| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:30 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the rpx package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rpx.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1746/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rpx 2.7.4 (landing page) Laurent Gatto
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | ERROR | skipped | ||||||||||
| Package: rpx |
| Version: 2.7.4 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rpx.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings rpx_2.7.4.tar.gz |
| StartedAt: 2023-04-11 23:08:57 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 23:09:46 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 49.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: rpx.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rpx.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings rpx_2.7.4.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/rpx.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘rpx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rpx’ version ‘2.7.4’
* 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 ‘rpx’ 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
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘rpx-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PXDataset2
> ### Title: New PXDataset (v2) to find and download proteomics data
> ### Aliases: PXDataset2 class:PXDataset2 PXDataset pxtitle
> ### pxfiles,PXDataset2-method pxfiles pxget,PXDataset2-method pxget
> ### pxid,PXDataset2-method pxid pxref,PXDataset2-method pxref
> ### pxtax,PXDataset2-method pxtax pxurl,PXDataset2-method pxurl
> ### show,PXDataset2-method pxCacheInfo,PXdataset-method pxCacheInfo
> ### pxinstruments pxSubmissionDate pxPublicationDate pxptms pxprotocols
> ### pxCacheInfo,PXDataset2-method
>
> ### ** Examples
>
>
> px <- PXDataset("PXD000001")
Loading PXD000001 from cache.
> px
Project PXD000001 with 11 files
Resource ID BFC60 in cache in /home/biocbuild/.cache/R/rpx.
[1] 'F063721.dat' ... [11] 'erwinia_carotovora.fasta'
Use 'pxfiles(.)' to see all files.
> pxtax(px)
[1] "Erwinia carotovora"
> pxurl(px)
[1] "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001"
> pxref(px)
[1] "Gatto L, Christoforou A; Using R and Bioconductor for proteomics data analysis., Biochim Biophys Acta, 2013 May 18, doi:10.1016/j.bbapap.2013.04.032 PMID:23692960"
> pxfiles(px)
Project PXD000001 files (11):
[remote] F063721.dat
[local] F063721.dat-mztab.txt
[remote] PRIDE_Exp_Complete_Ac_22134.xml.gz
[remote] PRIDE_Exp_mzData_Ac_22134.xml.gz
[remote] PXD000001_mztab.txt
[remote] README.txt
[local] TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML
[remote] TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML
[local] TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML
[remote] TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw
...
> pxfiles(px, as.vector = FALSE)
ID NAME
1 1 F063721.dat
2 2 F063721.dat-mztab.txt
3 3 PRIDE_Exp_Complete_Ac_22134.xml.gz
4 4 PRIDE_Exp_mzData_Ac_22134.xml.gz
5 5 PXD000001_mztab.txt
6 6 README.txt
7 7 TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML
8 8 TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML
9 9 TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML
10 10 TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw
11 11 erwinia_carotovora.fasta
URI
1 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/F063721.dat
2 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/F063721.dat-mztab.txt
3 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/PRIDE_Exp_Complete_Ac_22134.xml.gz
4 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/PRIDE_Exp_mzData_Ac_22134.xml.gz
5 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/PXD000001_mztab.txt
6 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/README.txt
7 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML
8 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML
9 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML
10 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw
11 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/erwinia_carotovora.fasta
TYPE MAPPINGS PX
1 id - PXD000001
2 mztab - PXD000001
3 xml - PXD000001
4 xml - PXD000001
5 mztab - PXD000001
6 doc - PXD000001
7 raw - PXD000001
8 raw - PXD000001
9 raw - PXD000001
10 rawbin - PXD000001
11 fas - PXD000001
>
> pxCacheInfo(px)
Resource ID BFC60 in cache in /home/biocbuild/.cache/R/rpx.
>
> fas <- pxget(px, "erwinia_carotovora.fasta")
Error in fix_issue_17(x) : Can't access URL(s):
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/erwinia_carotovora.fasta
ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/erwinia_carotovora.fasta
Calls: pxget ... pxget -> .local -> pxget1 -> get_url -> fix_issue_17
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_px2.R:10:1'): (code run outside of `test_that()`) ──────────────
Error in `fix_issue_17(x)`: Can't access URL(s):
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001
ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001
Backtrace:
▆
1. └─rpx::PXDataset2("PXD000001") at test_px2.R:10:0
2. └─rpx:::get_url(px_metadata[["_links"]]$datasetFtpUrl$href)
3. └─rpx:::fix_issue_17(x)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
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 ...
‘rpx.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘rpx.Rmd’ using rmarkdown
Quitting from lines 42-46 (rpx.Rmd)
Error: processing vignette 'rpx.Rmd' failed with diagnostics:
Can't access URL(s):
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001
ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001
--- failed re-building ‘rpx.Rmd’
SUMMARY: processing the following file failed:
‘rpx.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 3 ERRORs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/rpx.Rcheck/00check.log’
for details.
rpx.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL rpx ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘rpx’ ... ** using staged installation ** R ** 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 (rpx)
rpx.Rcheck/tests/testthat.Rout.fail
R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 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(rpx)
>
> test_check("rpx")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_px2.R:10:1'): (code run outside of `test_that()`) ──────────────
Error in `fix_issue_17(x)`: Can't access URL(s):
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001
ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001
Backtrace:
▆
1. └─rpx::PXDataset2("PXD000001") at test_px2.R:10:0
2. └─rpx:::get_url(px_metadata[["_links"]]$datasetFtpUrl$href)
3. └─rpx:::fix_issue_17(x)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted
rpx.Rcheck/rpx-Ex.timings
| name | user | system | elapsed |