Laurent Gatto
| Snapshot Date: 2019-10-17 09:00:12 -0400 (Thu, 17 Oct 2019) |
| URL: https://git.bioconductor.org/packages/pRolocdata |
| Branch: RELEASE_3_9 |
| Last Commit: 16ac667 |
| Last Changed Date: 2019-05-02 11:56:29 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 experimental data |
This page was generated on 2019-10-17 16:51:25 -0400 (Thu, 17 Oct 2019).
| Package 269/371 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pRolocdata 1.22.0 Laurent Gatto
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |
| Package: pRolocdata |
| Version: 1.22.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings pRolocdata_1.22.0.tar.gz |
| StartedAt: 2019-10-17 13:39:16 -0400 (Thu, 17 Oct 2019) |
| EndedAt: 2019-10-17 13:42:01 -0400 (Thu, 17 Oct 2019) |
| EllapsedTime: 164.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pRolocdata.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings pRolocdata_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/pRolocdata.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 ‘pRolocdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pRolocdata’ version ‘1.22.0’
* 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 ‘pRolocdata’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 137.6Mb
sub-directories of 1Mb or more:
data 43.8Mb
extdata 93.4Mb
* checking package 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
print.pRolocmetadata
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
andreyev2010 4.933 0.129 7.24
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.9-data-experiment/meat/pRolocdata.Rcheck/00check.log’
for details.
pRolocdata.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL pRolocdata ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘pRolocdata’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (pRolocdata)
pRolocdata.Rcheck/tests/testthat.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.
> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(MSnbase)
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: 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: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: ProtGenerics
This is MSnbase version 2.10.1
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
> library(pRolocdata)
This is pRolocdata version 1.22.0.
Use 'pRolocdata()' to list available data sets.
>
> test_check("pRolocdata")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 79 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
10.886 0.422 11.296
pRolocdata.Rcheck/pRolocdata-Ex.timings
| name | user | system | elapsed | |
| E14TG2a | 0.041 | 0.000 | 0.041 | |
| andreyev2010 | 4.933 | 0.129 | 7.240 | |
| andy2011 | 0.065 | 0.000 | 0.065 | |
| at_chloro | 0.087 | 0.004 | 0.091 | |
| baers2018 | 0.236 | 0.000 | 0.236 | |
| beltran2016 | 0.339 | 0.000 | 0.339 | |
| dunkley2006 | 0.012 | 0.000 | 0.012 | |
| fabre2015 | 0.201 | 0.000 | 0.201 | |
| foster2006 | 0.031 | 0.000 | 0.031 | |
| groen2014 | 2.326 | 0.007 | 2.334 | |
| hall2009 | 0.129 | 0.004 | 0.133 | |
| havugimana2012 | 0.591 | 0.004 | 0.596 | |
| hirst2018 | 0.371 | 0.004 | 0.375 | |
| hyperLOPIT2015 | 4.348 | 0.024 | 4.373 | |
| hyperLOPITU2OS2017 | 0.965 | 0.008 | 0.984 | |
| itzhak2016 | 0.413 | 0.008 | 0.421 | |
| itzhak2017 | 1.009 | 0.008 | 1.016 | |
| kirkwood2013 | 0.036 | 0.004 | 0.039 | |
| kristensen2012 | 0.022 | 0.000 | 0.022 | |
| lopimsSyn2 | 0.272 | 0.008 | 0.323 | |
| mulvey2015 | 2.924 | 0.052 | 2.977 | |
| nikolovski2012 | 0.274 | 0.000 | 0.274 | |
| nikolovski2014 | 0.286 | 0.004 | 0.289 | |
| pRolocdata | 0.013 | 0.032 | 0.093 | |
| pRolocmetadata | 0.017 | 0.000 | 0.017 | |
| rodriguez2012r1 | 0.470 | 0.028 | 0.695 | |
| stekhoven2014 | 0.226 | 0.008 | 0.234 | |
| tan2009 | 0.018 | 0.000 | 0.018 | |
| trotter2010 | 0.294 | 0.028 | 0.321 | |
| yeast | 0.273 | 0.005 | 0.279 | |