| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L M N O P Q [R] S T U V W X Y Z |
This page was generated on 2017-08-16 13:23:05 -0400 (Wed, 16 Aug 2017).
| Package 1146/1382 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| rpx 1.12.1 Laurent Gatto
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | ERROR | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | ||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: rpx |
| Version: 1.12.1 |
| Command: rm -rf rpx.buildbin-libdir rpx.Rcheck && mkdir rpx.buildbin-libdir rpx.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rpx.buildbin-libdir rpx_1.12.1.tar.gz >rpx.Rcheck\00install.out 2>&1 && cp rpx.Rcheck\00install.out rpx-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=rpx.buildbin-libdir --install="check:rpx-install.out" --force-multiarch --no-vignettes --timings rpx_1.12.1.tar.gz |
| StartedAt: 2017-08-16 02:37:17 -0400 (Wed, 16 Aug 2017) |
| EndedAt: 2017-08-16 02:39:57 -0400 (Wed, 16 Aug 2017) |
| EllapsedTime: 159.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: rpx.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf rpx.buildbin-libdir rpx.Rcheck && mkdir rpx.buildbin-libdir rpx.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rpx.buildbin-libdir rpx_1.12.1.tar.gz >rpx.Rcheck\00install.out 2>&1 && cp rpx.Rcheck\00install.out rpx-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=rpx.buildbin-libdir --install="check:rpx-install.out" --force-multiarch --no-vignettes --timings rpx_1.12.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/rpx.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rpx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rpx' version '1.12.1'
* 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 '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
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
PXDataset-class 4.96 0.22 14.8
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
PXDataset-class 5.58 0.18 14.83
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 1
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
2. Failure: PXD version (@test_px.R#44) ----------------------------------------
p@formatVersion not identical to "1.2.0".
1/1 mismatches
x[1]: "1.3.0"
y[1]: "1.2.0"
testthat results ================================================================
OK: 19 SKIPPED: 0 FAILED: 2
1. Failure: PXD000001 (@test_px.R#26)
2. Failure: PXD version (@test_px.R#44)
Error: testthat unit tests failed
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 1
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
2. Failure: PXD version (@test_px.R#44) ----------------------------------------
p@formatVersion not identical to "1.2.0".
1/1 mismatches
x[1]: "1.3.0"
y[1]: "1.2.0"
testthat results ================================================================
OK: 19 SKIPPED: 0 FAILED: 2
1. Failure: PXD000001 (@test_px.R#26)
2. Failure: PXD version (@test_px.R#44)
Error: testthat unit tests failed
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: 2 ERRORs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/rpx.Rcheck/00check.log'
for details.
testthat.Rout.fail:
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 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.
> # 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")
Object of class "PXDataset"
Id: PXD000001 with 12 files
[1] 'F063721.dat' ... [12] 'generated'
Use 'pxfiles(.)' to see all files.
1. Failure: PXD000001 (@test_px.R#26) ------------------------------------------
pxref(px1) not identical to `ref`.
1/1 mismatches
x[1]: "<!DOCTYPE HTML PUBLIC \"-//IETF//DTD HTML 2.0//EN\"> <html><head> <title>
x[1]: 301 Moved Permanently</title> </head><body> <h1>Moved Permanently</h1> <p>
x[1]: The document has moved <a href=\"https://eutils.ncbi.nlm.nih.gov/entrez/eu
x[1]: tils/efetch.fcgi/efetch.fcgi?db=pubmed&id=23692960&rettype=docsum&
x[1]: amp;retmode=text\">here</a>.</p> </body></html>"
y[1]: "Gatto L, Christoforou A. Using R and Bioconductor for proteomics data ana
y[1]: lysis. Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):42-51. Review"
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/erwinia_carotovora.fasta'
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.......... ........
downloaded 1.6 MB
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/erwinia_carotovora.fasta'
.......... .......... .......... .......... ..........
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downloaded 1.6 MB
2. Failure: PXD version (@test_px.R#44) ----------------------------------------
p@formatVersion not identical to "1.2.0".
1/1 mismatches
x[1]: "1.3.0"
y[1]: "1.2.0"
testthat results ================================================================
OK: 19 SKIPPED: 0 FAILED: 2
1. Failure: PXD000001 (@test_px.R#26)
2. Failure: PXD version (@test_px.R#44)
Error: testthat unit tests failed
Execution halted
testthat.Rout.fail:
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 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.
> # 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")
Object of class "PXDataset"
Id: PXD000001 with 12 files
[1] 'F063721.dat' ... [12] 'generated'
Use 'pxfiles(.)' to see all files.
1. Failure: PXD000001 (@test_px.R#26) ------------------------------------------
pxref(px1) not identical to `ref`.
1/1 mismatches
x[1]: "<!DOCTYPE HTML PUBLIC \"-//IETF//DTD HTML 2.0//EN\"> <html><head> <title>
x[1]: 301 Moved Permanently</title> </head><body> <h1>Moved Permanently</h1> <p>
x[1]: The document has moved <a href=\"https://eutils.ncbi.nlm.nih.gov/entrez/eu
x[1]: tils/efetch.fcgi/efetch.fcgi?db=pubmed&id=23692960&rettype=docsum&
x[1]: amp;retmode=text\">here</a>.</p> </body></html>"
y[1]: "Gatto L, Christoforou A. Using R and Bioconductor for proteomics data ana
y[1]: lysis. Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):42-51. Review"
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/erwinia_carotovora.fasta'
.......... .......... .......... .......... ..........
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downloaded 1.6 MB
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/erwinia_carotovora.fasta'
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downloaded 1.6 MB
2. Failure: PXD version (@test_px.R#44) ----------------------------------------
p@formatVersion not identical to "1.2.0".
1/1 mismatches
x[1]: "1.3.0"
y[1]: "1.2.0"
testthat results ================================================================
OK: 19 SKIPPED: 0 FAILED: 2
1. Failure: PXD000001 (@test_px.R#26)
2. Failure: PXD version (@test_px.R#44)
Error: testthat unit tests failed
Execution halted
rpx.Rcheck/00install.out:
install for i386 * installing *source* package 'rpx' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'rpx' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'rpx' as rpx_1.12.1.zip * DONE (rpx)
rpx.Rcheck/examples_i386/rpx-Ex.timings:
| name | user | system | elapsed | |
| PXDataset-class | 4.96 | 0.22 | 14.80 | |
| pxannounced | 0.45 | 0.12 | 1.23 | |
rpx.Rcheck/examples_x64/rpx-Ex.timings:
| name | user | system | elapsed | |
| PXDataset-class | 5.58 | 0.18 | 14.83 | |
| pxannounced | 0.43 | 0.08 | 0.97 | |