Laurent Gatto
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Pbase |
| Branch: RELEASE_3_10 |
| Last Commit: fffa65a |
| Last Changed Date: 2019-10-29 13:09:00 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:40:14 -0400 (Wed, 15 Apr 2020).
| Package 1233/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Laurent Gatto
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: Pbase |
| Version: 0.26.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pbase.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pbase_0.26.0.tar.gz |
| StartedAt: 2020-04-15 04:28:51 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:37:05 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 494.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: Pbase.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pbase.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pbase_0.26.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/Pbase.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pbase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pbase’ version ‘0.26.0’
* 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 ‘Pbase’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'Pbase' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/Pbase.Rcheck/00install.out’ for details.
* 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
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Pbase-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: etrid2grl
> ### Title: From a transcript identifier to 'GRanges' object
> ### Aliases: etrid2grl
>
> ### ** Examples
>
> id <- c("ENST00000612959", "ENST00000317091")
> grl1 <- etrid2grl(id[1])
Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery, :
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_99: DBI connect('database=ensembl_mart_99;host=127.0.0.1;port=5316','ensro',...) failed: Lost connection to MySQL server at 'reading initial communication packet', system error: 2 at /net/isilonP/public/ro/ensweb/live/mart/www_99/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
Calls: etrid2grl -> select -> select -> getBM -> .processResults
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 1 ERROR, 1 WARNING
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/Pbase.Rcheck/00check.log’
for details.
Pbase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Pbase ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘Pbase’ ... ** using staged installation ** R ** data ** 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 Warning: Package 'Pbase' is deprecated and will be removed from Bioconductor version 3.11 ** testing if installed package can be loaded from final location Warning: Package 'Pbase' is deprecated and will be removed from Bioconductor version 3.11 ** testing if installed package keeps a record of temporary installation path * DONE (Pbase)
Pbase.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
> test_check("Pbase")
Loading required package: Pbase
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: Rcpp
Loading required package: Gviz
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 170 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
Package 'Pbase' is deprecated and will be removed from Bioconductor
version 3.11
>
> proc.time()
user system elapsed
31.443 2.784 36.509
Pbase.Rcheck/Pbase-Ex.timings
| name | user | system | elapsed | |
| Pparams-class | 0.004 | 0.000 | 0.004 | |
| Proteins-class | 15.217 | 0.594 | 16.044 | |
| calculateHeavyLabels | 0.283 | 0.006 | 0.295 | |