes
==================================================
downloaded 8833 bytes

trying URL 'http://duffel.rail.bio/recount/SRP002001/SRP002001.tsv'
Content type 'text/tab-separated-values' length 629 bytes
==================================================
downloaded 629 bytes

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/files_info.tsv'
Content type 'text/tab-separated-values' length 705 bytes
==================================================
downloaded 705 bytes

trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/SRR036661.bw'
Content type 'text/plain; charset=UTF-8' length 19539759 bytes (18.6 MB)
==================================================
downloaded 18.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Content type 'text/plain; charset=UTF-8' length 50936703 bytes (48.6 MB)
==================================================
downloaded 48.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Content type 'text/plain; charset=UTF-8' length 50936703 bytes (48.6 MB)
==================================================
downloaded 48.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/SRR036661.bw'
Content type 'text/plain; charset=UTF-8' length 19539759 bytes (18.6 MB)
==================================================
downloaded 18.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/SRP002001.tsv'
Content type 'text/tab-separated-values' length 629 bytes
==================================================
downloaded 629 bytes

trying URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true'
Content type 'application/octet-stream' length 2531337 bytes (2.4 MB)
==================================================
downloaded 2.4 MB

trying URL 'http://duffel.rail.bio/recount/SRP036843/SRP036843.tsv'
Content type 'text/tab-separated-values' length 1278 bytes
==================================================
downloaded 1278 bytes

trying URL 'http://duffel.rail.bio/recount/SRP029334/SRP029334.tsv'
Content type 'text/tab-separated-values' length 50296 bytes (49 KB)
==================================================
downloaded 49 KB

trying URL 'http://duffel.rail.bio/recount/SRP050563/SRP050563.tsv'
Content type 'text/tab-separated-values' length 1296 bytes
==================================================
downloaded 1296 bytes

trying URL 'http://duffel.rail.bio/recount/SRP055438/SRP055438.tsv'
Content type 'text/tab-separated-values' length 13953 bytes (13 KB)
==================================================
downloaded 13 KB

trying URL 'http://duffel.rail.bio/recount/SRP055749/SRP055749.tsv'
Content type 'text/tab-separated-values' length 4823 bytes
==================================================
downloaded 4823 bytes

trying URL 'http://duffel.rail.bio/recount/SRP058120/SRP058120.tsv'
Content type 'text/tab-separated-values' length 9768 bytes
==================================================
downloaded 9768 bytes

trying URL 'http://duffel.rail.bio/recount/SRP005342/SRP005342.tsv'
Content type 'text/tab-separated-values' length 3628 bytes
==================================================
downloaded 3628 bytes

trying URL 'http://duffel.rail.bio/recount/SRP007508/SRP007508.tsv'
Content type 'text/tab-separated-values' length 1801 bytes
==================================================
downloaded 1801 bytes

trying URL 'http://duffel.rail.bio/recount/SRP015668/SRP015668.tsv'
Content type 'text/tab-separated-values' length 11186 bytes (10 KB)
==================================================
downloaded 10 KB

trying URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_tcga.Rdata?raw=true'
Content type 'application/octet-stream' length 16334695 bytes (15.6 MB)
==================================================
downloaded 15.6 MB

trying URL 'https://github.com/leekgroup/recount-website/blob/master/predictions/PredictedPhenotypes_v0.0.06.rda?raw=true'
Content type 'application/octet-stream' length 548129 bytes (535 KB)
==================================================
downloaded 535 KB

Loading objects:
  PredictedPhenotypes
trying URL 'http://duffel.rail.bio/recount/v2/DRP000499/rse_gene.Rdata'
Content type 'application/octet-stream' length 4636353 bytes (4.4 MB)
==================================================
downloaded 4.4 MB

trying URL 'http://duffel.rail.bio/recount/v2/DRP000366/files_info.tsv_fake'
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 62 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
167.312   8.113 438.938

Example timings

recount.Rcheck/recount-Ex.timings

nameusersystemelapsed
abstract_search0.0880.0080.096
add_metadata2.3730.0444.113
add_predictions0.7910.0312.612
all_metadata0.9120.0322.031
browse_study0.0750.0000.074
coverage_matrix4.1000.1199.339
download_retry0.0060.0000.393
download_study0.0040.0000.004
expressed_regions2.7700.1134.153
find_geo0.2790.0192.144
geo_characteristics1.0150.0406.371
geo_info0.1520.0000.152
getRPKM0.6530.0680.722
getTPM0.1270.0080.135
read_counts1.8410.0532.906
reproduce_ranges000
scale_counts0.1840.0000.183
snaptron_query 0.286 0.01112.696